RECQL4

gene
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Also known as RecQ4

Summary

RECQL4 (RecQ like helicase 4, HGNC:9949) is a protein-coding gene on chromosome 8q24.3, encoding ATP-dependent DNA helicase Q4 (O94761). An ATP-dependent DNA helicase which unwinds dsDNA with a 3’-overhang in a 3’-5’ direction.

The protein encoded by this gene is a DNA helicase that belongs to the RecQ helicase family. DNA helicases unwind double-stranded DNA into single-stranded DNAs and may modulate chromosome segregation. This gene is predominantly expressed in thymus and testis. Mutations in this gene are associated with Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes.

Source: NCBI Gene 9401 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Rothmund-Thomson syndrome (Definitive, ClinGen) — +6 more curated relationships
  • GWAS associations: 4
  • Clinical variants (ClinVar): 5,153 total — 276 pathogenic, 68 likely-pathogenic
  • Phenotypes (HPO): 215
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
  • MANE Select transcript: NM_004260

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9949
Approved symbolRECQL4
NameRecQ like helicase 4
Location8q24.3
Locus typegene with protein product
StatusApproved
AliasesRecQ4
Ensembl geneENSG00000160957
Ensembl biotypeprotein_coding
OMIM603780
Entrez9401

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000301323, ENST00000524998, ENST00000529424, ENST00000531875, ENST00000532846, ENST00000534270, ENST00000534538, ENST00000534626, ENST00000617875, ENST00000621189, ENST00000688394, ENST00000887977, ENST00000922086, ENST00000922087, ENST00000971710

RefSeq mRNA: 27 — MANE Select: NM_004260 NM_001413017, NM_001413018, NM_001413019, NM_001413020, NM_001413021, NM_001413022, NM_001413023, NM_001413024, NM_001413025, NM_001413027, NM_001413028, NM_001413029, NM_001413030, NM_001413031, NM_001413032, NM_001413033, NM_001413034, NM_001413035, NM_001413036, NM_001413037, NM_001413038, NM_001413039, NM_001413040, NM_001413041, NM_001413042, NM_001413043, NM_004260

CCDS: CCDS75804

Canonical transcript exons

ENST00000617875 — 21 exons

ExonStartEnd
ENSE00003497080144512847144513138
ENSE00003577229144515764144515890
ENSE00003627709144512392144512561
ENSE00003645517144512642144512771
ENSE00003703912144515326144515457
ENSE00003706019144514189144514362
ENSE00003706081144513928144514107
ENSE00003706299144517050144517190
ENSE00003706451144514442144514525
ENSE00003709211144512144144512324
ENSE00003710143144515150144515242
ENSE00003716048144517701144517833
ENSE00003720833144514936144515072
ENSE00003722249144517414144517508
ENSE00003726054144517602144517635
ENSE00003730309144515988144516764
ENSE00003744392144511681144511789
ENSE00003746399144513218144513480
ENSE00003748671144511911144512067
ENSE00003789763144513571144513712
ENSE00003901898144511288144511555

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 97.70.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.8112 / max 166.4055, expressed in 1422 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
9569310.11371203
956922.1749628
956941.5227756

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583497.70gold quality
ventricular zoneUBERON:000305392.85gold quality
mucosa of transverse colonUBERON:000499192.62gold quality
right testisUBERON:000453492.29gold quality
left testisUBERON:000453391.73gold quality
right hemisphere of cerebellumUBERON:001489090.12gold quality
ganglionic eminenceUBERON:000402390.05gold quality
cerebellar hemisphereUBERON:000224589.42gold quality
cerebellar cortexUBERON:000212989.09gold quality
testisUBERON:000047388.53gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.44gold quality
endometrium epitheliumUBERON:000481188.04gold quality
cerebellumUBERON:000203786.49gold quality
esophagus mucosaUBERON:000246985.10gold quality
right frontal lobeUBERON:000281084.70gold quality
cortical plateUBERON:000534383.87gold quality
transverse colonUBERON:000115783.71gold quality
stromal cell of endometriumCL:000225583.08gold quality
esophagusUBERON:000104382.35gold quality
putamenUBERON:000187481.42gold quality
embryoUBERON:000092281.41gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.31gold quality
caudate nucleusUBERON:000187381.22gold quality
tendon of biceps brachiiUBERON:000818881.20silver quality
small intestine Peyer’s patchUBERON:000345480.92gold quality
Brodmann (1909) area 9UBERON:001354080.62gold quality
nucleus accumbensUBERON:000188280.51gold quality
muscle layer of sigmoid colonUBERON:003580580.49gold quality
metanephros cortexUBERON:001053380.44gold quality
right lobe of thyroid glandUBERON:000111980.34gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-GEOD-99795no77.81
E-ANND-3no2.93

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1, HDAC1, SP1, TFAP2A, TP53

miRNA regulators (miRDB)

3 targeting RECQL4, 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-20A-3P99.4469.101575
HSA-MIR-473697.9665.891287
HSA-MIR-4778-5P97.9668.061634

Literature-anchored findings (GeneRIF, showing 40)

