RCCD1

gene
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Also known as MGC14386

Summary

RCCD1 (RCC1 domain containing 1, HGNC:30457) is a protein-coding gene on chromosome 15q26.1, encoding RCC1 domain-containing protein 1 (A6NED2). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8.

Predicted to be involved in chromatin organization. Located in cytosol and plasma membrane.

Source: NCBI Gene 91433 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 72 total
  • MANE Select transcript: NM_001017919

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30457
Approved symbolRCCD1
NameRCC1 domain containing 1
Location15q26.1
Locus typegene with protein product
StatusApproved
AliasesMGC14386
Ensembl geneENSG00000166965
Ensembl biotypeprotein_coding
OMIM617997
Entrez91433

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 18 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000394258, ENST00000554302, ENST00000555155, ENST00000555737, ENST00000556333, ENST00000556618, ENST00000556774, ENST00000557266, ENST00000557750, ENST00000850874, ENST00000852981, ENST00000852982, ENST00000852983, ENST00000852984, ENST00000852985, ENST00000852986, ENST00000852987, ENST00000852988, ENST00000935355, ENST00000935356, ENST00000935357, ENST00000935358, ENST00000970828, ENST00000970829

RefSeq mRNA: 2 — MANE Select: NM_001017919 NM_001017919, NM_033544

CCDS: CCDS32333

Canonical transcript exons

ENST00000394258 — 8 exons

ExonStartEnd
ENSE000013101349096161890963125
ENSE000013718119095711390957503
ENSE000017448959095661290956900
ENSE000024855089095488490954948
ENSE000036122639096102590961054
ENSE000036140919095760490957725
ENSE000036342159095990090959998
ENSE000036800389096032890960498

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 93.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.9598 / max 188.3527, expressed in 1693 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1485305.52721556
1485310.9520458
1485370.7808105
1485350.6954412
1485320.6120352
1485330.3012167
1485360.091226

Top tissues by expression

237 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065593.37gold quality
oocyteCL:000002392.76gold quality
ileal mucosaUBERON:000033192.35silver quality
pancreatic ductal cellCL:000207986.99silver quality
mucosa of transverse colonUBERON:000499186.69gold quality
pigmented layer of retinaUBERON:000178285.55gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.02gold quality
right adrenal gland cortexUBERON:003582785.00gold quality
right adrenal glandUBERON:000123384.72gold quality
right hemisphere of cerebellumUBERON:001489084.69gold quality
left ventricle myocardiumUBERON:000656684.46gold quality
cerebellar hemisphereUBERON:000224584.30gold quality
cerebellar cortexUBERON:000212984.17gold quality
lower esophagus mucosaUBERON:003583483.82gold quality
left adrenal gland cortexUBERON:003582583.59gold quality
left adrenal glandUBERON:000123483.58gold quality
cerebellumUBERON:000203783.49gold quality
adrenal cortexUBERON:000123583.38gold quality
ventricular zoneUBERON:000305383.37gold quality
epithelial cell of pancreasCL:000008383.22gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.85gold quality
kidney epitheliumUBERON:000481982.57gold quality
body of pancreasUBERON:000115082.54gold quality
parotid glandUBERON:000183182.53gold quality
adrenal glandUBERON:000236982.34gold quality
transverse colonUBERON:000115782.04gold quality
left ovaryUBERON:000211981.99gold quality
stromal cell of endometriumCL:000225581.96gold quality
trabecular bone tissueUBERON:000248381.91gold quality
right ovaryUBERON:000211881.63gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.00
E-MTAB-4850no123.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

58 targeting RCCD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-651-3P99.9473.485177
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-589-3P99.9169.622088
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-17-5P99.8973.832665
HSA-MIR-95-5P99.8972.173973
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-44899.7972.372103
HSA-MIR-205299.7969.372031
HSA-MIR-2681-5P99.7567.641655
HSA-MIR-674599.7465.331321
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-3934-5P99.6764.04846
HSA-MIR-29899.6367.561916
HSA-MIR-1212399.5271.792990
HSA-MIR-568999.5071.261154
HSA-MIR-239299.4367.50708
HSA-MIR-2115-3P99.3169.682026
HSA-MIR-5589-3P99.2968.301443
HSA-MIR-1273H-3P99.2967.55980

Literature-anchored findings (GeneRIF, showing 5)

