WDFY4
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Also known as KIAA1607Em:AC060234.3FLJ45748
Summary
WDFY4 (WDFY family member 4, HGNC:29323) is a protein-coding gene on chromosome 10q11.23, encoding WD repeat- and FYVE domain-containing protein 4 (Q6ZS81). Plays a critical role in the regulation of cDC1-mediated cross-presentation of viral and tumor antigens in dendritic cells.
Predicted to be involved in antigen processing and presentation. Predicted to act upstream of or within with a positive effect on CD8-positive, alpha-beta T cell activation. Predicted to act upstream of or within cellular response to virus. Predicted to be located in early endosome and endoplasmic reticulum.
Source: NCBI Gene 57705 — RefSeq curated summary.
At a glance
- Gene–disease (curated): complex neurodevelopmental disorder (Limited, GenCC)
- GWAS associations: 21
- Clinical variants (ClinVar): 554 total
- Druggable target: yes
- MANE Select transcript:
NM_001394531
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:29323 |
| Approved symbol | WDFY4 |
| Name | WDFY family member 4 |
| Location | 10q11.23 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | KIAA1607, Em:AC060234.3, FLJ45748 |
| Ensembl gene | ENSG00000128815 |
| Ensembl biotype | protein_coding |
| OMIM | 613316 |
| Entrez | 57705 |
Gene structure
Transcript identifiers
Ensembl transcripts: 7 — 4 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined
ENST00000325239, ENST00000360890, ENST00000374161, ENST00000465910, ENST00000490507, ENST00000497480, ENST00000858472
RefSeq mRNA: 3 — MANE Select: NM_001394531
NM_001370154, NM_001394531, NM_020945
CCDS: CCDS44385, CCDS91241
Canonical transcript exons
ENST00000325239 — 62 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001228474 | 48709716 | 48709966 |
| ENSE00001603847 | 48760347 | 48760440 |
| ENSE00001614039 | 48788530 | 48788675 |
| ENSE00001641025 | 48735880 | 48736070 |
| ENSE00001647261 | 48742968 | 48743548 |
| ENSE00001694351 | 48786639 | 48786870 |
| ENSE00001715860 | 48778611 | 48778832 |
| ENSE00001717590 | 48774458 | 48774672 |
| ENSE00001719080 | 48790727 | 48790917 |
| ENSE00001769365 | 48779941 | 48780119 |
| ENSE00001780432 | 48776750 | 48776984 |
| ENSE00001788437 | 48796298 | 48796450 |
| ENSE00001799961 | 48777419 | 48777495 |
| ENSE00001802112 | 48789874 | 48789985 |
| ENSE00001804246 | 48775712 | 48775806 |
| ENSE00003559852 | 48982509 | 48982956 |
| ENSE00003791740 | 48963842 | 48964054 |
| ENSE00003791805 | 48890579 | 48890727 |
| ENSE00003792379 | 48877033 | 48877199 |
| ENSE00003792628 | 48803286 | 48803359 |
| ENSE00003793024 | 48978309 | 48978393 |
| ENSE00003793143 | 48832573 | 48832709 |
| ENSE00003793522 | 48807859 | 48807958 |
| ENSE00003793526 | 48959722 | 48959813 |
| ENSE00003793697 | 48970131 | 48970289 |
| ENSE00003793779 | 48826671 | 48826909 |
| ENSE00003793843 | 48974862 | 48975041 |
| ENSE00003794712 | 48828778 | 48828896 |
| ENSE00003795195 | 48810530 | 48810735 |
| ENSE00003795900 | 48946040 | 48946157 |
| ENSE00003795960 | 48875089 | 48875140 |
| ENSE00003796446 | 48820234 | 48820437 |
| ENSE00003796460 | 48943330 | 48943449 |
| ENSE00003796561 | 48946860 | 48946969 |
| ENSE00003796625 | 48805260 | 48805421 |
| ENSE00003796712 | 48867265 | 48867342 |
| ENSE00003797064 | 48813957 | 48814082 |
| ENSE00003797149 | 48969064 | 48969248 |
| ENSE00003797185 | 48806004 | 48806095 |
| ENSE00003797195 | 48966526 | 48966673 |
