RCCD1
gene geneOn this page
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
| Field | Value |
|---|---|
| HGNC ID | HGNC:30457 |
| Approved symbol | RCCD1 |
| Name | RCC1 domain containing 1 |
| Location | 15q26.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | MGC14386 |
| Ensembl gene | ENSG00000166965 |
| Ensembl biotype | protein_coding |
| OMIM | 617997 |
| Entrez | 91433 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001310134 | 90961618 | 90963125 |
| ENSE00001371811 | 90957113 | 90957503 |
| ENSE00001744895 | 90956612 | 90956900 |
| ENSE00002485508 | 90954884 | 90954948 |
| ENSE00003612263 | 90961025 | 90961054 |
| ENSE00003614091 | 90957604 | 90957725 |
| ENSE00003634215 | 90959900 | 90959998 |
| ENSE00003680038 | 90960328 | 90960498 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 148530 | 5.5272 | 1556 |
| 148531 | 0.9520 | 458 |
| 148537 | 0.7808 | 105 |
| 148535 | 0.6954 | 412 |
| 148532 | 0.6120 | 352 |
| 148533 | 0.3012 | 167 |
| 148536 | 0.0912 | 26 |
Top tissues by expression
237 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| secondary oocyte | CL:0000655 | 93.37 | gold quality |
| oocyte | CL:0000023 | 92.76 | gold quality |
| ileal mucosa | UBERON:0000331 | 92.35 | silver quality |
| pancreatic ductal cell | CL:0002079 | 86.99 | silver quality |
| mucosa of transverse colon | UBERON:0004991 | 86.69 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 85.55 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 85.02 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 85.00 | gold quality |
| right adrenal gland | UBERON:0001233 | 84.72 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 84.69 | gold quality |
| left ventricle myocardium | UBERON:0006566 | 84.46 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 84.30 | gold quality |
| cerebellar cortex | UBERON:0002129 | 84.17 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 83.82 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 83.59 | gold quality |
| left adrenal gland | UBERON:0001234 | 83.58 | gold quality |
| cerebellum | UBERON:0002037 | 83.49 | gold quality |
| adrenal cortex | UBERON:0001235 | 83.38 | gold quality |
| ventricular zone | UBERON:0003053 | 83.37 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 83.22 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 82.85 | gold quality |
| kidney epithelium | UBERON:0004819 | 82.57 | gold quality |
| body of pancreas | UBERON:0001150 | 82.54 | gold quality |
| parotid gland | UBERON:0001831 | 82.53 | gold quality |
| adrenal gland | UBERON:0002369 | 82.34 | gold quality |
| transverse colon | UBERON:0001157 | 82.04 | gold quality |
| left ovary | UBERON:0002119 | 81.99 | gold quality |
| stromal cell of endometrium | CL:0002255 | 81.96 | gold quality |
| trabecular bone tissue | UBERON:0002483 | 81.91 | gold quality |
| right ovary | UBERON:0002118 | 81.63 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 3.00 |
| E-MTAB-4850 | no | 123.42 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-485-3P | 99.98 | 70.68 | 1585 |
| HSA-MIR-539-3P | 99.98 | 70.74 | 1616 |
| HSA-MIR-651-3P | 99.94 | 73.48 | 5177 |
| HSA-MIR-6835-3P | 99.93 | 70.49 | 2904 |
| HSA-MIR-6721-5P | 99.93 | 68.92 | 2981 |
| HSA-MIR-6768-5P | 99.92 | 67.36 | 1942 |
| HSA-MIR-589-3P | 99.91 | 69.62 | 2088 |