  • The RECQL4 gene structure is unusual because it contains many small introns <100 bp. We describe a proband with Rothmund-Thomson syndrome who has a novel 11-bp intronic deletion; this mutation results in a 66-bp intron too small for proper splicing. (PMID:12016592)
  • Two novel exonic single nucleotiude polymorphisms and a minisatellite repeat are characterized. (PMID:12601557)
  • RECQL4 mutations were not found in poikiloderma with neutropenia in Navajo and non-Navajo patients (PMID:12673665)
  • RECQL4 gene is not a frequent target for somatic mutations in sporadic osteosarcoma. (PMID:15221963)
  • RECQL4 from HeLa cells interacts with ubiquitin ligases UBR1 and UBR2. (PMID:15317757)
  • The human diseases connected with RECQL4 mutations appear distinct in their clinical phenotypes from Bloom or Werner’s symdrome. (PMID:15960976)
  • Baller-Gerold syndrome (BGS) in a subgroup of patients is due to RECQL4 mutations and could be integrated into a clinical spectrum that encompasses Rothmund-Thomson syndrome (RTS) and RAPADILINO syndrome. (PMID:15964893)
  • Findings suggest a role for RECQL4 in the repair of DNA double-strand breaks by homologous recombination and shed new light onto RECQL4’s function in human cells. (PMID:16141230)
  • RECQ4 lacks a detectable DNA helicase activity and is mutated in Rothmund-Thomson syndrome (PMID:16214424)
  • It is especially difficult to draw precise genotype-phenotype correlations in RECQL4 related syndromes. This is likely due to the complex and multiple cellular networks RECQL4 is associated with. (PMID:16617241)
  • These results suggest that enhanced oxidant sensitivity in RECQL4 deficient fibroblasts derived from RTS patients could be attributed to abnormal DNA metabolism and proliferation failure. (PMID:16678792)
  • These results demonstrate changes in the intracellular localization of RECQL4 in response to oxidative stress and identify an interaction between RECQL4 and PARP-1 (PMID:16949575)
  • RecQL4 may have a unique role in replication fork arrest. (PMID:17184169)
  • A greater role for the RECQL4 protein in DNA replication as opposed to repair of exogenous damage. (PMID:18504617)
  • RECQL4 polymorphisms and mutations are associated with Rothmund-Thomson Syndrome. (PMID:18616953)
  • genotype-phenotype analysis showed a significant correlation between RECQL4 mutational status and the presence of skeletal abnormalities (p < 0.0001) in Rothmund-Thomson syndrome patients (PMID:18647888)
  • RecQ4 has a role in the repair of UV-induced DNA damages in human cells (PMID:18693251)
  • Study reports that RAPADILINO patients identified as carriers of the c.1390+2delT mutation (p.Ala420_Ala463del) are at increased risk to develop lymphoma or osteosarcoma (6 out of 15 patients). (PMID:18716613)
  • RECQ4 exhibits DNA helicase activity. Importantly, two distinct regions of the protein, the conserved helicase motifs and the Sld2-like N-terminal domain, each independently promote ATP-dependent DNA unwinding. (PMID:19177149)
  • All osteosarcomas overexpressed RECQL4 in comparison to controls (PMID:19242607)
  • p300-mediated acetylation of the Rothmund-Thomson-syndrome gene product RECQL4 regulates its subcellular localization. (PMID:19299466)
  • Purified hRECQL4 protein (expressed in an insect expression system) is associated with both DNA helicase activity and single-stranded DNA-dependent ATPase activity. (PMID:19451148)
  • RECQL4 specifically stimulates the apurinic endonuclease activity of APE1, the DNA strand displacement activity of DNA polymerase beta, and incision of a 1- or 10-nucleotide flap DNA substrate by Flap Endonuclease I. (PMID:19567405)
  • MCM10 interacts directly with RECQ4 and regulates its DNA unwinding activity. (PMID:19696745)
  • Assembly of the Cdc45-Mcm2-7-GINS complex requires the Ctf4/And-1, RecQL4, and Mcm10 proteins. (PMID:19805216)
  • These results indicate that RECQ1 and RECQ4 are integral components of the human replication complex and play distinct roles in DNA replication initiation and replication fork progression in vivo. (PMID:20065033)
  • shows that RECQL4 is recruited early to laser-induced double-strand breaks and remains for a shorter duration than WRN and BLM (PMID:20222902)
  • Together, these data indicate that specific biochemical activities and protein partners of RecQ4 are conserved with those of the other RecQ helicases. (PMID:20451470)
  • Study shows that RecQL4 is an essential factor for prostate carcinogenesis. (PMID:21045146)
  • The N-terminal domain of RECQL4 is sufficient for cell viability. The C-terminal region including the helicase domain of RECQL4 is implicated in DNA repair. (PMID:21256165)
  • RecQL4, the N-terminal portion of which shares similarity with Sld2 known to be required for assembly of a replication complex in yeasts, is unique in that it has been shown to be essential for the initiation phase of normal DNA replication. (PMID:21436139)
  • Single Nucleotide Polymorphisms in RECQL4 gene is associated with glioblastoma. (PMID:22017238)
  • function of RECQL4 in telomere maintenance (PMID:22039056)
  • Measurements of mitochondrial bioenergetics showed a reduction in the mitochondrial reserve capacity after lentiviral knockdown of RECQL4 in two different primary cell lines. (PMID:22296597)
  • RECQL4 is essential for the transport of p53 to mitochondria. (PMID:22357944)
  • study concludes that the function of the RecQ helicases has diverged during evolution, with RecQL4 acquiring a function that allows cells to negotiate DNA replication templates that have been damaged by ionizing radiation (PMID:22508716)
  • BLM and RECQL4 interact physically and functionally in vivo and in vitro. (PMID:22544709)
  • Despite low-sequence homology, the N-terminus of the human RecQL4 helicase was determined to be a well-defined structure that carries an overall helical fold similar to homeodomain DNA-binding proteins but lacks their archetypical, minor groove-binding N-terminal extension. (PMID:22730300)
  • Nuclear exporting signals -mediated RecQL4 export to the cytoplasm is essential for the maintenance of mitochondrial genome stability. (PMID:22824301)
  • These observations help explain the underlying molecular etiology of the disease and our findings provide insight into the genotype and phenotype association among RECQL4 syndromes (PMID:22885111)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorecql4ENSDARG00000077516
mus_musculusRecql4ENSMUSG00000033762
rattus_norvegicusRecql4ENSRNOG00000032446
drosophila_melanogasterRecQ4FBGN0040290

