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RAD21

gene
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Also known as KIAA0078hHR21SCC1

Summary

RAD21 (RAD21 cohesin complex component, HGNC:9811) is a protein-coding gene on chromosome 8q24.11, encoding Double-strand-break repair protein rad21 homolog (O60216). As a member of the cohesin complex, involved in sister chromatid cohesion from the time of DNA replication in S phase to their segregation in mitosis, a function that is essential for proper chromosome segregation, post-replicative DNA repair, and the prevention of inappropriate…. It is a common-essential gene (DepMap: required in 99.5% of cancer cell lines) and haploinsufficient (ClinGen: sufficient evidence).

The protein encoded by this gene is highly similar to the gene product of Schizosaccharomyces pombe rad21, a gene involved in the repair of DNA double-strand breaks, as well as in chromatid cohesion during mitosis. This protein is a nuclear phospho-protein, which becomes hyperphosphorylated in cell cycle M phase. The highly regulated association of this protein with mitotic chromatin specifically at the centromere region suggests its role in sister chromatid cohesion in mitotic cells.

Source: NCBI Gene 5885 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Cornelia de Lange syndrome (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 2
  • Clinical variants (ClinVar): 555 total — 40 pathogenic, 19 likely-pathogenic (top 6% of genes corpus-wide)
  • Regional missense constraint (gnomAD): 2 of 5 regions constrained (≈34% of expected missense variation)
  • GTEx eGene: eQTL in 27 tissues, sQTL in 3 (q < 0.05)
  • Phenotypes (HPO): 160
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 2 cancer types (inferred from mutation patterns)
  • Cancer dependency (DepMap): dependent in 99.5% of screened cell lines (common-essential)
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.34 (highly constrained)
  • MANE Select transcript: NM_006265
  • Interaction hub: 4,476 STRING partners (top 1% of genes corpus-wide)

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9811
Approved symbolRAD21
NameRAD21 cohesin complex component
Location8q24.11
Locus typegene with protein product
StatusApproved
AliasesKIAA0078, hHR21, SCC1
Ensembl geneENSG00000164754
Ensembl biotypeprotein_coding
OMIM606462
Entrez5885

Gene structure

Transcript identifiers

Ensembl transcripts: 43 — 24 protein_coding, 12 retained_intron, 6 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000297338

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 3, TSL 3: 3, TSL 4: 2

ENST00000297338, ENST00000517485, ENST00000517749, ENST00000518055, ENST00000519469, ENST00000519837, ENST00000520992, ENST00000522699, ENST00000523547, ENST00000523986, ENST00000685972, ENST00000686622, ENST00000687122, ENST00000687358, ENST00000687902, ENST00000688033, ENST00000689124, ENST00000689154, ENST00000689504, ENST00000690166, ENST00000690189, ENST00000900008, ENST00000900009, ENST00000900010, ENST00000900011, ENST00000927337, ENST00000927338, ENST00000927339, ENST00000927340, ENST00000927341, ENST00000958516, ENST00000958517, ENST00000958518, ENST00000958519, ENST00001006742, ENST00001011649, ENST00001011654, ENST00001074827, ENST00001074829, ENST00001109555, ENST00001129034, ENST00001129035, ENST00001135351

RefSeq mRNA: 1 — MANE Select: NM_006265 NM_006265

CCDS: CCDS6321

Canonical transcript exons

ENST00000297338 — 14 exons

ExonStartEnd
ENSE00001087180116848946116849029
ENSE00001087181116857267116857473
ENSE00001087182116856646116856771
ENSE00001087184116851948116852096
ENSE00001087186116856166116856288
ENSE00001087189116850618116850767
ENSE00001087190116854245116854468
ENSE00001087191116852549116852708
ENSE00001276365116845934116847691
ENSE00001356828116874611116874776
ENSE00003464321116861841116861940
ENSE00003464650116866586116866761
ENSE00003525419116863130116863259
ENSE00003579379116858352116858458

Expression profiles

Bgee: expression breadth ubiquitous, 301 present calls, max score 99.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 84.2621 / max 1535.8367, expressed in 1822 samples.

Highest expression (Bgee): ventricular zone, ganglionic eminence, superficial temporal artery, endometrium epithelium, epithelium of nasopharynx.

Genetic regulation across tissues (GTEx eQTL / sQTL)

RAD21 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 27 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 30 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Thyroideqtl4.9e-26-0.498:116876671:T:A
Nerve Tibialeqtl1.4e-21-0.178:116885085:C:T
Skin Sun Exposed Lower legeqtl4.5e-14-0.128:116896606:T:TC
Artery Tibialeqtl1.1e-13-0.148:116885085:C:T
Skin Not Sun Exposed Suprapubiceqtl4.4e-13-0.118:116846150:G:A
Muscle Skeletaleqtl3.0e-12-0.198:116828792:T:A
Testissqtl2.8e-11+0.688:116882227:A:G
Breast Mammary Tissueeqtl9.9e-11-0.148:116886972:A:G
Artery Aortaeqtl2.5e-10-0.148:116885085:C:T
Pituitaryeqtl1.4e-08-0.218:116841534:G:C
Whole Bloodeqtl2.0e-08-0.098:116868416:C:T
Esophagus Mucosaeqtl2.1e-07-0.088:116885085:C:T
Adipose Subcutaneouseqtl6.4e-07-0.088:116885085:C:T
Cells Cultured fibroblastseqtl1.0e-06-0.088:116846367:C:CAT
Esophagus Musculariseqtl2.6e-06-0.108:116919448:T:C
Lungeqtl6.3e-06-0.118:116885085:C:T
Colon Transverseeqtl1.4e-05-0.118:116846367:C:CAT
Heart Atrial Appendageeqtl5.4e-05-0.098:116846367:C:CAT
Heart Left Ventricleeqtl9.5e-05-0.098:116891826:A:G
Testiseqtl2.6e-04-0.118:116895581:G:A

FANTOM5 promoters

showing 10 of 14 alternative TSS:

Promoter IDTPM avgSamples expressed
9455084.26211822
945435.26531378
945493.13391109
945420.7315177
945470.2810112
945450.2576132
945460.136041
945440.133536
945480.077025
945350.05342