| ENSE00003797860 | 48897454 | 48897574 |
| ENSE00003798148 | 48957129 | 48957282 |
| ENSE00003798275 | 48981367 | 48981478 |
| ENSE00003798700 | 48900221 | 48900306 |
| ENSE00003798857 | 48976797 | 48976979 |
| ENSE00003799284 | 48941806 | 48941848 |
| ENSE00003799357 | 48873491 | 48873697 |
| ENSE00003800099 | 48821062 | 48821176 |
| ENSE00003800150 | 48830700 | 48830885 |
| ENSE00003800241 | 48822380 | 48822537 |
| ENSE00003800634 | 48901801 | 48901863 |
| ENSE00003800763 | 48811539 | 48811708 |
| ENSE00003800802 | 48817245 | 48817409 |
| ENSE00003804697 | 48733931 | 48734035 |
| ENSE00003805575 | 48729432 | 48729589 |
| ENSE00003805919 | 48731110 | 48731562 |
| ENSE00003808399 | 48723433 | 48723567 |
| ENSE00003808751 | 48727470 | 48727659 |
| ENSE00003809180 | 48721261 | 48721367 |
| ENSE00003809586 | 48720011 | 48720125 |
| ENSE00003810435 | 48725881 | 48726070 |
| ENSE00003937228 | 48684873 | 48685001 |
Expression profiles
Bgee: expression breadth ubiquitous, 186 present calls, max score 91.95.
FANTOM5 (CAGE): breadth broad, TPM avg 9.2045 / max 423.3553, expressed in 487 samples.
FANTOM5 promoters (11 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 104859 | 6.3969 | 430 |
| 104858 | 1.2880 | 299 |
| 104860 | 0.8073 | 198 |
| 104857 | 0.2054 | 111 |
| 104861 | 0.1452 | 74 |
| 104862 | 0.1307 | 59 |
| 205862 | 0.0617 | 1 |
| 104870 | 0.0577 | 22 |
| 104863 | 0.0561 | 26 |
| 104869 | 0.0436 | 19 |
Top tissues by expression
238 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| superficial temporal artery | UBERON:0001614 | 91.95 | silver quality |
| lymph node | UBERON:0000029 | 89.43 | gold quality |
| spleen | UBERON:0002106 | 89.36 | gold quality |
| granulocyte | CL:0000094 | 87.94 | gold quality |
| bone marrow cell | CL:0002092 | 87.30 | gold quality |
| blood | UBERON:0000178 | 87.25 | gold quality |
| vermiform appendix | UBERON:0001154 | 85.52 | gold quality |
| ileal mucosa | UBERON:0000331 | 85.06 | gold quality |
| leukocyte | CL:0000738 | 84.99 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 84.89 | gold quality |
| monocyte | CL:0000576 | 84.74 | gold quality |
| sperm | CL:0000019 | 83.34 | silver quality |
| trabecular bone tissue | UBERON:0002483 | 83.17 | gold quality |
| bone marrow | UBERON:0002371 | 80.72 | gold quality |
| caecum | UBERON:0001153 | 80.57 | gold quality |
| tonsil | UBERON:0002372 | 80.43 | gold quality |
| buccal mucosa cell | CL:0002336 | 79.22 | silver quality |
| visceral pleura | UBERON:0002401 | 79.20 | silver quality |
| epithelium of nasopharynx | UBERON:0001951 | 78.68 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 78.22 | gold quality |
| upper arm skin | UBERON:0004263 | 77.34 | gold quality |
| parietal pleura | UBERON:0002400 | 76.13 | silver quality |
| small intestine Peyer’s patch | UBERON:0003454 | 75.25 | gold quality |
| myocardium | UBERON:0002349 | 74.94 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 74.69 | gold quality |
| right lung | UBERON:0002167 | 74.69 | gold quality |
| gall bladder | UBERON:0002110 | 74.48 | gold quality |
| kidney epithelium | UBERON:0004819 | 74.48 | gold quality |
| left testis | UBERON:0004533 | 74.46 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 73.96 | gold quality |
Single-cell (SCXA)
Detected in 7 experiment(s), a significant marker in 7.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-9801 | yes | 2704.26 |
| E-MTAB-6678 | yes | 1787.05 |