Paralogs (4): RECQL (ENSG00000004700), RECQL5 (ENSG00000108469), WRN (ENSG00000165392), BLM (ENSG00000197299)

Protein

Protein identifiers

ATP-dependent DNA helicase Q4O94761 (reviewed: O94761)

Alternative names: DNA 3’-5’ helicase RecQ4, DNA helicase, RecQ-like type 4, RTS, RecQ protein-like 4

All UniProt accessions (8): O94761, A0A087WTJ0, A0A087X072, V9GY28, V9GY60, V9GYA3, V9GYB6, V9GZ64

UniProt curated annotations — full annotation on UniProt →

Function. An ATP-dependent DNA helicase which unwinds dsDNA with a 3’-overhang in a 3’-5’ direction. Does not unwind more than 18 bp of dsDNA. May modulate chromosome segregation. The N-terminal domain (residues 1-54) binds DNA Y-shaped DNA better than ss- or dsDNA. The core helicase domain binds ssDNA.

Subunit / interactions. Interacts with UBR1 and UBR2. Interacts with MCM10; this interaction regulates RECQL4 unwinding activity. Interacts (via residues 1-54) with TOPBP1.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Ubiquitously expressed, with highest levels in thymus and testis.

Disease relevance. RAPADILINO syndrome (RAPADILINOS) [MIM:266280] Disease characterized by radial and patellar aplasia or hypoplasia. The disease is caused by variants affecting the gene represented in this entry. Baller-Gerold syndrome (BGS) [MIM:218600] An autosomal recessive syndrome characterized by short stature, craniosynostosis, absent or hypoplastic radii, short and curved ulna, fused carpal bones and absent carpals, metacarpals and phalanges. Some patients manifest poikiloderma. Cases reported as Baller-Gerold syndrome have phenotypic overlap with several other disorders, including Saethre-Chotzen syndrome. The disease is caused by variants affecting the gene represented in this entry. Rothmund-Thomson syndrome 2 (RTS2) [MIM:268400] A form of Rothmund-Thomson syndrome, a disorder characterized by sparse hair, eyebrows and eyelashes, juvenile cataracts, and poikiloderma, a genodermatosis presenting with mottled pigmentation, telangiectasia and epidermal atrophy. Additional features are short stature, dysplastic nails, and skeletal and dental abnormalities. RTS2 is an autosomal recessive form frequently accompanied by an increased risk of osteosarcoma in childhood and skin cancer later in life. The disease is caused by variants affecting the gene represented in this entry.

Cofactor. Binds a Zn(2+) ion per subunit.

Induction. Up-regulated in actively dividing cells.

Similarity. Belongs to the helicase family. RecQ subfamily.

RefSeq proteins (27): NP_001399946, NP_001399947, NP_001399948, NP_001399949, NP_001399950, NP_001399951, NP_001399952, NP_001399953, NP_001399954, NP_001399956, NP_001399957, NP_001399958, NP_001399959, NP_001399960, NP_001399961, NP_001399962, NP_001399963, NP_001399964, NP_001399965, NP_001399966, NP_001399967, NP_001399968, NP_001399969, NP_001399970, NP_001399971, NP_001399972, NP_004251* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001650Helicase_C-likeDomain
IPR004589DNA_helicase_ATP-dep_RecQFamily
IPR011545DEAD/DEAH_box_helicase_domDomain
IPR014001Helicase_ATP-bdDomain
IPR021110DNA_rep_checkpnt_proteinFamily
IPR027417P-loop_NTPaseHomologous_superfamily

Pfam: PF00270, PF00271, PF11719

Enzyme classification (BRENDA):

  • EC 3.6.4.12 — DNA helicase (BRENDA: 0 organisms, 0 substrates, 0 inhibitors, 0 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 1 shown:

  • ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)

UniProt features (119 total): sequence variant 33, helix 29, strand 23, turn 8, binding site 5, region of interest 5, mutagenesis site 5, compositionally biased region 4, modified residue 3, domain 2, chain 1, short sequence motif 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5LSTX-RAY DIFFRACTION2.75
2KMUSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O94761-F168.320.33

Functional residue map

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

Ligand- & substrate-binding residues (5): 502–509; 853; 855; 897; 900

Post-translational modifications (3): 27, 178, 180

Mutagenesis-validated functional residues (5):

PositionPhenotype
508no helicase activity (in a fragment of residues 427-1208).
605no helicase activity (in a fragment of residues 427-1208).
618loss of helicase activity, 20% atpase activity (in a fragment of residues 427-1208).
944–1032about 50% reduction in helicase velocity (in a fragment of residues 427-1208).
1117–1208decreases helicase activity 5-fold, decreased ssdna-binding (in a fragment of residues 427-1208).