Top tissues by expression

showing 100 of 301 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305399.47gold quality
ganglionic eminenceUBERON:000402399.04gold quality
superficial temporal arteryUBERON:000161498.85gold quality
endometrium epitheliumUBERON:000481198.81gold quality
epithelium of nasopharynxUBERON:000195198.79gold quality
germinal epithelium of ovaryUBERON:000130498.76gold quality
cerebellar vermisUBERON:000472098.76gold quality
substantia nigra pars reticulataUBERON:000196698.69gold quality
subthalamic nucleusUBERON:000190698.66gold quality
substantia nigra pars compactaUBERON:000196598.66gold quality
embryoUBERON:000092298.63gold quality
trabecular bone tissueUBERON:000248398.53gold quality
inferior vagus X ganglionUBERON:000536398.53gold quality
seminal vesicleUBERON:000099898.51gold quality
superior vestibular nucleusUBERON:000722798.47gold quality
corpus callosumUBERON:000233698.44gold quality
adult organismUBERON:000702398.44gold quality
lower lobe of lungUBERON:000894998.38gold quality
pigmented layer of retinaUBERON:000178298.34gold quality
retinaUBERON:000096698.31gold quality
colonic epitheliumUBERON:000039798.29gold quality
middle frontal gyrusUBERON:000270298.20gold quality
lateral globus pallidusUBERON:000247698.19gold quality
medulla oblongataUBERON:000189698.16gold quality
thymusUBERON:000237098.15gold quality
trigeminal ganglionUBERON:000167598.13gold quality
bone marrowUBERON:000237198.11gold quality
bone elementUBERON:000147498.10gold quality
mucosa of paranasal sinusUBERON:000503098.10gold quality
paraflocculusUBERON:000535198.06gold quality
caput epididymisUBERON:000435897.99gold quality
cortical plateUBERON:000534397.99gold quality
frontal poleUBERON:000279597.98gold quality
adrenal tissueUBERON:001830397.95gold quality
corpus epididymisUBERON:000435997.93gold quality
lymph nodeUBERON:000002997.92gold quality
ponsUBERON:000098897.92gold quality
oocyteCL:000002397.91gold quality
parietal pleuraUBERON:000240097.90gold quality
oral cavityUBERON:000016797.85gold quality
heart right ventricleUBERON:000208097.85gold quality
mucosa of sigmoid colonUBERON:000499397.82gold quality
Brodmann (1909) area 10UBERON:001354197.81gold quality
ventral tegmental areaUBERON:000269197.76gold quality
dorsal plus ventral thalamusUBERON:000189797.75gold quality
jejunumUBERON:000211597.74gold quality
choroid plexus epitheliumUBERON:000391197.74gold quality
renal medullaUBERON:000036297.73gold quality
cauda epididymisUBERON:000436097.73gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099197.69gold quality
jejunal mucosaUBERON:000039997.68gold quality
penisUBERON:000098997.68gold quality
colonic mucosaUBERON:000031797.66gold quality
secondary oocyteCL:000065597.65gold quality
dorsal root ganglionUBERON:000004497.62gold quality
bone marrow cellCL:000209297.60gold quality
dorsal motor nucleus of vagus nerveUBERON:000287097.60gold quality
islet of LangerhansUBERON:000000697.57gold quality
visceral pleuraUBERON:000240197.57gold quality
superior surface of tongueUBERON:000737197.56gold quality
urethraUBERON:000005797.53gold quality
pleuraUBERON:000097797.53gold quality
mammary ductUBERON:000176597.51gold quality
synovial jointUBERON:000221797.48gold quality
pylorusUBERON:000116697.47gold quality
CA1 field of hippocampusUBERON:000388197.43gold quality
rectumUBERON:000105297.41gold quality
tonsilUBERON:000237297.39gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451197.39gold quality
caecumUBERON:000115397.34gold quality
midbrainUBERON:000189197.33gold quality
myocardiumUBERON:000234997.33gold quality
cartilage tissueUBERON:000241897.30gold quality
calcaneal tendonUBERON:000370197.30gold quality
orbitofrontal cortexUBERON:000416797.29gold quality
epithelium of mammary glandUBERON:000324497.28gold quality
endometriumUBERON:000129597.25gold quality
skin of hipUBERON:000155497.25gold quality
substantia nigraUBERON:000203897.25gold quality
globus pallidusUBERON:000187597.22gold quality
spinal cordUBERON:000224097.21gold quality
pericardiumUBERON:000240797.21gold quality
cardia of stomachUBERON:000116297.20gold quality
upper leg skinUBERON:000426297.20gold quality
thoracic mammary glandUBERON:000520097.19gold quality
mammary glandUBERON:000191197.17gold quality
lateral nuclear group of thalamusUBERON:000273697.16gold quality
parietal lobeUBERON:000187297.15gold quality
cardiac muscle of right atriumUBERON:000337997.15gold quality
vermiform appendixUBERON:000115497.12gold quality
postcentral gyrusUBERON:000258197.10gold quality
C1 segment of cervical spinal cordUBERON:000646997.07gold quality
urinary bladderUBERON:000125597.02gold quality
vastus lateralisUBERON:000137997.00gold quality
right lungUBERON:000216797.00gold quality
tongueUBERON:000172396.97gold quality
gingivaUBERON:000182896.97gold quality
placentaUBERON:000198796.93gold quality
medial globus pallidusUBERON:000247796.93gold quality
hypothalamusUBERON:000189896.92gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-CURD-112yes37.08
E-CURD-122yes23.02
E-GEOD-125970yes16.52
E-MTAB-6678yes8.21
E-MTAB-10553yes7.48
E-GEOD-106540no818.43
E-ANND-3no0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Thymustissue151.4
Corpus callosumtissue140.5
Hippocampal formationtissue138.8
Thalamustissue135.3
Superior colliculitissue128.7
Midbraintissue126.3
Cerebral cortextissue124.1high
Motor cortextissue124.1
Prefrontal cortextissue115.8
Bone marrowtissue115.5high
Retrosplenial cortextissue111.7
Amygdalatissue111.3
Hypothalamustissue110.9
Ponstissue110.0
Entorhinal cortextissue107.8
Retrosplenial and cingulate cortextissue106.4
Cerebellumtissue105.6high
Insular cortextissue104.1
Occipital cortextissue103.8
Somatosensory cortextissue102.7
Tonsiltissue102.2high
Lymph nodetissue101.7high
Septumtissue97.2
Substantia nigratissue97.0
Temporal cortextissue95.6
Periaqueductal graytissue94.6
Medulla oblongatatissue93.3
Putamentissue92.1
Olfactory bulbtissue90.2
Ventral forebraintissue89.6
Spinal cordtissue87.8
Tonguetissue86.9
Retinatissue84.9
Heart muscletissue80.8medium
Nucleus accumbenstissue77.5
Locus coeruleustissue77.1
Placentatissue76.3high
Frontal cortextissue75.2
Caudate putamentissue73.7
Parathyroid glandtissue73.5high
Testistissue73.4high
Basal gangliatissue72.0high
Adrenal glandtissue70.7high
Rectumtissue69.6high
Thyroid glandtissue69.3high
Hippocampustissue68.1high
Skeletal muscletissue66.7high
Adipose tissuetissue65.2high
Choroid plexustissue64.9
Colontissue62.9high
Ovarytissue62.2high
Appendixtissue62.1high
Kidneytissue61.7high
Esophagustissue61.3high
Spleentissue60.8high
Postcentral gyrustissue60.1
Breasttissue59.7high
Livertissue58.1low
Lungtissue56.1high
Seminal vesicletissue55.8high

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — White matter (140.5), Subiculum (138.8), Corpus callosum, genu (white matter) (131.6), Parieto-temporal junction (white matter) (126.2), Cerebellar white matter (122.8).