  • RCCD1 and KDM8 form a histone demethylase complex. (PMID:24981860)
  • Expression of RCCD1 in whole blood was also suggestively associated with disease risk (p-value: 1.2x10-05), as were expression of ACAP1 (p-value: 1.9x10-05) and LRRC25 (p-value: 5.2x10-05). While genome-wide association studies (GWAS) have implicated RCCD1 and ANKLE1 in breast cancer risk, they have not identified the remaining three genes (PMID:28362817)
  • RCCD1 as a novel regulator of TGF-beta-induced epithelial mesenchymal transformation and cell migration in non-small lung carcinoma cells. (PMID:28455245)
  • JMJD5 catalyzes stereoselective C-3 hydroxylation of arginine residues in sequences from human RCCD1 and ribosomal protein S6. (PMID:29563586)
  • miR-519b-3p binds to LINC01419 and has a role in upregulating RCCD1 in lung adenocarcinoma cells (PMID:31582214)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_reriorccd1ENSDARG00000071074
danio_rerioherc7ENSDARG00000098906
ENSDARG00000104505
mus_musculusRccd1ENSMUSG00000038930
rattus_norvegicusRccd1ENSRNOG00000042059
drosophila_melanogastercaFBGN0000247
drosophila_melanogasterRcc1FBGN0002638
drosophila_melanogasterCG7420FBGN0031344
drosophila_melanogasterCG6678FBGN0038917
caenorhabditis_elegansWBGENE00004304
caenorhabditis_elegansK11D2.1WBGENE00010768

Paralogs (9): ALS2 (ENSG00000003393), HERC1 (ENSG00000103657), SERGEF (ENSG00000129158), RCBTB1 (ENSG00000136144), RCBTB2 (ENSG00000136161), RPGR (ENSG00000156313), RCC2 (ENSG00000179051), RCC1 (ENSG00000180198), RCC1L (ENSG00000274523)

Protein

Protein identifiers

RCC1 domain-containing protein 1A6NED2 (reviewed: A6NED2)

All UniProt accessions (3): A6NED2, G3V2I3, G3V3Q4

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8. Possibly together with KDM8, is involved in proper mitotic spindle organization and chromosome segregation. Plays a role in regulating alpha-tubulin deacetylation and cytoskeletal microtubule stability, thereby promoting cell migration and TGF-beta-induced epithelial to mesenchymal transition (EMT), potentially through the inhibition of KDM8.

Subunit / interactions. Found in a complex with KDM8. Interacts (via N-terminus) with KDM8 (via N-terminus).

Subcellular location. Chromosome.

Post-translational modifications. Specifically hydroxylated (with R stereochemistry) at C-3 of ARG-141 by KDM8.

RefSeq proteins (2): NP_001017919, NP_291022 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000408Reg_chr_condensRepeat
IPR009091RCC1/BLIP-IIHomologous_superfamily
IPR052830RCC1_domain-containingFamily

Pfam: PF00415

UniProt features (10 total): repeat 4, chain 1, region of interest 1, modified residue 1, sequence variant 1, mutagenesis site 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
6F4TX-RAY DIFFRACTION1.22
6F4RX-RAY DIFFRACTION1.3
6F4SX-RAY DIFFRACTION1.46

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A6NED2-F187.750.73

Functional residue map

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

Post-translational modifications (1): 141

Mutagenesis-validated functional residues (1):

PositionPhenotype
141abolishes hydroxylation by kdm8.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9629569Protein hydroxylation

MSigDB gene sets: 90 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, CADWELL_ATG16L1_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, chr15q26, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, WHITFIELD_CELL_CYCLE_G2, FOSTER_KDM1A_TARGETS_DN, REACTOME_GAMMA_CARBOXYLATION_HYPUSINYLATION_HYDROXYLATION_AND_ARYLSULFATASE_ACTIVATION, GSE14415_INDUCED_TREG_VS_FOXP3_KO_INDUCED_TREG_UP, CREB3L4_TARGET_GENES, E2F5_TARGET_GENES, ELF2_TARGET_GENES, HOXA13_TARGET_GENES

GO Biological Process (1): chromatin organization (GO:0006325)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): chromosome (GO:0005694), cytosol (GO:0005829), plasma membrane (GO:0005886)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular component organization1
binding1
intracellular membraneless organelle1
cytoplasm1
cellular anatomical structure1
membrane1
cell periphery1

Protein interactions and networks

STRING

1084 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RCCD1KDM8Q8N371668
RCCD1WDFY4Q6ZS81469
RCCD1LRRC25Q8N386465
RCCD1CZIBQ9NWV4447
RCCD1ANKLE1Q8NAG6441
RCCD1TMEM220Q6QAJ8433
RCCD1ZNF433Q8N7K0420
RCCD1ACAP1Q15027401
RCCD1TYW5A2RUC4397
RCCD1FLACC1Q96Q35396
RCCD1LRRC37AA6NMS7393
RCCD1LRRC37A3O60309390
RCCD1ZDHHC11BP0C7U3382
RCCD1C11orf24Q96F05371
RCCD1ZNF530Q6P9A1369