| E-CURD-120 | yes | 585.02 |
| E-HCAD-1 | yes | 21.55 |
| E-MTAB-6701 | yes | 21.38 |
| E-ANND-3 | yes | 13.98 |
| E-MTAB-8498 | yes | 12.26 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): YY1
miRNA regulators (miRDB)
24 targeting WDFY4, 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-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-146A-5P | 99.96 | 68.93 | 988 |
| HSA-MIR-146B-5P | 99.96 | 69.13 | 977 |
| HSA-MIR-4666A-3P | 99.96 | 71.71 | 3434 |
| HSA-MIR-7153-5P | 99.94 | 68.89 | 1006 |
| HSA-MIR-4659A-3P | 99.80 | 72.62 | 4248 |
| HSA-MIR-4659B-3P | 99.80 | 72.62 | 4248 |
| HSA-MIR-148A-3P | 99.74 | 73.77 | 1700 |
| HSA-MIR-148B-3P | 99.74 | 73.75 | 1700 |
| HSA-MIR-152-3P | 99.74 | 73.75 | 1703 |
| HSA-MIR-7161-5P | 99.68 | 68.92 | 1592 |
| HSA-MIR-548U | 99.65 | 67.78 | 1463 |
| HSA-MIR-3182 | 99.40 | 68.15 | 2454 |
| HSA-MIR-4687-5P | 99.14 | 66.26 | 488 |
| HSA-MIR-129-1-3P | 98.86 | 68.41 | 779 |
| HSA-MIR-129-2-3P | 98.86 | 68.41 | 779 |
| HSA-MIR-6829-5P | 98.86 | 65.12 | 1480 |
| HSA-MIR-4290 | 98.51 | 65.17 | 907 |
| HSA-MIR-5008-5P | 98.42 | 65.87 | 1019 |
| HSA-MIR-10226 | 98.25 | 66.50 | 811 |
| HSA-MIR-6779-3P | 97.51 | 65.82 | 789 |
| HSA-MIR-938 | 97.41 | 68.28 | 656 |
| HSA-MIR-1587 | 96.95 | 64.03 | 932 |
| HSA-MIR-3651 | 95.62 | 64.67 | 287 |
Literature-anchored findings (GeneRIF, showing 7)
- Genetic variants in ETS1 and WDFY4 were found to be associated with systemic lupus erythematosus, in the Asian population studied. (PMID:20169177)
- rs877819 SNP in WDFY4 may be associated with systemic lupus erythematosus by reduced binding of YY1 and downregulating WDFY4 expression. (PMID:22972472)
- A significantly increased risk for RA associated with the WDFY4 rs7097397 AG genotype. (PMID:24549174)
- We identified a variant in WDFY4 that was significantly associated with clinically amyopathic dermatomyositis (CADM). This variant had a cis-splicing quantitative trait locus effect for a truncated WDFY4isoform (tr-WDFY4), with higher expression in the risk allele. (PMID:29331962)
- BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes. (PMID:33189404)
- Analysis of WDFY4 rs7097397 and PHLDB1 rs7389 polymorphisms in Chinese patients with systemic lupus erythematosus. (PMID:35188604)
- WDFY4 polymorphisms in Chinese patients with anti-MDA5 dermatomyositis is associated with rapid progressive interstitial lung disease. (PMID:36637178)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | wdfy4 | ENSDARG00000077009 |
| mus_musculus | Wdfy4 | ENSMUSG00000051506 |
| rattus_norvegicus | Wdfy4 | ENSRNOG00000029662 |
| caenorhabditis_elegans | WBGENE00004760 | |
| caenorhabditis_elegans | WBGENE00007752 |
Paralogs (7): NSMAF (ENSG00000035681), LYST (ENSG00000143669), NBEAL1 (ENSG00000144426), NBEAL2 (ENSG00000160796), WDFY3 (ENSG00000163625), NBEA (ENSG00000172915), LRBA (ENSG00000198589)
Protein
Protein identifiers
WD repeat- and FYVE domain-containing protein 4 — Q6ZS81 (reviewed: Q6ZS81)
All UniProt accessions (2): Q6ZS81, A0A1W2PQ91
UniProt curated annotations — full annotation on UniProt →
Function. Plays a critical role in the regulation of cDC1-mediated cross-presentation of viral and tumor antigens in dendritic cells. Mechanistically, acts near the plasma membrane and interacts with endosomal membranes to promote endosomal-to-cytosol antigen trafficking. Also plays a role in B-cell survival through regulation of autophagy.