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets:

TargetRegulation
APOBRepression
RUNX1Repression

Upstream regulators (CollecTRI, top): CTCF, ESR1, MYC, NR5A1, TFAP2A, TFAP2C

miRNA regulators (miRDB)

Targeting RAD21 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 153 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4262100.0073.263931
HSA-MIR-188-3P100.0068.761240
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-574-5P100.0066.01989
HSA-MIR-3646100.0073.565283
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-511-3P99.9968.851467
HSA-MIR-318599.9968.121959
HSA-MIR-366299.9973.825684
HSA-MIR-477599.9875.006394
HSA-MIR-1213699.9872.815713
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-433-3P99.9869.371203
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.341, missense Z 3.65 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000297338 splits into 5 regions with different missense tolerance; 2 are missense-constrained (≈34% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
8:116,847,503–116,847,64534 / 59.90.57no
8:116,847,646–116,852,659225 / 218.31.03no
8:116,852,660–116,856,19742 / 117.20.36yes (p 3.7e-12)
8:116,856,198–116,861,863165 / 229.60.72no
8:116,861,864–116,866,72927 / 144.10.19yes (p 1.8e-22)
ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map
DepMap (CRISPR cell-line fitness): dependent in 99.5% of screened cell lines, common-essential.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): KLE (-2.844), NMC-G1 (-2.453), NCI-H226 (-2.367), RERF-GC-1B (-2.358), JM1 (-2.267), VCaP (-2.244), K-562 (-2.222), KP-N-YN (-2.217), ONCO-DG-1 (-2.204), KU812 (-2.2), NCI-H1092 (-2.191), TUHR10TKB (-2.174), SK-N-BE(2) (-2.16), SNU-449 (-2.125), IMR-32 (-2.109).

Literature-anchored findings (GeneRIF, showing 40)

  • Caspase proteolysis of the cohesin component RAD21 promotes apoptosis (PMID:11875078)
  • RAD21 subunit of the cohesin complex directly interacts with ATPase subunit SNF2; mapping of RAD21, SNF2 and Mi2 binding sites reveals specific association of these three proteins with DNA elements containing Alu sequences (PMID:12198550)
  • Scc1 is essential for the association of kinetochores with microtubules. (PMID:12200439)
  • plays a role in apoptosis, and its cleavage during apoptosis may act as a nuclear signal to initiate cytoplasmic events involved in the apoptotic pathway (PMID:12417729)
  • RAD21 shows increased expression in clinical prostate carcinomas and is also amplified in 30-40% of xenografts and hormone-refractory tumors. (PMID:14603436)
  • Phosphorylation of SA2 is essential for cohesin dissociation during prophase and prometaphase, but is not required for cohesin cleavage by separase. (PMID:15737063)
  • RAD21 suppression enhances the antitumor activity of chemotherapeutic agents acting via induction of DNA damage (PMID:15767545)
  • The RAD21 gene was closely related to the invasion and metastasis of cancer cells. (PMID:16416296)
  • As compared to the telomerase group, the alternative lengthening of telomeres group presents higher expression of hRad21, thinner tumor invasion depth, and higher survival rate. (PMID:18197499)
  • These data argue that the regulation of the IL-3 and the GM-CSF promoters depends on the positions of their enhancers relative to the conserved CTCF/cohesin-binding sites. (PMID:19158269)
  • The depletion of either CTCF or RAD21 disrupts the chromatin loop structure, together with significant changes in the APO expression. (PMID:19322193)
  • Ectopic expression of Rad21 repressed CTCF-regulated transcription of KSHV lytic genes. (PMID:19369356)
  • hRAD21 was significantly differently expressed in cells maintaining telomere length through a telomerase-independent mechanism, termed the alternative lengthening of telomeres (ALT). (PMID:20364118)
  • Rad21 protein depletion causes centrosome defects in interphase and prophase of mitosis. (PMID:20404533)
  • Rad21 protein are cleaved by separase are required for the localization of Rad21 to the centrosome. (PMID:20404544)
  • RAD21 expression confers poor prognosis and resistance to chemotherapy in high grade luminal, basal and HER2 breast cancers. (PMID:21255398)
  • Rad21 cleavage by calpain-1 promotes separation of chromosome arms, which coincides with a calcium-induced partial loss of cohesin at several chromosomal loci. (PMID:21876002)
  • RAD21 expression is associated with a poorer prognosis in BRCA2, but not in BRCA1 breast cancers. (PMID:22537934)
  • RAD21 mutations cause a human cohesinopathy (PMID:22633399)
  • show that the Smc5/6 subunit Mms21 sumoylates multiple lysines of the cohesin subunit Scc1 (PMID:22751501)
  • ASURA specifically binds to chromatin when Scc1 is associated with chromatin. (PMID:23548868)
  • Rad21 binds to SA proteins through two SA-binding motifs on Rad21. (PMID:23874961)
  • -RAD21 and EIF3H, both on chromosome 8q23, CHRAC1 on chromosome 8q24.3 and TANC2 on chromosome 17q23-were confirmed to be driver genes regulating the proliferation/survival of clonogenic breast cancer cells (PMID:24148822)
  • This study reports the first intragenic deletion and frameshift mutations identified in RAD21 in two patients presenting with atypical Cornelia de Lange syndrome. (PMID:24378232)
  • CTCF and Rad21 act as host cell restriction factors for Kaposi’s sarcoma-associated herpesvirus (KSHV) lytic replication by modulating viral gene transcription. (PMID:24415941)
  • RAD21 expression in CRC is associated with aggressive disease especially in KRAS mutant tumours and resistance to chemoradiotherapy. (PMID:24548858)
  • Cross-sectional deep-sequencing analysis for clonal hierarchy demonstrated STAG2, SMC3, and RAD21 mutations to be ancestral in 18%, 18%, and 47% of cases, respectively, and each expanded to clonal dominance concordant with disease transformation (PMID:25006131)
  • Studied the role of looping in large-scale (supra Mb) folding of human chromosomes by knocking down the gene that codes for CTCF and the one coding for Rad21, an essential subunit of cohesin. (PMID:25299688)
  • cohesin’s proposed DNA exit gate is formed by interactions between Scc1 and the coiled-coil region of Smc3. (PMID:25414306)
  • Elevated RAD21 expression tracks with reactivation of L1 expression in human sporadic colorectal cancer. (PMID:25464844)
  • Some patients with chronic intestinal pseudo-obstruction carry mutations in RAD21 that disrupt the ability of its product to regulate genes such as RUNX1 and APOB. (PMID:25575569)
  • found well-positioned CTCF and RAD21 peaks approximately 60-80 bp upstream of the TSS in the unidirectional genes. The peak heights were related to the amount of antisense transcription. Results provide insights into the distribution of histone modifications at promoters and suggest a novel role of CTCF and cohesin as regulators of transcriptional direction. (PMID:25881024)
  • Reduced RAD21 destabilizes high-level gene amplification by disrupting pre-replication complex bindings in human cancers with chromosomal instability. (PMID:26420833)
  • Data indicate that RAD21 plays an important role in cellular senescence breast cancer cells, mainly through RB1 pathway activation via c-Myc downregulation. (PMID:26529363)
  • This study together with previous reports suggests incomplete penetrance associated with RAD21 variants and these individuals may therefore be underdiagnosed. (PMID:27882533)
  • With tissue microarrays of hepatocellular carcinoma (HCC) patients, we determined the prognostic values of the core genes in the network and found that RAD21, CDK1, and HDAC2 expression levels were negatively associated with overall survival for HCC patients. (PMID:28434945)
  • evidence for a possible pathogenetic role of RAD21 promoter methylation in the development of chronic lymphocytic leukemia. (PMID:29587287)
  • depletion of Rad21 in a Pds5-deficient background rescues the phenotype observed upon Pds5 depletion alone. These findings support a model where loss of either component of the cohesin releasin complex perturbs cohesin dynamics on replication forks, hindering fork progression and promoting MRE11-dependent fork slowing (PMID:29917110)
  • A subset of PGP9.5- and HuC/D-IR neuronal cell bodies and nerve fibers in the myenteric plexus of human and mouse small intestine also displayed cytoplasmic RAD21 (PMID:30069982)
  • We demonstrate that infection of hepatoma cells with HCV leads to up regulation of the expression of the RAD21 cohesin subunit and changes cohesin residency on the chromatin. (PMID:30698808)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriorad21aENSDARG00000006092
danio_reriorad21bENSDARG00000035655
mus_musculusRad21ENSMUSG00000022314
rattus_norvegicusRad21ENSRNOG00000004420
drosophila_melanogastervtdFBGN0260987
caenorhabditis_elegansWBGENE00004737