| HSA-MIR-106A-5P | 99.90 | 73.94 | 2683 |
| HSA-MIR-17-5P | 99.89 | 73.83 | 2665 |
| HSA-MIR-95-5P | 99.89 | 72.17 | 3973 |
| HSA-MIR-106B-5P | 99.88 | 74.72 | 2795 |
| HSA-MIR-20A-5P | 99.88 | 74.76 | 2769 |
| HSA-MIR-20B-5P | 99.88 | 74.01 | 2621 |
| HSA-MIR-519D-3P | 99.88 | 73.97 | 2607 |
| HSA-MIR-526B-3P | 99.88 | 74.06 | 2587 |
| HSA-MIR-93-5P | 99.88 | 73.98 | 2606 |
| HSA-MIR-6756-5P | 99.82 | 67.97 | 2466 |
| HSA-MIR-448 | 99.79 | 72.37 | 2103 |
| HSA-MIR-2052 | 99.79 | 69.37 | 2031 |
| HSA-MIR-2681-5P | 99.75 | 67.64 | 1655 |
| HSA-MIR-6745 | 99.74 | 65.33 | 1321 |
| HSA-MIR-6766-5P | 99.68 | 67.70 | 2325 |
| HSA-MIR-3934-5P | 99.67 | 64.04 | 846 |
| HSA-MIR-298 | 99.63 | 67.56 | 1916 |
| HSA-MIR-12123 | 99.52 | 71.79 | 2990 |
| HSA-MIR-5689 | 99.50 | 71.26 | 1154 |
| HSA-MIR-2392 | 99.43 | 67.50 | 708 |
| HSA-MIR-2115-3P | 99.31 | 69.68 | 2026 |
| HSA-MIR-5589-3P | 99.29 | 68.30 | 1443 |
| HSA-MIR-1273H-3P | 99.29 | 67.55 | 980 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | rccd1 | ENSDARG00000071074 |
| danio_rerio | herc7 | ENSDARG00000098906 |
| ENSDARG00000104505 | ||
| mus_musculus | Rccd1 | ENSMUSG00000038930 |
| rattus_norvegicus | Rccd1 | ENSRNOG00000042059 |
| drosophila_melanogaster | ca | FBGN0000247 |
| drosophila_melanogaster | Rcc1 | FBGN0002638 |
| drosophila_melanogaster | CG7420 | FBGN0031344 |
| drosophila_melanogaster | CG6678 | FBGN0038917 |
| caenorhabditis_elegans | WBGENE00004304 | |
| caenorhabditis_elegans | K11D2.1 | WBGENE00010768 |
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 1 — A6NED2 (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)
| ID | Name | Type |
|---|---|---|
| IPR000408 | Reg_chr_condens | Repeat |
| IPR009091 | RCC1/BLIP-II | Homologous_superfamily |
| IPR052830 | RCC1_domain-containing | Family |
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.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 6F4T | X-RAY DIFFRACTION | 1.22 |
| 6F4R | X-RAY DIFFRACTION | 1.3 |
| 6F4S | X-RAY DIFFRACTION | 1.46 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-A6NED2-F1 | 87.75 | 0.73 |
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):
| Position | Phenotype |
|---|---|
| 141 | abolishes hydroxylation by kdm8. |
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-9629569 | Protein 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:
| Category | Pathways |
|---|---|
| Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular component organization | 1 |
| binding | 1 |
| intracellular membraneless organelle | 1 |
| cytoplasm | 1 |
| cellular anatomical structure | 1 |
| membrane | 1 |
| cell periphery | 1 |
Protein interactions and networks
STRING
1084 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| RCCD1 | KDM8 | Q8N371 | 668 |
| RCCD1 | WDFY4 | Q6ZS81 | 469 |
| RCCD1 | LRRC25 | Q8N386 | 465 |
| RCCD1 | CZIB | Q9NWV4 | 447 |
| RCCD1 | ANKLE1 | Q8NAG6 | 441 |
| RCCD1 | TMEM220 | Q6QAJ8 | 433 |
| RCCD1 | ZNF433 | Q8N7K0 | 420 |
| RCCD1 | ACAP1 | Q15027 | 401 |
| RCCD1 | TYW5 | A2RUC4 | 397 |
| RCCD1 | FLACC1 | Q96Q35 | 396 |
| RCCD1 | LRRC37A | A6NMS7 | 393 |
| RCCD1 | LRRC37A3 | O60309 | 390 |
| RCCD1 | ZDHHC11B | P0C7U3 | 382 |
| RCCD1 | C11orf24 | Q96F05 | 371 |
| RCCD1 | ZNF530 | Q6P9A1 | 369 |
IntAct