Subunit / interactions. Interacts with HSP90AB1.
Subcellular location. Early endosome. Endoplasmic reticulum.
Isoforms (5)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q6ZS81-1 | 1 | yes |
| Q6ZS81-2 | 2 | |
| Q6ZS81-3 | 3 | |
| Q6ZS81-4 | 4 | |
| Q6ZS81-5 | 5 |
RefSeq proteins (3): NP_001357083, NP_001381460, NP_065996 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000409 | BEACH_dom | Domain |
| IPR001680 | WD40_rpt | Repeat |
| IPR011989 | ARM-like | Homologous_superfamily |
| IPR011993 | PH-like_dom_sf | Homologous_superfamily |
| IPR015943 | WD40/YVTN_repeat-like_dom_sf | Homologous_superfamily |
| IPR016024 | ARM-type_fold | Homologous_superfamily |
| IPR019775 | WD40_repeat_CS | Conserved_site |
| IPR023362 | PH-BEACH_dom | Domain |
| IPR036322 | WD40_repeat_dom_sf | Homologous_superfamily |
| IPR036372 | BEACH_dom_sf | Homologous_superfamily |
| IPR051944 | BEACH_domain_protein | Family |
Pfam: PF00400, PF02138
UniProt features (31 total): splice variant 7, repeat 6, region of interest 5, sequence conflict 4, compositionally biased region 3, sequence variant 3, domain 2, chain 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
No AlphaFold model available for Q6ZS81 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 123 (showing top):
GOBP_CELLULAR_RESPONSE_TO_VIRUS, GOBP_ANTIGEN_PROCESSING_AND_PRESENTATION, TGANTCA_AP1_C, GOBP_ALPHA_BETA_T_CELL_ACTIVATION, RYTTCCTG_ETS2_B, ELK1_01, P300_01, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, NERF_Q2, GOBP_RESPONSE_TO_VIRUS, PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN, MGGAAGTG_GABP_B, CHEN_METABOLIC_SYNDROM_NETWORK, GOBP_LYMPHOCYTE_ACTIVATION
GO Biological Process (4): autophagy (GO:0006914), antigen processing and presentation (GO:0019882), CD8-positive, alpha-beta T cell activation (GO:0036037), cellular response to virus (GO:0098586)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (3): early endosome (GO:0005769), endoplasmic reticulum (GO:0005783), endosome (GO:0005768)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| endomembrane system | 2 |
| catabolic process | 1 |
| transmembrane transport | 1 |
| process utilizing autophagic mechanism | 1 |
| immune system process | 1 |
| alpha-beta T cell activation | 1 |
| response to virus | 1 |
| binding | 1 |
| endosome | 1 |
| cytoplasm | 1 |
| intracellular membrane-bounded organelle | 1 |
| cytoplasmic vesicle | 1 |
Protein interactions and networks
STRING
2802 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| WDFY4 | LRRC18 | Q8N456 | 700 |
| WDFY4 | WDFY2 | Q96P53 | 578 |
| WDFY4 | SNX22 | Q96L94 | 544 |
| WDFY4 | WDFY1 | Q8IWB7 | 522 |
| WDFY4 | IFIH1 | Q9BYX4 | 490 |
| WDFY4 | BANK1 | Q8NDB2 | 487 |
| WDFY4 | RCCD1 | A6NED2 | 469 |
| WDFY4 | TLR9 | Q9NR96 | 458 |
| WDFY4 | TMEM208 | Q9BTX3 | 453 |
| WDFY4 | TLR3 | O15455 | 441 |
| WDFY4 | BATF3 | Q9NR55 | 432 |
| WDFY4 | LAPTM5 | Q13571 | 430 |