Paralogs (2): REC8 (ENSG00000100918), RAD21L1 (ENSG00000244588)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:108016) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 9 distinct phenotype terms.

Mouse phenotype (MP)Records
reduced male fertility1
abnormal T cell differentiation1
abnormal CD4-positive, alpha beta T cell morphology1
decreased double-positive T cell number1
abnormal female meiosis1
abnormal CD4-positive, alpha-beta T cell physiology1
decreased CD4-positive, alpha-beta T cell number1
decreased CD8-positive, alpha-beta T cell number1
prenatal lethality, incomplete penetrance1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Bos taurusQ3SWX998.3%Diamond
Ailuropoda melanoleucaD2HSB384.9%Diamond
Xenopus laevisO9331083.6%Diamond
Schizosaccharomyces pombe 972h-P3077649.3%Diamond
Arabidopsis thalianaQ9FQ1949.3%Diamond
Saccharomyces cerevisiae S288CQ1215835.9%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
AARDprotein-coding441376
RAD21-AS1ncRNA644660
UTP23protein-coding84294
MIR3610ncRNA100500914
SLC30A8protein-coding169026
EIF3Hprotein-coding8667

Protein

Protein identifiers

Double-strand-break repair protein rad21 homolog — O60216 (reviewed: O60216)

Alternative names: Nuclear matrix protein 1, SCC1 homolog

All UniProt accessions (7): A0A8I5KWV3, E5RFV8, E5RG18, E5RIN7, E5RJK5, E5RJW1, O60216

UniProt curated annotations — full annotation on UniProt →

Function. As a member of the cohesin complex, involved in sister chromatid cohesion from the time of DNA replication in S phase to their segregation in mitosis, a function that is essential for proper chromosome segregation, post-replicative DNA repair, and the prevention of inappropriate recombination between repetitive regions. The cohesin complex may also play a role in spindle pole assembly during mitosis. In interphase, cohesins may function in the control of gene expression by binding to numerous sites within the genome. May control RUNX1 gene expression. Binds to and represses APOB gene promoter. May play a role in embryonic gut development, possibly through the regulation of enteric neuron development. May promote apoptosis.

Subunit / interactions. Component of the cohesin complex, which consists of an SMC1A/B and SMC3 heterodimer core and 2 non-Smc subunits RAD21 and STAG1/SA1, STAG2/SA2 or STAG3/SA3. Interacts (via C-terminus) with SMC1A and (via N-terminus) with SMC3; these interactions are direct. The cohesin complex interacts with NUMA1. The cohesin complex also interacts with CDCA5, PDS5A and PDS5B; this interaction might regulate the ability of the cohesin complex to mediate sister chromatid cohesion. The interaction with PDS5B is direct and is stimulated by STAG1/SA1. The cohesin complex interacts with the cohesin loading complex subunits NIPBL/Scc2 (via HEAT repeats) and MAU2/Scc4. NIPBL directly contacts all members of the complex, RAD21, SMC1A/B, SMC3 and STAG1. The cohesin complex interacts with DDX11/ChIR1. Directly interacts with WAPL; this interaction is stimulated by STAG1/SA1. Interacts with the ISWI chromatin remodeling complex component SMARCA5/SNF2h; the interaction is direct. Interacts with the NuRD complex component CHD4; the interaction is direct.

Subcellular location. Nucleus. Nucleus matrix. Chromosome. Centromere. Cytoplasm. Cytoskeleton. Spindle pole Cytoplasm. Cytosol.

Tissue specificity. Expressed in the gut (at protein level).

Post-translational modifications. Cleaved by separase/ESPL1 at the onset of anaphase; this cleavage is required for sister chromatid separation and cytokinesis. Cleaved by caspase-3/CASP3 or caspase-7/CASP7 at the beginning of apoptosis. Phosphorylated; becomes hyperphosphorylated in M phase of cell cycle. The large dissociation of cohesin from chromosome arms during prophase may be partly due to its phosphorylation by PLK1.

Disease relevance. Cornelia de Lange syndrome 4 with or without midline brain defects (CDLS4) [MIM:614701] A form of Cornelia de Lange syndrome, a clinically heterogeneous developmental disorder associated with malformations affecting multiple systems. It is characterized by facial dysmorphisms, abnormal hands and feet, growth delay, cognitive retardation, hirsutism, gastroesophageal dysfunction and cardiac, ophthalmologic and genitourinary anomalies. The disease is caused by variants affecting the gene represented in this entry. Mungan syndrome (MGS) [MIM:611376] An autosomal recessive disease characterized by visceral neuromyopathy, intestinal dysmotility and chronic intestinal pseudoobstruction, megaduodenum, long-segment Barrett esophagus, and a variety of cardiac valve or septal defects such as membranous ventricular septal defect, pulmonary and tricuspid valve regurgitation. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The C-terminal part associates with the ATPase head of SMC1A, while the N-terminal part binds to the ATPase head of SMC3.

Similarity. Belongs to the rad21 family.