IntAct

34 interactions, top by confidence:

ABTypeScore
KDM8RCCD1psi-mi:“MI:0915”(physical association)0.710
ALDH3A1RCCD1psi-mi:“MI:0914”(association)0.640
RCCD1SPAG9psi-mi:“MI:0914”(association)0.640
POLR2LRCCD1psi-mi:“MI:0914”(association)0.640
MAPK8IP3RCCD1psi-mi:“MI:0914”(association)0.640
YJU2BRCCD1psi-mi:“MI:0914”(association)0.530
INPP5ARCCD1psi-mi:“MI:0914”(association)0.530
ZNF219RCCD1psi-mi:“MI:0914”(association)0.530
SLC27A3RCCD1psi-mi:“MI:0914”(association)0.350
RCCD1ZNF609psi-mi:“MI:0914”(association)0.350
ZNF219psi-mi:“MI:0914”(association)0.350
CDC73RCCD1psi-mi:“MI:0914”(association)0.350
CTR9RCCD1psi-mi:“MI:0914”(association)0.350
DDX6RCCD1psi-mi:“MI:0914”(association)0.350
EZH1RCCD1psi-mi:“MI:0914”(association)0.350
CSTL1DENND11psi-mi:“MI:0914”(association)0.350
UBL3RCCD1psi-mi:“MI:0914”(association)0.350
RCCD1IFT56psi-mi:“MI:0914”(association)0.350
MAPK8IP3SHTN1psi-mi:“MI:0914”(association)0.350
MRPS17RCCD1psi-mi:“MI:0914”(association)0.350
AFG2BRCCD1psi-mi:“MI:0914”(association)0.350

BioGRID (89): RCCD1 (Affinity Capture-MS), KCTD9 (Affinity Capture-MS), KDM8 (Affinity Capture-MS), MAPK8IP3 (Affinity Capture-MS), RCCD1 (Affinity Capture-MS), SPAG9 (Affinity Capture-MS), TSC22D3 (Affinity Capture-MS), POLR2L (Affinity Capture-MS), DDHD2 (Affinity Capture-MS), C5orf34 (Affinity Capture-MS), RCCD1 (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), RAB3GAP1 (Affinity Capture-MS), RCCD1 (Affinity Capture-MS), ZNF609 (Affinity Capture-MS)

ESM2 similar proteins: A1A4I4, A5PKD8, A6NED2, A8MQ27, O35465, O60294, O75808, O94819, O95382, P70268, Q0MW30, Q14318, Q16512, Q2T9J0, Q32NY4, Q32P44, Q3B7U9, Q3MHW0, Q3U5Q7, Q3USL1, Q4R828, Q561R2, Q5EBM0, Q5EBP3, Q5PQP9, Q60806, Q63433, Q6PAT0, Q7T0L4, Q8BNW9, Q8BTU7, Q8BYR1, Q8IYL2, Q8N5A5, Q8NEP7, Q8VC03, Q8VHS5, Q8WXI3, Q91ZT7, Q96C12

Diamond homologs: A6NED2, F1RD40, F2Z461, O74881, O75592, O95714, P18754, P23800, Q15034, Q4R828, Q4U2R1, Q52KW8, Q5GLZ8, Q5PQN1, Q6NRS1, Q6PAV2, Q7TPH6, Q80YD6, Q8BTU7, Q8IVU3, Q8VE37, Q9FN03, Q9NB71, Q9P2D0, Q9UII4, D3ZGQ5, O95199, P0C5Y8, P25171, P25183, P58544, Q15751, Q5BIW4, Q5DX34, Q5RCZ7, Q6NXM2, Q6NYE2, Q6ZPR6, Q7ZZC8, Q86SG6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance59
Likely benign1
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1487 predictions. Top by Δscore:

VariantEffectΔscore
15:90959894:TTTCA:Tacceptor_loss1.0000
15:90959896:TCAGA:Tacceptor_loss1.0000
15:90959897:CA:Cacceptor_loss1.0000
15:90959898:A:AGacceptor_gain1.0000
15:90959898:A:Cacceptor_loss1.0000
15:90959899:G:GAacceptor_gain1.0000
15:90959899:G:GTacceptor_loss1.0000
15:90959899:GA:Gacceptor_gain1.0000
15:90959899:GAGA:Gacceptor_gain1.0000
15:90959995:G:Tdonor_gain1.0000
15:90955791:AAC:Aacceptor_gain0.9900
15:90955793:C:CAacceptor_gain0.9900
15:90956896:GACCC:Gdonor_gain0.9900
15:90956901:G:GGdonor_gain0.9900
15:90957723:GTG:Gdonor_gain0.9900
15:90959887:T:Aacceptor_gain0.9900
15:90959899:GAGAC:Gacceptor_gain0.9900
15:90959996:A:Tdonor_gain0.9900
15:90959996:AAGG:Adonor_loss0.9900
15:90959997:AG:Adonor_loss0.9900
15:90959998:GG:Gdonor_loss0.9900
15:90959999:GTGAG:Gdonor_loss0.9900
15:90960000:T:Adonor_loss0.9900
15:90955220:G:Tdonor_gain0.9800
15:90955787:A:AGacceptor_gain0.9800
15:90955792:AC:Aacceptor_gain0.9800
15:90956897:ACCC:Adonor_gain0.9800
15:90957721:GAGTG:Gdonor_gain0.9800
15:90959995:G:GTdonor_gain0.9800
15:90960001:G:GGdonor_loss0.9800