| WDFY4 | MYCBP2 | O75592 | 427 |
| WDFY4 | MPPE1 | Q53F39 | 426 |
| WDFY4 | SEC22B | O75396 | 425 |
IntAct
5 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| WDFY4 | PLOD1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| APBB1 | SSPOP | psi-mi:“MI:0914”(association) | 0.350 |
| NTRK1 | ILVBL | psi-mi:“MI:0914”(association) | 0.350 |
| WDFY4 | tktA | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (7): WDFY4 (Proximity Label-MS), WDFY4 (Affinity Capture-MS), HSPA8 (Cross-Linking-MS (XL-MS)), WDFY4 (Proximity Label-MS), WDFY4 (Affinity Capture-MS), WDFY4 (Affinity Capture-RNA), WDFY4 (Affinity Capture-MS)
ESM2 similar proteins: A0JMW6, A1L1L2, A1L2I9, A2A9C3, A4FV45, A8C756, B0I564, D3ZND0, E9Q2M9, G3HQ82, O15360, O35821, O70576, O75800, Q15021, Q1JPG0, Q24JP3, Q4KLN4, Q5T011, Q5U1Z0, Q5U249, Q66H56, Q6AXZ5, Q6GPP1, Q6NUQ4, Q6NXR4, Q6ZS81, Q7L4E1, Q8BGI5, Q8BK03, Q8BM55, Q8BMG7, Q8BTG3, Q8C3S2, Q8CJF7, Q8K2Z4, Q8K368, Q8WYP5, Q92574, Q99M76
Diamond homologs: A8XSV3, D4A929, E7FAW3, E9Q2M9, F4HZB2, F4IG73, F4JD14, F4JHT3, O35242, P0C6P0, P25356, P50851, P97412, Q19317, Q54PP7, Q54RQ8, Q55AV3, Q55DM1, Q562E7, Q5ND34, Q6VNB8, Q6ZNJ1, Q6ZQA0, Q6ZS30, Q6ZS81, Q7LKZ7, Q86JF2, Q8IZQ1, Q8NFP9, Q92636, Q99698, Q9DDD5, Q9EPN1, Q9ESE1, Q9TTK4, Q9W060, Q9W4E2, E7FEV0, F4I9T0, F4JY12
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
554 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 469 |
| Likely benign | 42 |
| Benign | 13 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
10723 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 10:48709965:AGGTT:A | donor_loss | 1.0000 |
| 10:48723512:T:TA | acceptor_gain | 1.0000 |
| 10:48723565:CAGG:C | donor_loss | 1.0000 |
| 10:48723567:GGT:G | donor_loss | 1.0000 |
| 10:48723568:G:GC | donor_loss | 1.0000 |
| 10:48723569:T:A | donor_loss | 1.0000 |
| 10:48725879:A:AG | acceptor_gain | 1.0000 |
| 10:48725879:AGAT:A | acceptor_gain | 1.0000 |
| 10:48725880:G:GA | acceptor_gain | 1.0000 |
| 10:48725880:G:GC | acceptor_loss | 1.0000 |
| 10:48725880:GAT:G | acceptor_gain | 1.0000 |
| 10:48725880:GATG:G | acceptor_gain | 1.0000 |
| 10:48725880:GATGT:G | acceptor_gain | 1.0000 |
| 10:48725997:G:GT | donor_gain | 1.0000 |
| 10:48726060:G:GG | donor_gain | 1.0000 |
| 10:48726067:CAGGG:C | donor_loss | 1.0000 |
| 10:48726069:GG:G | donor_gain | 1.0000 |
| 10:48726070:GG:G | donor_gain | 1.0000 |
| 10:48726071:GTAT:G | donor_loss | 1.0000 |
| 10:48726072:T:G | donor_loss | 1.0000 |
| 10:48727468:A:AG | acceptor_gain | 1.0000 |
| 10:48727469:G:GA | acceptor_gain | 1.0000 |
| 10:48727658:CGGTA:C | donor_loss | 1.0000 |
| 10:48727659:GGTAA:G | donor_loss | 1.0000 |
| 10:48727660:G:GG | donor_gain | 1.0000 |
| 10:48727660:GTAAG:G | donor_loss | 1.0000 |
| 10:48727661:T:G | donor_loss | 1.0000 |
| 10:48731108:AGG:A | acceptor_gain | 1.0000 |
| 10:48731109:GGG:G | acceptor_gain | 1.0000 |
| 10:48731534:G:GT | donor_gain | 1.0000 |