RefSeq proteins (1): NP_006256* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006909Rad21/Rec8_C_euDomain
IPR006910Rad21_Rec8_NDomain
IPR023093ScpA-like_CHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily
IPR039781Rad21/Rec8-likeFamily
IPR049589NXP1_M-likeDomain

Pfam: PF04824, PF04825

UniProt features (66 total): helix 19, modified residue 8, region of interest 7, mutagenesis site 7, sequence variant 5, compositionally biased region 4, strand 4, site 3, cross-link 3, turn 3, chain 2, sequence conflict 1

Structure

Experimental structures (PDB)

showing 30 of 37 structures by resolution:

PDBTitleMethodResolution (Å)
8ROEHuman cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-bound conformationX-RAY DIFFRACTION1.36
8RODHuman cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Open/closed P-loop conformationX-RAY DIFFRACTION1.5
8ROFHuman cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-Mg-bound conformationX-RAY DIFFRACTION1.65
8RO9Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformationX-RAY DIFFRACTION1.77
8ROCHuman cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Apo closed P-loop conformationX-RAY DIFFRACTION1.85
8RO8Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Apo closed P-loop conformationX-RAY DIFFRACTION1.9
8ROGHuman cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformationX-RAY DIFFRACTION1.94
8RO7Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Open/closed P-loop conformationX-RAY DIFFRACTION2.09
8RO6Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Apo closed P-loop conformationX-RAY DIFFRACTION2.2
8ROKHuman cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1X-RAY DIFFRACTION2.25
6RRCCrystal structure of the N-terminal region of human cohesin subunit STAG1 in complex with …X-RAY DIFFRACTION2.37
8ROAHuman cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ADP-bound conformationX-RAY DIFFRACTION2.44
8ROIHuman cohesin SMC3-HD(EQ)/RAD21-N complex - ADP-bound conformationX-RAY DIFFRACTION2.45
8ROBHuman cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformationX-RAY DIFFRACTION2.5
8ROHHuman cohesin SMC3-HD(EQ)/RAD21-N complex - Apo conformationX-RAY DIFFRACTION2.6
6QNXStructure of the SA2/SCC1/CTCF complexX-RAY DIFFRACTION2.7
9HN0Cryo-EM structure of human separase bound to SCC1 (310-550 aa)ELECTRON MICROSCOPY2.8
4PJWcrystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid …X-RAY DIFFRACTION2.85
9HMVCryo-EM structure of SA2-SCC1 complex at 2.9 angstromELECTRON MICROSCOPY2.9
9HN4Cryo-EM structure of human separase bound to phosphorylated SCC1 (310-550 aa)ELECTRON MICROSCOPY2.93
4PK7crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid …X-RAY DIFFRACTION2.95
9HN5Cryo-EM structure of human separase bound to phosphorylated SCC1 (100-320 aa)ELECTRON MICROSCOPY2.96
8ROJHuman cohesin SMC3-HD/RAD21-N complex - ADP-Mg-bound conformationX-RAY DIFFRACTION3
4PJUcrystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid …X-RAY DIFFRACTION3.05
9HX9Structure of the SA2/SCC1/MCM3 complexX-RAY DIFFRACTION3.07
9EP3Structure of the SA2/SCC1/WAPL complexX-RAY DIFFRACTION3.08
8ROLHuman cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 2X-RAY DIFFRACTION3.11
6RRKCrystal structure of the central region of human cohesin subunit STAG1 in complex with …X-RAY DIFFRACTION3.17
7ZJSStructural basis of centromeric cohesion protection by SGO1X-RAY DIFFRACTION3.24
9HMSCryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2ELECTRON MICROSCOPY3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O60216-F161.490.20

Human Protein Atlas

Protein class: Predicted intracellular proteins, Cancer-related genes, Mutated cancer genes, Mutational cancer driver genes, Disease related genes, Human disease related genes, Congenital malformations, Other congenital malformations, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH supported · IF enhanced

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3)

PositionRole
172–173cleavage; by espl1
279–280cleavage; by caspase-3 or caspase-7
450–451cleavage; by espl1

Post-translational modifications (11)

TypePositions
Phosphoserine46, 153, 175, 249, 454, 545
Phosphothreonine394, 623
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)48, 216, 418

Mutagenesis-validated functional residues (7)

PositionPhenotype
1–126abolishes interaction with smc1.
126–282abolishes binding to smarca5.
172abolishes first cleavage by espl1, no effect on nuclear localization.
276–280loss of cleavage by caspase-3 or caspase-7.
279loss of cleavage by caspase-3 or caspase-7.
282no effect on cleavage by caspase-3 or caspase-7.
450abolishes second cleavage by espl1, no effect on nuclear localization.

Function

Pathways and Gene Ontology

Reactome pathways

6 curated (TAS) of 24; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

24 pathways:

IDPathwayEvidence
R-HSA-2470946Cohesin Loading onto Chromatincurated
R-HSA-2468052Establishment of Sister Chromatid Cohesioncurated
R-HSA-9018519Estrogen-dependent gene expressioncurated
R-HSA-2500257Resolution of Sister Chromatid Cohesioncurated
R-HSA-3108214SUMOylation of DNA damage response and repair proteinscurated
R-HSA-2467813Separation of Sister Chromatidscurated
R-HSA-1640170Cell Cycle—
R-HSA-69278Cell Cycle, Mitotic—
R-HSA-8939211ESR-mediated signaling—
R-HSA-68886M Phase—
R-HSA-1500620Meiosis—
R-HSA-1221632Meiotic synapsiselectronic
R-HSA-392499Metabolism of proteins—
R-HSA-68882Mitotic Anaphase—
R-HSA-2555396Mitotic Metaphase and Anaphase—
R-HSA-68877Mitotic Prometaphase—
R-HSA-68884Mitotic Telophase/Cytokinesis—
R-HSA-597592Post-translational protein modification—
R-HSA-1474165Reproduction—
R-HSA-69242S Phase—
R-HSA-3108232SUMO E3 ligases SUMOylate target proteins—
R-HSA-2990846SUMOylation—
R-HSA-162582Signal Transduction—
R-HSA-9006931Signaling by Nuclear Receptors—

MSigDB gene sets: 742 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, MORF_MTA1, GOBP_CHROMOSOME_ORGANIZATION, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, FREAC2_01, MORF_MBD4, TGCGCANK_UNKNOWN, REACTOME_MEIOTIC_SYNAPSIS, GOBP_REGULATION_OF_NUCLEAR_DIVISION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GEORGES_CELL_CYCLE_MIR192_TARGETS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MORF_RAD21

GO Biological Process (26): response to hypoxia (GO:0001666), double-strand break repair (GO:0006302), DNA recombination (GO:0006310), DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), apoptotic process (GO:0006915), chromosome segregation (GO:0007059), sister chromatid cohesion (GO:0007062), reciprocal meiotic recombination (GO:0007131), negative regulation of G2/M transition of mitotic cell cycle (GO:0010972), negative regulation of interleukin-1 beta production (GO:0032691), negative regulation of tumor necrosis factor production (GO:0032720), positive regulation of interleukin-10 production (GO:0032733), establishment of mitotic sister chromatid cohesion (GO:0034087), establishment of meiotic sister chromatid cohesion (GO:0034089), negative regulation of glial cell apoptotic process (GO:0034351), negative regulation of neuron apoptotic process (GO:0043524), negative regulation of mitotic metaphase/anaphase transition (GO:0045841), positive regulation of sister chromatid cohesion (GO:0045876), cell division (GO:0051301), protein localization to chromatin (GO:0071168), replication-born double-strand break repair via sister chromatid exchange (GO:1990414), DNA repair (GO:0006281), DNA damage response (GO:0006974), positive regulation of gene expression (GO:0010628), negative regulation of gene expression (GO:0010629)