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 567 (showing top): GOBP_CHROMOSOME_ORGANIZATION, FISCHER_G1_S_CELL_CYCLE, ENK_UV_RESPONSE_KERATINOCYTE_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_TELOMERE_ORGANIZATION, KAUFFMANN_DNA_REPAIR_GENES, PATIL_LIVER_CANCER, PUJANA_CHEK2_PCC_NETWORK, MODULE_118, MUELLER_PLURINET, DOANE_RESPONSE_TO_ANDROGEN_DN, BILD_E2F3_ONCOGENIC_SIGNATURE, GOBP_DNA_DAMAGE_RESPONSE, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP

GO Biological Process (7): telomere maintenance (GO:0000723), double-strand break repair via homologous recombination (GO:0000724), DNA replication (GO:0006260), DNA repair (GO:0006281), telomeric D-loop disassembly (GO:0061820), DNA recombination (GO:0006310), chromosome organization (GO:0051276)

GO Molecular Function (17): bubble DNA binding (GO:0000405), helicase activity (GO:0004386), ATP binding (GO:0005524), four-way junction helicase activity (GO:0009378), ATP hydrolysis activity (GO:0016887), oxidized purine DNA binding (GO:0032357), metal ion binding (GO:0046872), telomeric D-loop binding (GO:0061821), DNA/DNA annealing activity (GO:1990814), nucleotide binding (GO:0000166), nucleic acid binding (GO:0003676), DNA binding (GO:0003677), protein binding (GO:0005515), hydrolase activity (GO:0016787), isomerase activity (GO:0016853), catalytic activity, acting on DNA (GO:0140097), catalytic activity, acting on a nucleic acid (GO:0140640)

GO Cellular Component (6): chromosome, telomeric region (GO:0000781), nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA metabolic process4
catalytic activity3
cellular anatomical structure3
catalytic activity, acting on a nucleic acid2
ATP-dependent activity2
binding2
telomere organization1
recombinational repair1
double-strand break repair1
DNA biosynthetic process1
DNA damage response1
telomeric loop disassembly1
organelle organization1
DNA secondary structure binding1
nucleic acid conformation isomerase activity1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
DNA helicase activity1
ribonucleoside triphosphate phosphatase activity1
oxidized DNA binding1
cation binding1
D-loop DNA binding1
single-stranded DNA binding1
catalytic activity, acting on DNA1
annealing activity1
nucleoside phosphate binding1
heterocyclic compound binding1
nucleic acid binding1
chromosomal region1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular membraneless organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

4671 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RECQL4MCM10Q7L590962
RECQL4TICRRQ7Z2Z1958
RECQL4FEN1P39748956
RECQL4TOPBP1Q92547939
RECQL4CDC45O75419931
RECQL4XPAP23025918
RECQL4UBR2Q8IWV8917
RECQL4USB1Q9BQ65912
RECQL4UBR1Q8IWV7865
RECQL4RAD51Q06609855
RECQL4APEX1P27695842
RECQL4DNA2P51530813
RECQL4ATMQ13315793
RECQL4EXO1Q9UQ84782
RECQL4TOP3AQ13472772

IntAct

101 interactions, top by confidence:

ABTypeScore
RFXANKRFXAPpsi-mi:“MI:0914”(association)0.780
NEUROG3GXYLT2psi-mi:“MI:0914”(association)0.640
VWCEZNF316psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
FBLZNF316psi-mi:“MI:0914”(association)0.530
KCTD17CBX4psi-mi:“MI:0914”(association)0.530
ZNF764SH3PXD2Bpsi-mi:“MI:0914”(association)0.530
ZNRD2MYO9Apsi-mi:“MI:0914”(association)0.530
PTGES3AIPpsi-mi:“MI:0914”(association)0.530
PRKAG3PFDN6psi-mi:“MI:0914”(association)0.530
NOTCH2ZNF316psi-mi:“MI:0914”(association)0.530
PNMA2CCDC85Cpsi-mi:“MI:0914”(association)0.530
TERF1RECQL4psi-mi:“MI:0915”(physical association)0.510
PPP2R2BDDX3Xpsi-mi:“MI:0914”(association)0.460
RAD51RECQL4psi-mi:“MI:0915”(physical association)0.400
RECQL4PLECpsi-mi:“MI:0915”(physical association)0.400
Recql4RECQL4psi-mi:“MI:0915”(physical association)0.400
TERF2IPRECQL4psi-mi:“MI:0915”(physical association)0.370
ACDRECQL4psi-mi:“MI:0915”(physical association)0.370
POT1RECQL4psi-mi:“MI:0915”(physical association)0.370
ARHGAP25UBA6psi-mi:“MI:0914”(association)0.350
FBLGXYLT2psi-mi:“MI:0914”(association)0.350
NLGN3TMEM131Lpsi-mi:“MI:0914”(association)0.350
CDC16KRBA1psi-mi:“MI:0914”(association)0.350
P4HA2CCDC85Cpsi-mi:“MI:0914”(association)0.350
KCTD17CBX4psi-mi:“MI:0914”(association)0.350
SKAP1MYO9Apsi-mi:“MI:0914”(association)0.350
LZTS2MYO9Apsi-mi:“MI:0914”(association)0.350

BioGRID (1558): RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS), RECQL4 (Affinity Capture-MS)

ESM2 similar proteins: A1L3T7, A2A3L6, A4IFI1, A7E3N7, A8MYJ7, A8VU90, O94761, O94812, O95153, O95382, P97680, Q0P5G1, Q13671, Q14154, Q3UYR4, Q4V896, Q53GL7, Q569K6, Q58CQ5, Q58EX7, Q66H85, Q6DT37, Q6F5E8, Q6ZVH7, Q76MJ5, Q7TNF8, Q7Z3H0, Q80UU1, Q80UW5, Q8BWA8, Q8BXP5, Q8BYG0, Q8CIE4, Q8CJ00, Q8IYJ3, Q8NAG6, Q8TE82, Q91WA6, Q91WE1, Q921Q7