AlphaMissense
20855 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 10:48974928:A:C | S2999R | 0.998 |
| 10:48974930:C:A | S2999R | 0.998 |
| 10:48974930:C:G | S2999R | 0.998 |
| 10:48941843:T:A | W2542R | 0.997 |
| 10:48941843:T:C | W2542R | 0.997 |
| 10:48941845:G:C | W2542C | 0.997 |
| 10:48941845:G:T | W2542C | 0.997 |
| 10:48943423:T:A | W2575R | 0.997 |
| 10:48943423:T:C | W2575R | 0.997 |
| 10:48982532:G:A | G3171D | 0.997 |
| 10:48982558:T:A | W3180R | 0.996 |
| 10:48982558:T:C | W3180R | 0.996 |
| 10:48943347:T:A | N2549K | 0.995 |
| 10:48943347:T:G | N2549K | 0.995 |
| 10:48959769:T:A | W2727R | 0.995 |
| 10:48959769:T:C | W2727R | 0.995 |
| 10:48963881:T:A | W2755R | 0.995 |
| 10:48963881:T:C | W2755R | 0.995 |
| 10:48981462:G:C | A3158P | 0.995 |
| 10:48810567:T:A | W1626R | 0.994 |
| 10:48810567:T:C | W1626R | 0.994 |
| 10:48969145:C:A | A2889D | 0.994 |
| 10:48976978:G:C | R3097P | 0.994 |
| 10:48780027:T:A | W1162R | 0.993 |
| 10:48780027:T:C | W1162R | 0.993 |
| 10:48897563:T:C | F2476L | 0.993 |
| 10:48897565:C:A | F2476L | 0.993 |
| 10:48897565:C:G | F2476L | 0.993 |
| 10:48943386:A:C | R2562S | 0.993 |
| 10:48943386:A:T | R2562S | 0.993 |
dbSNP variants (sampled 300 via entrez): RS1000023381 (10:48931463 C>T), RS1000028419 (10:48973845 C>T), RS1000028490 (10:48770882 T>C), RS1000035752 (10:48806523 C>T), RS1000042724 (10:48821573 C>T), RS1000045285 (10:48845958 C>T), RS1000053469 (10:48859178 T>G), RS1000055905 (10:48968369 C>T), RS1000061102 (10:48748621 G>A), RS1000081782 (10:48974162 G>A,T), RS1000082851 (10:48924620 A>G), RS1000114558 (10:48810543 A>C,G,T), RS1000118694 (10:48865514 G>T), RS1000131428 (10:48901176 C>T), RS1000140397 (10:48691707 A>G,T)
Disease associations
OMIM: gene MIM:613316 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| complex neurodevelopmental disorder | Limited | Autosomal recessive |
Mondo (1): complex neurodevelopmental disorder (MONDO:0100038)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
21 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000216_2 | Systemic lupus erythematosus | 3.000000e-06 |
| GCST000507_14 | Systemic lupus erythematosus | 7.000000e-12 |
| GCST000592_2 | Systemic lupus erythematosus | 8.000000e-12 |
| GCST001308_6 | Response to anti-depressant treatment in major depressive disorder | 2.000000e-07 |
| GCST001795_25 | Systemic lupus erythematosus | 8.000000e-09 |
| GCST002318_166 | Rheumatoid arthritis | 3.000000e-09 |
| GCST002724_18 | Airway responsiveness in chronic obstructive pulmonary disease | 7.000000e-06 |
| GCST002987_21 | Stroke | 9.000000e-08 |
| GCST002987_9 | Stroke | 9.000000e-08 |
| GCST003155_9 | Systemic lupus erythematosus | 5.000000e-09 |
| GCST003156_2 | Systemic lupus erythematosus | 9.000000e-12 |
| GCST003252_27 | Systemic lupus erythematosus | 1.000000e-06 |
| GCST003599_11 | Systemic lupus erythematosus | 2.000000e-09 |