GO Molecular Function (6): cis-regulatory region sequence-specific DNA binding (GO:0000987), chromatin binding (GO:0003682), lncRNA binding (GO:0106222), DNA-binding transcription factor binding (GO:0140297), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (12): chromosome, centromeric region (GO:0000775), chromatin (GO:0000785), condensed nuclear chromosome (GO:0000794), spindle pole (GO:0000922), nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), cytosol (GO:0005829), cohesin complex (GO:0008278), membrane (GO:0016020), nuclear matrix (GO:0016363), meiotic cohesin complex (GO:0030893)

Reactome top-level categories

15 top-level categories:

CategoryPathways
M Phase3
Meiosis1
Mitotic Anaphase1
S Phase1
Mitotic Telophase/Cytokinesis1
Mitotic Prometaphase1
SUMO E3 ligases SUMOylate target proteins1
ESR-mediated signaling1
Reproduction1
Cell Cycle1
Post-translational protein modification1
SUMOylation1
Metabolism of proteins1
Mitotic Metaphase and Anaphase1
Cell Cycle, Mitotic1

GO top-level categories

showing 60 of 67 GO namespaces:

CategoryTerms
cellular anatomical structure6
cell cycle process2
negative regulation of mitotic cell cycle phase transition2
establishment of sister chromatid cohesion2
negative regulation of apoptotic process2
binding2
chromosome2
nuclear lumen2
response to stress1
response to decreased oxygen levels1
DNA repair1
DNA metabolic process1
gene expression1
RNA biosynthetic process1
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
chromosome organization1
meiosis I1
reciprocal homologous recombination1
meiotic cell cycle process1
G2/M transition of mitotic cell cycle1
regulation of G2/M transition of mitotic cell cycle1
negative regulation of cell cycle G2/M phase transition1
interleukin-1 beta production1
regulation of interleukin-1 beta production1
negative regulation of interleukin-1 production1
tumor necrosis factor production1
regulation of tumor necrosis factor production1
negative regulation of tumor necrosis factor superfamily cytokine production1
positive regulation of cytokine production1
interleukin-10 production1
regulation of interleukin-10 production1
mitotic cell cycle1
mitotic sister chromatid cohesion1
mitotic cell cycle process1
meiotic sister chromatid cohesion1
glial cell apoptotic process1
regulation of glial cell apoptotic process1
regulation of neuron apoptotic process1
neuron apoptotic process1
metaphase/anaphase transition of mitotic cell cycle1
regulation of mitotic metaphase/anaphase transition1
negative regulation of mitotic nuclear division1
negative regulation of metaphase/anaphase transition of cell cycle1
negative regulation of mitotic sister chromatid separation1
sister chromatid cohesion1
regulation of sister chromatid cohesion1
positive regulation of cell cycle process1
positive regulation of chromosome organization1
cellular process1
transcription cis-regulatory region binding1
RNA binding1
transcription factor binding1
nucleic acid binding1
chromosomal region1
nuclear chromosome1
condensed chromosome1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 7 of 44 annotations. The rest are phylogenetic / computational / electronic (IEA).

7 experimentally-supported GO terms:

GO termNSEvidence
positive regulation of sister chromatid cohesionBPmutant phenotype
protein localization to chromatinBPmutant phenotype
regulation of transcription by RNA polymerase IIBPdirect assay
cohesin complexCCdirect assay
membraneCChigh-throughput assay
nuclear matrixCCdirect assay
nucleoplasmCCdirect assay

Protein interactions and networks

STRING

showing 15 of 4,476 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
RAD21SMC3Q9UQE7993
RAD21ESPL1Q14674982
RAD21SMC1AQ14683971
RAD21NIPBLQ6KC79970
RAD21STAG2Q8N3U4966
RAD21STAG1Q8WVM7958
RAD21PDS5AQ29RF7953
RAD21WAPLQ7Z5K2937
RAD21SMC4Q9NTJ3884
RAD21CTCFP49711875
RAD21ESCO1Q5FWF5872
RAD21SGO1Q5FBB7851
RAD21ESCO2Q56NI9826
RAD21SGO2Q562F6807
RAD21CHTF18Q8WVB6806

IntAct

Human interaction partners of RAD21 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 38 partners by confidence:

PartnerInteraction typeMIscoreRecords
STAG2association0.97015
SMC3physical association0.96010
SMC1Aphysical association0.93015
STAG1association0.9307
WAPLcolocalization0.91014
PDS5Bassociation0.8606
PDS5Aassociation0.8603
SGO1physical association0.7406
SSU72physical association0.6707
FHL3physical association0.6704
CDCA5association0.6403
ESPL1direct interaction0.6203
CPNE5association0.5301
NIPBLphysical association0.4902
AIREphysical association0.4001
CTCFphysical association0.4001
HAND2physical association0.4001
ARL5Bassociation0.3502
REC8association0.3502
BRCA2association0.3501
CITED1association0.3501
CPNE9association0.3501
GOLGA7association0.3501
HSD17B1association0.3501
KLHL20association0.3501
RABIFassociation0.3501
SMC2association0.3501
FBXW7proximity0.2704
SMARCA4proximity0.2704
SPOPproximity0.2704

BioGRID (616 interactions; top human partners by supporting records in a sample of 600 records): SMC3 (Co-fractionation; 28 records), SMC1A (Co-fractionation; 24 records), STAG2 (Co-fractionation; 21 records), STAG1 (Co-fractionation; 18 records), WAPAL (Affinity Capture-MS; 13 records), CDCA5 (Affinity Capture-MS; 9 records), PDS5A (Affinity Capture-MS; 9 records), PDS5B (Affinity Capture-Western; 9 records), USP13 (Affinity Capture-MS; 5 records), CCAR2 (Affinity Capture-MS; 3 records), CDC34 (Affinity Capture-MS; 3 records), FHL3 (Two-hybrid; 3 records), HIST1H4A (Affinity Capture-MS; 3 records), MCM7 (Co-fractionation; 3 records), NSMCE2 (Biochemical Activity; 3 records)

SIGNOR signaling

showing 12 of 13 signaling interactions:

AEffectBMechanism
PRSS21up-regulatesRAD21cleavage
RAD21“down-regulates quantity by repression”RUNX1“transcriptional regulation”
RAD21“down-regulates quantity”APOB“transcriptional regulation”
STAG2“up-regulates quantity by stabilization”RAD21binding
RAD21“down-regulates activity”GATA2relocalization
RAD21“down-regulates activity”RUNX1relocalization
RAD21“down-regulates activity”ERGrelocalization
PLK1“down-regulates quantity by destabilization”RAD21dephosphorylation
ESPL1“down-regulates quantity by destabilization”RAD21cleavage
RAD21“up-regulates activity”DNA_repair
RAD21“form complex”“Cohesin complex”binding
CC2D1A“up-regulates activity”RAD21binding

Protein complexes (CORUM) (6)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

6 complexes by size:

ComplexSubunitsMembers
★ SNF2h-cohesin-NuRD complex16MBD2, MTA2, RBBP7, SMARCA5, MTA1, RBBP4, HDAC2, RAD21, SMC3, STAG1, STAG2, BAZ1A, HDAC1, MBD3, SMC1A, CHD3
Sororin-cohesin complex6SMC1A, SMC3, CDCA5, PDS5A, PDS5B, RAD21
Cohesin-SA1 complex4SMC3, STAG1, RAD21, SMC1A
Cohesin-SA2 complex4SMC3, STAG2, RAD21, SMC1A
DDX11-RAD21-SMC1A-SMC3 complex4SMC1A, SMC3, DDX11, RAD21
NIPBL-RAD21-SMC1A complex3NIPBL, RAD21, SMC1A

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 38 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Meiosis546.0×2e-06
S Phase635.1×5e-07
Reproduction530.7×1e-05
Resolution of Sister Chromatid Cohesion1027.9×1e-10
Meiotic synapsis522.7×6e-05
Mitotic Metaphase and Anaphase721.9×7e-07
Mitotic Anaphase721.9×7e-07
Separation of Sister Chromatids1121.6×1e-10

GO biological processes:

GO termPartnersFoldFDR
mitotic sister chromatid cohesion6177.4×3e-10
sister chromatid cohesion6121.0×1e-09
cell division1113.4×5e-08
positive regulation of ERK1 and ERK2 cascade511.2×3e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 2 cancer types — AML, LUSC.

intOGen’s role is a computational inference from cohort mutation patterns and may diverge from the gene’s curated/literature role; read it alongside the evidence above.

Genetic variants

Variant evidence for RAD21: 555 ClinVar records (59 pathogenic / likely pathogenic); 2 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

555 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic40
Likely pathogenic19
Uncertain significance213
Likely benign170
Benign50

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 59 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
802434NM_006265.3(RAD21):c.144+1G>APathogeniccriteria provided, multiple submitters, no conflicts2
985588NM_006265.3(RAD21):c.1222G>T (p.Gly408Ter)Pathogeniccriteria provided, multiple submitters, no conflicts2
1805433NM_006265.3(RAD21):c.1635del (p.Gly547fs)Pathogeniccriteria provided, multiple submitters, no conflicts2
2631614NM_006265.3(RAD21):c.160C>T (p.Arg54Trp)Likely pathogeniccriteria provided, multiple submitters, no conflicts3
998067NM_006265.3(RAD21):c.9C>A (p.Tyr3Ter)Likely pathogeniccriteria provided, multiple submitters, no conflicts2
560415NM_006265.3(RAD21):c.1864G>A (p.Ala622Thr)Pathogeniccriteria provided, single submitter2
864835NM_006265.3(RAD21):c.589C>T (p.Gln197Ter)Pathogeniccriteria provided, single submitter2
864836NM_006265.3(RAD21):c.1217_1224del (p.Lys406fs)Pathogeniccriteria provided, single submitter2
1185049NM_006265.3(RAD21):c.943_946del (p.Glu315fs)Pathogeniccriteria provided, single submitter2
211993NM_006265.3(RAD21):c.56_62del (p.Leu19fs)Pathogeniccriteria provided, single submitter1
211994NM_006265.3(RAD21):c.579dup (p.Glu194fs)Pathogeniccriteria provided, single submitter1
211995NM_006265.3(RAD21):c.592_593dup (p.Ser198fs)Pathogeniccriteria provided, single submitter1
280268NM_006265.3(RAD21):c.578T>A (p.Leu193Ter)Pathogeniccriteria provided, single submitter1
418706NM_006265.3(RAD21):c.1651del (p.Gln551fs)Pathogeniccriteria provided, single submitter1
436481NM_006265.3(RAD21):c.181_182dup (p.Gly62fs)Pathogeniccriteria provided, single submitter1

Per-variant reference — Sugi Variant

Explore RAD21’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 1,123):

Position(s)EffectΔscoreSites
8:116847692–116847693acceptor_loss1.00002
8:116850768–116850769acceptor_loss1.00005
8:116850769acceptor_gain1.0000
8:116850776–116850777acceptor_gain1.00002
8:116851946–116851947donor_loss1.00005
8:116852097acceptor_loss1.0000
8:116852101–116852103acceptor_gain1.00002
8:116852109–116852111acceptor_gain1.00003
8:116852511donor_gain1.0000
8:116852709–116852710acceptor_loss1.00006

AlphaMissense

2,123 missense substitutions predicted likely pathogenic (of 4,235 scored), across 406 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M36190.9961.000
M8790.9490.999
M5190.9261.000
H2281.0001.000
H5881.0001.000
D7781.0001.000
D32781.0001.000
F8980.9991.000
F280.9981.000
D9580.9981.000
D34680.9970.999
D35280.9950.998
F11780.9941.000
F30480.9941.000
H3180.9910.999
F11480.9871.000
D2480.9861.000
D11680.9860.998
F3380.9851.000
F59780.9841.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

CancerPrognosticp-value
Kidney Renal Clear Cell Carcinoma (TCGA)favorable2.87e-05
Kidney Chromophobe (TCGA)unfavorable3.58e-05
Liver Hepatocellular Carcinoma (validation)unfavorable0.000622
Lung Adenocarcinoma (TCGA)unfavorable0.000923

Disease associations

OMIM: gene MIM:606462 | disease phenotypes: MIM:614701, MIM:122470, MIM:611376

GenCC curated gene-disease

3 curated gene-disease records:

DiseaseClassificationInheritanceRecords
Cornelia de Lange syndrome 4DefinitiveAutosomal dominant4
Cornelia de Lange syndromeDefinitiveAutosomal dominant2
Mungan syndromeStrongAutosomal recessive2

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

1 validity classifications:

DiseaseClassificationInheritance
Cornelia de Lange syndromeDefinitiveAD

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (15 panels, 11 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

15 panels:

PanelRating
Cerebral malformationgreen
Cleftinggreen
DDG2Pgreen
Fetal anomaliesgreen
Haematological malignancies cancer susceptibilitygreen
Holoprosencephalygreen
Hypotonic infantgreen
IUGR and IGF abnormalitiesgreen
Intellectual disabilitygreen
Leukodystrophy, childhood onsetgreen
Severe microcephalygreen
Paediatric disordersamber
Paediatric pseudo-obstruction syndromeamber
Radial dysplasiaamber
Skeletal dysplasiaamber

Mondo (5): Cornelia de Lange syndrome 4 (MONDO:0013864), Cornelia de Lange syndrome (MONDO:0016033), Cornelia de Lange syndrome 1 (MONDO:0007387), Mungan syndrome (MONDO:0012657), acute megakaryoblastic leukemia in down syndrome (MONDO:0020526)

Orphanet (2): Cornelia de Lange syndrome (Orphanet:199), Acute megakaryoblastic leukemia in children with Down syndrome (Orphanet:99887)

HPO phenotypes

showing 60 of 160 phenotypes (HPO-id order):