Diamond homologs: A2XVF7, A3AVH5, A4RK80, A8WK63, D4ACP5, G2TRN7, O09053, O18017, O34748, O88700, O93530, O94761, O94762, P0CQ88, P0CQ89, P15043, P35187, P40724, P46063, P50729, P54132, P71359, P73421, Q09811, Q0WVW7, Q14191, Q19546, Q5RF63, Q5UPX0, Q6AYJ1, Q75NR7, Q7RZH4, Q8L840, Q8VID5, Q9CL21, Q9DEY9, Q9FT70, Q9FT72, Q9FT73, Q9FT74

SIGNOR signaling

6 interactions.

AEffectBMechanism
UBR1up-regulatesRECQL4binding
UBR2up-regulatesRECQL4binding
MCM10down-regulatesRECQL4binding
RECQL4“up-regulates activity”DNA_repair
CDK2“up-regulates activity”RECQL4phosphorylation
CDK1“up-regulates activity”RECQL4phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 123 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
Cellular Senescence612.3×6e-04
Meiotic synapsis510.5×4e-03
Cellular responses to stress105.5×7e-04
Cellular responses to stimuli115.2×6e-04

GO biological processes:

GO termPartnersFoldFDR
telomere maintenance via telomerase534.2×2e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — STAD.

Clinical variants and AI predictions

ClinVar

5153 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic276
Likely pathogenic68
Uncertain significance2781
Likely benign1671
Benign51

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1029808NM_004260.4(RECQL4):c.615dup (p.Lys206fs)Pathogenic
1065954NM_004260.4(RECQL4):c.3236G>T (p.Ser1079Ile)Pathogenic
1068625NM_004260.4(RECQL4):c.652_653del (p.Gln218fs)Pathogenic
1069365NM_004260.4(RECQL4):c.3284_3287dup (p.Ser1097fs)Pathogenic
1069662NM_004260.4(RECQL4):c.897del (p.Glu301fs)Pathogenic
1069990NM_004260.4(RECQL4):c.3331G>T (p.Glu1111Ter)Pathogenic
1070028NM_004260.4(RECQL4):c.1089C>A (p.Tyr363Ter)Pathogenic
1070092NM_004260.4(RECQL4):c.1561del (p.Arg521fs)Pathogenic
1070117NM_004260.4(RECQL4):c.2631C>G (p.Tyr877Ter)Pathogenic
1070337NM_004260.4(RECQL4):c.2083A>T (p.Lys695Ter)Pathogenic
1070691NM_004260.4(RECQL4):c.988_1004del (p.Ala330fs)Pathogenic
1070864NC_000008.10:g.(?145738945)(145743168_?)delPathogenic
1070865NC_000008.10:g.(?_145737562)_145739175delPathogenic
1071000NM_004260.4(RECQL4):c.3163del (p.Leu1055fs)Pathogenic
1071942NM_004260.4(RECQL4):c.2096del (p.Asn699fs)Pathogenic
1072153NM_004260.4(RECQL4):c.670G>T (p.Glu224Ter)Pathogenic
1072762NM_004260.4(RECQL4):c.2092C>T (p.Gln698Ter)Pathogenic
1072952NM_004260.4(RECQL4):c.2026del (p.Leu676fs)Pathogenic
1073755NM_004260.4(RECQL4):c.1078C>T (p.Gln360Ter)Pathogenic
1073779NM_004260.4(RECQL4):c.3321C>G (p.Tyr1107Ter)Pathogenic
1073983NM_004260.4(RECQL4):c.2305del (p.Val769fs)Pathogenic
1074685NM_004260.4(RECQL4):c.1390+2T>CPathogenic
1075387NM_004260.4(RECQL4):c.3223C>T (p.Gln1075Ter)Pathogenic
1075388NM_004260.4(RECQL4):c.55C>T (p.Arg19Ter)Pathogenic
1075795NM_004260.4(RECQL4):c.3035G>A (p.Trp1012Ter)Pathogenic
1076095NM_004260.4(RECQL4):c.1922_1923del (p.Thr641fs)Pathogenic
1076587NM_004260.4(RECQL4):c.694_707del (p.Ala232fs)Pathogenic
1076598NM_004260.4(RECQL4):c.1048del (p.Arg350fs)Pathogenic
1076729NM_004260.4(RECQL4):c.3184dup (p.Arg1062fs)Pathogenic
1076922NM_004260.4(RECQL4):c.3265del (p.Leu1089fs)Pathogenic

SpliceAI

3139 predictions. Top by Δscore:

VariantEffectΔscore
8:144511552:CTTC:Cacceptor_gain1.0000
8:144511675:CCTCA:Cdonor_loss1.0000
8:144511676:CTCA:Cdonor_loss1.0000
8:144511678:CACCG:Cdonor_loss1.0000
8:144511679:A:ACdonor_gain1.0000
8:144511679:A:ATdonor_loss1.0000
8:144511680:C:CCdonor_gain1.0000
8:144511787:GAG:Gacceptor_gain1.0000
8:144511788:AG:Aacceptor_gain1.0000
8:144511789:GCTG:Gacceptor_loss1.0000
8:144511790:C:CCacceptor_gain1.0000
8:144511792:G:Cacceptor_gain1.0000
8:144511792:G:GCacceptor_gain1.0000
8:144511900:A:ACdonor_gain1.0000
8:144511901:C:CCdonor_gain1.0000
8:144511901:CTGCA:Cdonor_gain1.0000
8:144511909:A:ACdonor_gain1.0000
8:144511910:C:CCdonor_gain1.0000
8:144511910:CT:Cdonor_gain1.0000
8:144511942:T:TAdonor_gain1.0000
8:144511969:T:Adonor_gain1.0000
8:144511975:T:TAdonor_gain1.0000
8:144512063:CTACG:Cacceptor_gain1.0000
8:144512066:CG:Cacceptor_gain1.0000
8:144512068:C:CCacceptor_gain1.0000
8:144512640:A:ACdonor_gain1.0000
8:144512640:A:Cdonor_loss1.0000
8:144512641:C:CAdonor_loss1.0000
8:144512641:C:CCdonor_gain1.0000
8:144512769:TGG:Tacceptor_gain1.0000

AlphaMissense

7747 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:144514250:T:AE606V0.996
8:144514265:A:GF601S0.992
8:144514258:G:CC603W0.989
8:144514262:G:TA602D0.989
8:144513401:G:CF760L0.988
8:144513401:G:TF760L0.988
8:144513403:A:GF760L0.988
8:144514264:A:CF601L0.988
8:144514264:A:TF601L0.988
8:144514266:A:GF601L0.988
8:144514253:T:AD605V0.987
8:144514250:T:GE606A0.986
8:144514216:G:CF617L0.985
8:144514216:G:TF617L0.985
8:144514218:A:GF617L0.985
8:144514970:A:TV529D0.985
8:144514253:T:GD605A0.984
8:144514260:A:GC603R0.984
8:144513239:G:CC814W0.982
8:144514067:A:GL640P0.982
8:144514256:A:TI604N0.982
8:144515066:G:AS497F0.982
8:144515191:A:GF481S0.982
8:144513402:A:GF760S0.981
8:144515190:A:CF481L0.981
8:144515190:A:TF481L0.981
8:144515192:A:GF481L0.981
8:144511551:G:CS1169R0.980
8:144511551:G:TS1169R0.980
8:144511553:T:GS1169R0.980

dbSNP variants (sampled 300 via entrez): RS1000281324 (8:144513003 C>A,G,T), RS1000338840 (8:144517883 CCGGGGG>C), RS1000972788 (8:144518579 G>T), RS1001013778 (8:144518014 G>A), RS1001434106 (8:144516428 C>T), RS1001801628 (8:144516577 T>C), RS1001894022 (8:144517756 C>A,G,T), RS1002397552 (8:144515834 T>A,C), RS1002430382 (8:144515693 T>A,C,G), RS1003029779 (8:144514127 GGT>G), RS1003210065 (8:144514145 C>A,T), RS1003500353 (8:144511407 C>A,T), RS1004216290 (8:144518043 T>C), RS1004279093 (8:144512566 G>A), RS1004394987 (8:144515042 C>G,T)

Disease associations

OMIM: gene MIM:603780 | disease phenotypes: MIM:218600, MIM:266280, MIM:268400, MIM:167000, MIM:607174, MIM:130000, MIM:114480, MIM:254500

GenCC curated gene-disease

DiseaseClassificationInheritance
Rothmund-Thomson syndromeDefinitiveAutosomal recessive
Rothmund-Thomson syndrome type 2DefinitiveAutosomal recessive
Baller-Gerold syndromeDefinitiveAutosomal recessive
osteosarcomaStrongAutosomal recessive
rapadilino syndromeStrongAutosomal recessive
RECON progeroid syndromeLimitedAutosomal recessive
congenital heart diseaseNo Known Disease RelationshipAutosomal dominant

ClinGen Gene-Disease Validity (2)

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

DiseaseClassificationInheritance
congenital heart diseaseNo Known Disease RelationshipAD
Rothmund-Thomson syndromeDefinitiveAR

Mondo (17): Baller-Gerold syndrome (MONDO:0009039), hereditary neoplastic syndrome (MONDO:0015356), rapadilino syndrome (MONDO:0009955), Rothmund-Thomson syndrome type 2 (MONDO:0016369), ovarian cancer (MONDO:0008170), Rothmund-Thomson syndrome (MONDO:0010002), hepatoblastoma (MONDO:0018666), familial meningioma (MONDO:0011789), congenital heart disease (MONDO:0005453), breast cancer (MONDO:0007254), Ehlers-Danlos syndrome (MONDO:0020066), hereditary breast carcinoma (MONDO:0016419), high grade surface osteosarcoma (MONDO:0006246), undifferentiated pleomorphic sarcoma (MONDO:0002142), plasma cell myeloma (MONDO:0009693)

Orphanet (13): Baller-Gerold syndrome (Orphanet:1225), Inherited cancer-predisposing syndrome (Orphanet:140162), Rothmund-Thomson syndrome type 2 (Orphanet:221016), RAPADILINO syndrome (Orphanet:3021), Rare ovarian cancer (Orphanet:213500), Rothmund-Thomson syndrome (Orphanet:2909), Hepatoblastoma (Orphanet:449), Familial multiple meningioma (Orphanet:263662), Ehlers-Danlos syndrome (Orphanet:98249), Hereditary breast cancer (Orphanet:227535), Undifferentiated pleomorphic sarcoma (Orphanet:2023), Multiple myeloma (Orphanet:29073), AL amyloidosis (Orphanet:85443)