AlphaMissense

2378 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:90959920:T:AW234R0.994
15:90959920:T:CW234R0.994
15:90956768:T:CF12L0.993
15:90956770:C:AF12L0.993
15:90956770:C:GF12L0.993
15:90960487:C:AA313D0.992
15:90961045:T:AW324R0.992
15:90961045:T:CW324R0.992
15:90960486:G:CA313P0.991
15:90957711:C:TS222F0.990
15:90957710:T:CS222P0.989
15:90956774:T:CF14L0.988
15:90956776:C:AF14L0.988
15:90956776:C:GF14L0.988
15:90959931:T:AN237K0.988
15:90959931:T:GN237K0.988
15:90957490:T:AW182R0.987
15:90957490:T:CW182R0.987
15:90957618:G:AG191D0.987
15:90959930:A:TN237I0.987
15:90960472:G:AG308E0.987
15:90956772:G:AG13D0.986
15:90959923:G:CG235R0.986
15:90961048:G:CG325R0.986
15:90961728:T:AW364R0.986
15:90961728:T:CW364R0.986
15:90956783:T:CF17L0.984
15:90956785:C:AF17L0.984
15:90956785:C:GF17L0.984
15:90957711:C:AS222Y0.983

dbSNP variants (sampled 300 via entrez): RS1000110959 (15:90953864 G>A), RS1000139699 (15:90960562 GACGGAAAA>G), RS1000362431 (15:90962686 T>C), RS1000652566 (15:90955711 A>AC), RS1000797326 (15:90962483 T>C,G), RS1001061196 (15:90956997 G>T), RS1001283759 (15:90960635 A>C,G), RS1001393007 (15:90961262 C>G,T), RS1001419787 (15:90956121 G>T), RS1001492923 (15:90956293 A>AT), RS1001540351 (15:90956563 C>G), RS1002659509 (15:90955171 G>C), RS1002980751 (15:90961880 G>A), RS1003168491 (15:90957255 G>A), RS1003294040 (15:90962792 A>G)

Disease associations

OMIM: gene MIM:617997 | disease phenotypes: MIM:210900

GenCC curated gene-disease

Mondo (1): Bloom syndrome (MONDO:0008876)

Orphanet (1): Bloom syndrome (Orphanet:125)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

StudyTraitp-value
GCST006804_14Red cell distribution width1.000000e-110
GCST006914_16Sleep duration3.000000e-08
GCST90013466_16Height3.000000e-09
GCST90013466_37Height2.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009188Red cell distribution width

MeSH disease descriptors (1)

DescriptorNameTree numbers
D001816Bloom SyndromeC16.131.077.137; C16.320.798.313; C18.452.284.100; C20.673.795.313

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases expression3
Resveratrolaffects cotreatment, increases expression2
Benzo(a)pyreneaffects methylation, increases methylation2
Cisplatinaffects expression, affects cotreatment, increases expression2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
propionaldehydedecreases expression1
trichostatin Aaffects expression1
beta-lapachonedecreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
potassium chromate(VI)decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
abrinedecreases expression1
jinfukangaffects cotreatment, increases expression1
Decitabineaffects expression1
Leflunomidedecreases expression1
Acetaminophenincreases expression1
Arsenicaffects methylation1
Calcitrioldecreases expression, affects cotreatment1
Coumestrolaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Smokedecreases expression1
Sodium Dodecyl Sulfatedecreases expression1
Testosteroneaffects cotreatment, decreases expression1
Thiramdecreases expression1

Clinical trials (associated diseases)

3 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00021437Not specifiedCOMPLETEDBiological Significance of the Bloom’s Syndrome Protein
NCT04251325Not specifiedUNKNOWNSocio-demographic Characteristics of Basic Life Support Course Participants
NCT04353089Not specifiedUNKNOWNGeographical Association Between Basic Life Support Courses, Bystander Cardiopulmonary Resuscitation and Survival
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Bloom syndrome