HPOTerm
HP:0000003Multicystic kidney dysplasia
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000010Recurrent urinary tract infections
HP:0000028Cryptorchidism
HP:0000047Hypospadias
HP:0000059Hypoplastic labia majora
HP:0000076Vesicoureteral reflux
HP:0000083Renal insufficiency
HP:0000089Renal hypoplasia
HP:0000130Abnormality of the uterus
HP:0000164Abnormality of the dentition
HP:0000174Abnormal palate morphology
HP:0000175Cleft palate
HP:0000176Submucous cleft hard palate
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000220Velopharyngeal insufficiency
HP:0000233Thin vermilion border
HP:0000248Brachycephaly
HP:0000252Microcephaly
HP:0000294Low anterior hairline
HP:0000316Hypertelorism
HP:0000319Smooth philtrum
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000358Posteriorly rotated ears
HP:0000369Low-set ears
HP:0000381Stapes ankylosis
HP:0000400Macrotia
HP:0000405Conductive hearing impairment
HP:0000407Sensorineural hearing impairment
HP:0000411Protruding ear
HP:0000413Atresia of the external auditory canal
HP:0000414Bulbous nose
HP:0000431Wide nasal bridge
HP:0000453Choanal atresia
HP:0000463Anteverted nares
HP:0000470Short neck
HP:0000482Microcornea
HP:0000486Strabismus
HP:0000498Blepharitis
HP:0000501Glaucoma
HP:0000508Ptosis
HP:0000518Cataract
HP:0000527Long eyelashes
HP:0000545Myopia
HP:0000574Thick eyebrow
HP:0000582Upslanted palpebral fissure
HP:0000601Hypotelorism
HP:0000639Nystagmus
HP:0000664Synophrys
HP:0000667Phthisis bulbi
HP:0000684Delayed eruption of teeth
HP:0000687Widely spaced teeth
HP:0000717Autism
HP:0000722Compulsive behaviors
HP:0000739Anxiety
HP:0000767Pectus excavatum
HP:0000768Pectus carinatum

GWAS associations

2 associations:

StudyTraitp-value
GCST005863_11Menopause (age at onset)2e-8
GCST005863_29Menopause (age at onset)3e-7

EFO canonical traits (from GWAS)

1 canonical traits:

EFO IDTrait name
EFO:0004704age at menopause

MeSH disease descriptors

1 disease descriptors:

DescriptorNameTree numbers
C548078Mungan Syndrome *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

57 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsincreases abundance, increases expression, decreases expression3
Particulate Matterincreases abundance, affects expression, decreases expression3
bisphenol Adecreases expression, affects cotreatment, increases expression2
trichostatin Aaffects cotreatment, decreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
echimidineincreases metabolic processing, decreases expression1
TAK-243decreases sumoylation1
pradimicin-IRDdecreases expression1
2,4,6-tribromophenoldecreases expression1
lasiocarpinedecreases expression, increases metabolic processing1
triphenyl phosphateaffects expression1
riddelliinedecreases expression, increases metabolic processing1
beta-lapachonedecreases expression1
arseniteaffects binding, decreases reaction1
afimoxifeneaffects response to substance1
sodium arsenitedecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneincreases expression, affects cotreatment1
coumarindecreases phosphorylation1
beta-methylcholineaffects expression1
deguelinincreases expression1
nickel acetateaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
torcetrapibincreases expression1
ICG 001decreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
hexabrominated diphenyl ether 153decreases expression1
jinfukangdecreases expression1

Cellosaurus cell lines

32 cell lines: 29 cancer cell line, 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_0393LN-229Cancer cell lineFemale
CVCL_0589Kasumi-1Cancer cell lineMale
CVCL_1632P31/FUJCancer cell lineMale
CVCL_A5S0SEES3-1V human RAD21, clone1Embryonic stem cellMale
CVCL_A5S1SEES3-1V human RAD21, clone2Embryonic stem cellMale
CVCL_A5S2SEES3-1V human RAD21, clone3Embryonic stem cellMale
CVCL_A602CMYCancer cell lineMale
CVCL_A8V5LN229/CD20Cancer cell lineFemale
CVCL_D2R8LN229/mCCR3Cancer cell lineFemale
CVCL_D2RMLN229/mCD39Cancer cell lineFemale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 252 trials:

NCTPhaseStatusTitle
NCT05657860Phase 4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479Phase 4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829Phase 4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198Phase 4RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736Phase 3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT04381897Phase 2NOT_YET_RECRUITINGUse of N-Acetylcysteine in the Treatment of Repetitive and Self-Injurious Behaviors in Cornelia de Lange Syndrome
NCT02304302Phase 2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950Phase 2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226Phase 2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856Phase 2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT01773278Phase 2UNKNOWNCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT05273320Phase 1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361Phase 1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764Phase 1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827Phase 1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940Phase 1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT06789783Phase 2/3RECRUITINGCornelia De Lange Syndrome: Assessing Positive Effects of Lithium Treatment
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT03113877Not specifiedTERMINATEDEvaluation of Autonomic Function in Individuals With Cornelia de Lange Syndrome (CdLS)
NCT04463316Not specifiedRECRUITINGGROWing Up With Rare GENEtic Syndromes
NCT05829668Not specifiedRECRUITINGBehavioral Assessment and Treatment of Problem Behavior in Children With Cornelia de Lange Syndrome
NCT03479476Phase 2/3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796Phase 1/2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672Early Phase 1TERMINATEDClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394Not specifiedUNKNOWNFCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614Not specifiedCOMPLETEDPsychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405Not specifiedCOMPLETEDTMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders
NCT02862808Not specifiedCOMPLETEDMolecular Diagnosis of Syndromic or Isolated Severe Intellectual Disability Using Whole Exome Sequencing : a Pilot Study
NCT02881333Not specifiedUNKNOWNVarious Type of Genetic Events in Patients With Intellectual Disability
NCT02889068Not specifiedCOMPLETEDTargeted Next Generation Sequencing and Intellectual Disability
NCT02914951Not specifiedENROLLING_BY_INVITATIONCognitive-Behavioral Therapy for Irritability in Children With Autism Spectrum Disorder and Intellectual Disability
NCT02919826Not specifiedCOMPLETEDDialectical Behaviour Group Therapy for Adults With Intellectual Disabilities
NCT02934854Not specifiedWITHDRAWNBiomarker for Creatine Deficiency Syndromes (BioCDS)
NCT03033797Not specifiedUNKNOWNAugmentative and Alternative Communication in Games With Virtual Reality in Intellectual Disabilities
NCT03135236Not specifiedCOMPLETEDParents as the Primary Sexuality Educators for Their Young Adults With Down Syndrome
NCT03139760Not specifiedCOMPLETEDPOWERSforID: A Telehealth Weight Management System for Adults With Intellectual Disability
NCT03203226Not specifiedCOMPLETEDThe Feldenkrais Method for People With Intellectual Disability
NCT03212092Not specifiedCOMPLETEDReducing Aggression Among People With an Intellectual Disability
NCT03218462Not specifiedCOMPLETEDEffect of Sensory Adapted Dental Environment on Dental Anxiety of Children With Intellectual and Developmental Disabilities
NCT03234231Not specifiedUNKNOWNSupervised Brushing Programme for Intellectual Disabled Students