HPO phenotypes

215 total (30 of 215 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000028Cryptorchidism
HP:0000069Abnormality of the ureter
HP:0000076Vesicoureteral reflux
HP:0000077Abnormality of the kidney
HP:0000126Hydronephrosis
HP:0000135Hypogonadism
HP:0000143Rectovaginal fistula
HP:0000160Narrow mouth
HP:0000164Abnormality of the dentition
HP:0000175Cleft palate
HP:0000193Bifid uvula
HP:0000218High palate
HP:0000233Thin vermilion border
HP:0000238Hydrocephalus
HP:0000239Large fontanelles
HP:0000244Brachyturricephaly
HP:0000248Brachycephaly
HP:0000260Wide anterior fontanel
HP:0000262Turricephaly
HP:0000263Oxycephaly
HP:0000275Narrow face
HP:0000276Long face
HP:0000282Facial edema
HP:0000286Epicanthus
HP:0000303Mandibular prognathia
HP:0000316Hypertelorism
HP:0000331Short chin
HP:0000337Broad forehead
HP:0000347Micrognathia

GWAS associations

4 associations (top):

StudyTraitp-value
GCST002598_30Educational attainment9.000000e-06
GCST003795_8Age at first birth6.000000e-07
GCST006045_10Age at first birth6.000000e-09
GCST006269_1161General cognitive ability3.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004784self reported educational attainment
EFO:0009101age at first birth measurement
EFO:0004337intelligence

MeSH disease descriptors (13)

DescriptorNameTree numbers
D004535Ehlers-Danlos SyndromeC14.907.454.240; C15.378.463.515.240; C16.131.831.428; C16.320.850.260; C17.300.200.310; C17.800.804.428; C17.800.827.260
D006330Heart Defects, CongenitalC14.240.400; C14.280.400; C16.131.240.400
D018197HepatoblastomaC04.557.435.380
D051677Histiocytoma, Malignant FibrousC04.557.450.565.590.425.360; C04.557.450.795.400
D009101Multiple MyelomaC04.557.595.500; C14.907.454.460; C15.378.147.780.650; C15.378.463.515.460; C20.683.515.845; C20.683.780.650
D009386Neoplastic Syndromes, HereditaryC04.700; C16.320.700
D012516OsteosarcomaC04.557.450.565.575.650; C04.557.450.795.620
D010051Ovarian NeoplasmsC04.588.322.455; C12.050.351.500.056.630.705; C12.050.351.937.418.685; C12.100.250.056.630.705; C12.900.418.685; C19.344.410; C19.391.630.705
D011038Rothmund-Thomson SyndromeC16.131.831.775; C16.320.850.765; C16.614.760; C17.800.804.775; C17.800.827.775; C18.452.284.760
C562840Breast Cancer, Familial (supp.)
C536788Craniosynostosis radial aplasia syndrome (supp.)
C537443Meningioma, familial (supp.)
C535288Rapadilino syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression3
Resveratrolaffects cotreatment, increases expression, decreases expression2
Cisplatindecreases expression, increases expression2
Valproic Acidaffects expression, increases methylation2
aristolochic acid Iincreases expression1
GSK-J4decreases expression1
FR900359decreases phosphorylation1
fluorene-9-bisphenoldecreases expression1
propionaldehydedecreases expression1
bisphenol Adecreases expression1
lead acetateincreases expression1
2,2’-methylenebis(4-methyl-6-tert-butylphenol)affects expression, affects response to substance1
methylparabenincreases expression1
o,p’-DDTincreases methylation1
perfluorooctanoic aciddecreases expression1
sulindac sulfidedecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
cupric chlorideincreases expression1
hydroquinoneincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
monomethylarsonous aciddecreases expression1
ICG 001decreases expression1
abrinedecreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
jinfukangincreases expression1
NSC 689534affects binding, decreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Bortezomibincreases expression1

Cellosaurus cell lines

18 cell lines: 7 finite cell line, 4 cancer cell line, 4 transformed cell line, 3 induced pluripotent stem cell