| GCST003622_35 | Systemic lupus erythematosus | 9.000000e-11 |
| GCST003622_65 | Systemic lupus erythematosus | 5.000000e-07 |
| GCST005338_1 | Clinically amyopathic dermatomyositis | 2.000000e-08 |
| GCST005752_132 | Systemic lupus erythematosus | 7.000000e-10 |
| GCST006959_116 | Rheumatoid arthritis | 6.000000e-07 |
| GCST007400_29 | Systemic lupus erythematosus | 1.000000e-08 |
| GCST007843_19 | Rheumatoid arthritis | 3.000000e-08 |
| GCST011956_40 | Systemic lupus erythematosus | 2.000000e-40 |
EFO canonical traits (3, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0006320 | antidepressant-induced side effect |
| EFO:0006897 | airway responsiveness measurement |
| EFO:0008532 | clinically amyopathic dermatomyositis |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: yes
ChEMBL targets (1): CHEMBL4742299 (PROTEIN-PROTEIN INTERACTION)
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
22 total (human), top 22 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| (+)-JQ1 compound | decreases expression | 2 |
| Benzo(a)pyrene | affects methylation, decreases expression, increases methylation | 2 |
| aflatoxin B2 | decreases methylation | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| nutlin 3 | affects cotreatment, increases expression | 1 |
| abrine | increases expression | 1 |
| bisphenol S | decreases methylation | 1 |
| Air Pollutants | affects expression, increases abundance | 1 |
| Dactinomycin | affects cotreatment, increases expression | 1 |
| Ethyl Methanesulfonate | decreases expression | 1 |
| Formaldehyde | decreases expression | 1 |
| Methyl Methanesulfonate | decreases expression | 1 |
| Nickel | increases expression | 1 |
| Ozone | affects expression, increases abundance | 1 |
| Phthalic Acids | increases methylation | 1 |
| Tobacco Smoke Pollution | decreases methylation | 1 |
| Triclosan | increases expression | 1 |
| Valproic Acid | increases methylation | 1 |
| Antirheumatic Agents | decreases expression | 1 |
| Cadmium Chloride | increases expression | 1 |
| Magnetite Nanoparticles | increases expression | 1 |
ChEMBL screening assays
1 unique, capped per target: 1 binding
Representative assays (with source publication via chembl_document):
| Assay ID | Type | Description | Source paper |
|---|---|---|---|
| CHEMBL4713759 | Binding | Protac activity at CRBN/WDFY4 in human BxPC-3 cells assessed as WDFY4 degradation incubated for 16 hrs by proteomic analysis | Discovery of a Napabucasin PROTAC as an Effective Degrader of the E3 Ligase ZFP91. — J Med Chem |
Clinical trials (associated diseases)
2 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT06310681 | Not specified | COMPLETED | Pilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability |
| NCT07303049 | Not specified | NOT_YET_RECRUITING | Cognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder |
Related Atlas pages
- Associated diseases: complex neurodevelopmental disorder