34 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| KDM8 | RCCD1 | psi-mi:“MI:0915”(physical association) | 0.710 |
| ALDH3A1 | RCCD1 | psi-mi:“MI:0914”(association) | 0.640 |
| RCCD1 | SPAG9 | psi-mi:“MI:0914”(association) | 0.640 |
| POLR2L | RCCD1 | psi-mi:“MI:0914”(association) | 0.640 |
| MAPK8IP3 | RCCD1 | psi-mi:“MI:0914”(association) | 0.640 |
| YJU2B | RCCD1 | psi-mi:“MI:0914”(association) | 0.530 |
| INPP5A | RCCD1 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNF219 | RCCD1 | psi-mi:“MI:0914”(association) | 0.530 |
| SLC27A3 | RCCD1 | psi-mi:“MI:0914”(association) | 0.350 |
| RCCD1 | ZNF609 | psi-mi:“MI:0914”(association) | 0.350 |
| ZNF219 | psi-mi:“MI:0914”(association) | 0.350 | |
| CDC73 | RCCD1 | psi-mi:“MI:0914”(association) | 0.350 |
| CTR9 | RCCD1 | psi-mi:“MI:0914”(association) | 0.350 |
| DDX6 | RCCD1 | psi-mi:“MI:0914”(association) | 0.350 |
| EZH1 | RCCD1 | psi-mi:“MI:0914”(association) | 0.350 |
| CSTL1 | DENND11 | psi-mi:“MI:0914”(association) | 0.350 |
| UBL3 | RCCD1 | psi-mi:“MI:0914”(association) | 0.350 |
| RCCD1 | IFT56 | psi-mi:“MI:0914”(association) | 0.350 |
| MAPK8IP3 | SHTN1 | psi-mi:“MI:0914”(association) | 0.350 |
| MRPS17 | RCCD1 | psi-mi:“MI:0914”(association) | 0.350 |
| AFG2B | RCCD1 | psi-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):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 59 |
| Likely benign | 1 |
| Benign | 3 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1487 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 15:90959894:TTTCA:T | acceptor_loss | 1.0000 |
| 15:90959896:TCAGA:T | acceptor_loss | 1.0000 |
| 15:90959897:CA:C | acceptor_loss | 1.0000 |
| 15:90959898:A:AG | acceptor_gain | 1.0000 |
| 15:90959898:A:C | acceptor_loss | 1.0000 |
| 15:90959899:G:GA | acceptor_gain | 1.0000 |
| 15:90959899:G:GT | acceptor_loss | 1.0000 |
| 15:90959899:GA:G | acceptor_gain | 1.0000 |
| 15:90959899:GAGA:G | acceptor_gain | 1.0000 |
| 15:90959995:G:T | donor_gain | 1.0000 |
| 15:90955791:AAC:A | acceptor_gain | 0.9900 |
| 15:90955793:C:CA | acceptor_gain | 0.9900 |
| 15:90956896:GACCC:G | donor_gain | 0.9900 |
| 15:90956901:G:GG | donor_gain | 0.9900 |
| 15:90957723:GTG:G | donor_gain | 0.9900 |
| 15:90959887:T:A | acceptor_gain | 0.9900 |
| 15:90959899:GAGAC:G | acceptor_gain | 0.9900 |
| 15:90959996:A:T | donor_gain | 0.9900 |
| 15:90959996:AAGG:A | donor_loss | 0.9900 |
| 15:90959997:AG:A | donor_loss | 0.9900 |
| 15:90959998:GG:G | donor_loss | 0.9900 |
| 15:90959999:GTGAG:G | donor_loss | 0.9900 |
| 15:90960000:T:A | donor_loss | 0.9900 |
| 15:90955220:G:T | donor_gain | 0.9800 |
| 15:90955787:A:AG | acceptor_gain | 0.9800 |
| 15:90955792:AC:A | acceptor_gain | 0.9800 |
| 15:90956897:ACCC:A | donor_gain | 0.9800 |
| 15:90957721:GAGTG:G | donor_gain | 0.9800 |
| 15:90959995:G:GT | donor_gain | 0.9800 |
| 15:90960001:G:GG | donor_loss | 0.9800 |
AlphaMissense
2378 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 15:90959920:T:A | W234R | 0.994 |
| 15:90959920:T:C | W234R | 0.994 |
| 15:90956768:T:C | F12L | 0.993 |
| 15:90956770:C:A | F12L | 0.993 |
| 15:90956770:C:G | F12L | 0.993 |
| 15:90960487:C:A | A313D | 0.992 |
| 15:90961045:T:A | W324R | 0.992 |
| 15:90961045:T:C | W324R | 0.992 |
| 15:90960486:G:C | A313P | 0.991 |
| 15:90957711:C:T | S222F | 0.990 |
| 15:90957710:T:C | S222P | 0.989 |