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

CellosaurusNameCategorySex
CVCL_B5EGSK-DSRCT2Cancer cell lineMale
CVCL_C7PEAG28462Induced pluripotent stem cellMale
CVCL_TI71HAP1 RECQL4 (-) 1Cancer cell lineMale
CVCL_TI72HAP1 RECQL4 (-) 2Cancer cell lineMale
CVCL_TI73HAP1 RECQL4 (-) 3Cancer cell lineMale
CVCL_UG21CDMLi002-AInduced pluripotent stem cellFemale
CVCL_X812AG05013Finite cell lineMale
CVCL_X815AG17524Finite cell lineFemale
CVCL_X816AG18371Finite cell lineMale
CVCL_X817AG18372Transformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00668824PHASE4UNKNOWNImproved Diagnosis of Congenital Heart Disease by Magnetic Resonance Imaging Using Vasovist
NCT01368705PHASE4COMPLETEDNitrogen Balance in Infants After Post Cardiothoracic Surgery
NCT01619982PHASE4COMPLETEDPre-operative Prophylaxis With Vancomycin and Cefazolin in Pediatric Cardiovascular Surgery Patients
NCT02122679PHASE4WITHDRAWNTranexamic Acid Effect on Platelet Aggregation Following Infant Cardiopulmonary Bypass
NCT02527811PHASE4UNKNOWNUlinastatin Injection in in Pediatric Patients Undergoing Open Heart Surgery
NCT03014700PHASE4COMPLETEDFibrinogen Concentrate vs Cryoprecipitate
NCT03408340PHASE4TERMINATEDParavertebral Nerve Blocks in Neonates
NCT03630796PHASE4UNKNOWNEffect of Sevoflurane in Postoperative Troponin I Levels in Children Undergoing Congenital Heart Defects Surgery
NCT03667703PHASE4COMPLETEDStress Ulcer Prophylaxis Versus Placebo in Critically Ill Infants With Congenital Heart Disease
NCT04453761PHASE4UNKNOWNThiamine Influenced on Substrate Energy Effectiveness in Indonesian Children Undergoing Cardiopulmonary Bypass
NCT06668389PHASE4RECRUITINGSodium-Glucose Cotransporter 2 Inhibitors for Repaired Tetralogy of Fallot Patients for Enhancement of Cardio-Pulmonary Status Trial
NCT07499154PHASE4NOT_YET_RECRUITINGPerioperative Lidocaine for Lung Protection in Infants Undergoing Cardiac Surgery
NCT00190697PHASE4COMPLETEDA Study of LY353381 (Arzoxifene) for Patients Who Benefitted From This Drug in Other Oncology Trials and Wished to Continue Treatment
NCT00277160PHASE4COMPLETEDA Study of Primary Prophylaxis With Neulasta (Pegfilgrastim) Versus Secondary Prophylaxis After Chemotherapy in Elderly Subjects (>/= 65 Years Old) With Cancer
NCT00727961PHASE4COMPLETEDA Study to Evaluate Efficacy and Tolerance of Caelyx in Patients With Epithelial Ovarian Cancer. (Study P04072)(COMPLETED)
NCT00740116PHASE4COMPLETEDTranexamic Acid in Surgery of Advanced Ovarian Cancer
NCT00817479PHASE4COMPLETEDTumor Gene Expression in Women With Ovarian Cancer
NCT01432015PHASE4COMPLETEDFosaprepitant Versus Aprepitant in the Prevention of Chemotherapy Induced Nausea and Vomiting
NCT01706120PHASE4UNKNOWNStudy of Clinical and Biological Prognostic Factors in Patients With Ovarian Cancer Receiving Carboplatin +Paclitaxel With Bevacizumab
NCT01932125PHASE4COMPLETEDAn Interventional Study of Avastin (Bevacizumab) in Patients With Advanced/Metastatic Epithelial Ovarian Cancer, Fallopian Tube Cancer or Primary Peritoneal Cancer
NCT01953107PHASE4COMPLETEDOral Iron vs. Placebo in Newly Diagnosed Gynecologic Oncology Patients Who Are Surgical Candidates.
NCT02035345PHASE4TERMINATEDSlowed Carboplatin Infusion for Ovarian Cancer Patients Receiving Carboplatin Re-Treatment
NCT02243059PHASE4WITHDRAWNMagnetic Resonance Imaging for Lymph Node Staging in Ovarian Cancer
NCT03164980PHASE4TERMINATEDQoL-Comparison Between Trabectedin/PLD and Pt-based Therapy in Patients With Pt-sensitive Recurrent Ovarian Cancer
NCT03384511PHASE4COMPLETEDThe Use of 18F-ALF-NOTA-PRGD2 PET/CT Scan to Predict the Efficacy and Adverse Events of Apatinib in Malignancies.
NCT03543462PHASE4COMPLETEDDiaphragmatic Resection And Gynecological Ovarian Neoplasm
NCT03752216PHASE4COMPLETEDNIraparib and Quality of LifE is a Longitudinal Study Evaluating in Real Life the Tolerability of Niraparib.
NCT03858166PHASE4TERMINATEDEfficacy and Safety of PEG-rhG-CSF Secondary Prophylaxis vs. Therapeutic Administration in Patients With Ovarian Cancer
NCT04024254PHASE4COMPLETEDA Study of Serum Folate Levels in Patients Treated With Olaparib
NCT04330040PHASE4COMPLETEDProspective Multicentre Phase-IV Clinical Trial of Olaparib in Indian Patients With Ovarian and Metastatic Breast Cancer
NCT04352439PHASE4COMPLETEDAspirin for Prevention of Venous Thromboembolism Among Ovarian Cancer Patients Receiving Neoadjuvant Chemotherapy
NCT05187208PHASE4UNKNOWNPARP Inhibitor Oral Maintenance in Low-Risk Ovarian Cancer
NCT05606692PHASE4RECRUITINGInfluences of Propofol and Sevoflurane Anesthesia in Ovarian Cancer (Anesthetics)
NCT05926336PHASE4RECRUITINGThe Effects of Using Different Anesthetics on the Prognosis of Primary Tumors and Its Mechanism of Action
NCT06412120PHASE4RECRUITINGStudy Evaluating Safety, Tolerability, and Metabolism of Niraparib
NCT06871787PHASE4NOT_YET_RECRUITINGNear-Infrared Fluorescence Imaging With Indocyanine Green to Evaluate Bowel Anastomoses in Gynecologic Oncology Surgery
NCT06887933PHASE4NOT_YET_RECRUITINGA Trial to Evaluate the Safety of Niraparib Tablets in Adult Female Participants With Advanced or Relapsed Epithelial Ovarian Cancer
NCT07469202PHASE4NOT_YET_RECRUITINGCYTALUX Dose Extension Study
NCT00000470PHASE3COMPLETEDInfant Heart Surgery: Central Nervous System Sequelae of Circulatory Arrest
NCT00000494PHASE3COMPLETEDManagement of Patent Ductus in Premature Infants