| 15:90956774:T:C | F14L | 0.988 |
| 15:90956776:C:A | F14L | 0.988 |
| 15:90956776:C:G | F14L | 0.988 |
| 15:90959931:T:A | N237K | 0.988 |
| 15:90959931:T:G | N237K | 0.988 |
| 15:90957490:T:A | W182R | 0.987 |
| 15:90957490:T:C | W182R | 0.987 |
| 15:90957618:G:A | G191D | 0.987 |
| 15:90959930:A:T | N237I | 0.987 |
| 15:90960472:G:A | G308E | 0.987 |
| 15:90956772:G:A | G13D | 0.986 |
| 15:90959923:G:C | G235R | 0.986 |
| 15:90961048:G:C | G325R | 0.986 |
| 15:90961728:T:A | W364R | 0.986 |
| 15:90961728:T:C | W364R | 0.986 |
| 15:90956783:T:C | F17L | 0.984 |
| 15:90956785:C:A | F17L | 0.984 |
| 15:90956785:C:G | F17L | 0.984 |
| 15:90957711:C:A | S222Y | 0.983 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST006804_14 | Red cell distribution width | 1.000000e-110 |
| GCST006914_16 | Sleep duration | 3.000000e-08 |
| GCST90013466_16 | Height | 3.000000e-09 |
| GCST90013466_37 | Height | 2.000000e-07 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0009188 | Red cell distribution width |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D001816 | Bloom Syndrome | C16.131.077.137; 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.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects expression, decreases expression, increases expression | 3 |
| Resveratrol | affects cotreatment, increases expression | 2 |
| Benzo(a)pyrene | affects methylation, increases methylation | 2 |
| Cisplatin | affects expression, affects cotreatment, increases expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| GSK-J4 | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| propionaldehyde | decreases expression | 1 |
| trichostatin A | affects expression | 1 |
| beta-lapachone | decreases expression | 1 |
| sodium arsenite | decreases expression | 1 |
| butyraldehyde | decreases expression | 1 |
| potassium chromate(VI) | decreases expression | 1 |
| 2,3-bis(3’-hydroxybenzyl)butyrolactone | affects cotreatment, increases expression | 1 |
| aflatoxin B2 | decreases methylation | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| abrine | decreases expression | 1 |
| jinfukang | affects cotreatment, increases expression | 1 |
| Decitabine | affects expression | 1 |
| Leflunomide | decreases expression | 1 |
| Acetaminophen | increases expression | 1 |
| Arsenic | affects methylation | 1 |
| Calcitriol | decreases expression, affects cotreatment | 1 |
| Coumestrol | affects cotreatment, increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Plant Extracts | affects cotreatment, increases expression | 1 |
| Smoke | decreases expression | 1 |
| Sodium Dodecyl Sulfate | decreases expression | 1 |
| Testosterone | affects cotreatment, decreases expression | 1 |
| Thiram | decreases expression | 1 |
Clinical trials (associated diseases)
3 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00021437 | Not specified | COMPLETED | Biological Significance of the Bloom’s Syndrome Protein |
| NCT04251325 | Not specified | UNKNOWN | Socio-demographic Characteristics of Basic Life Support Course Participants |
| NCT04353089 | Not specified | UNKNOWN | Geographical Association Between Basic Life Support Courses, Bystander Cardiopulmonary Resuscitation and Survival |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Bloom syndrome