SCHIP1
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Also known as SCHIP-1
Summary
SCHIP1 (schwannomin interacting protein 1, HGNC:15678) is a protein-coding gene on chromosome 3q25.33, encoding Schwannomin-interacting protein 1 (P0DPB3).
Enables identical protein binding activity. Predicted to be involved in positive regulation of hippo signaling. Predicted to act upstream of or within several processes, including face morphogenesis; fibroblast migration; and luteinization. Located in several cellular components, including cell junction; cytosol; and nuclear body.
Source: NCBI Gene 29970 — RefSeq curated summary.
At a glance
- Gene–disease (curated): complex neurodevelopmental disorder (Limited, GenCC)
- GWAS associations: 23
- Clinical variants (ClinVar): 9 total
- MANE Select transcript:
NM_014575
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:15678 |
| Approved symbol | SCHIP1 |
| Name | schwannomin interacting protein 1 |
| Location | 3q25.33 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | SCHIP-1 |
| Ensembl gene | ENSG00000151967 |
| Ensembl biotype | protein_coding |
| OMIM | 619206 |
| Entrez | 29970 |
Gene structure
Transcript identifiers
Ensembl transcripts: 16 — 10 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay
ENST00000412423, ENST00000445224, ENST00000460298, ENST00000461058, ENST00000472483, ENST00000475932, ENST00000482804, ENST00000482885, ENST00000483730, ENST00000495954, ENST00000527095, ENST00000638311, ENST00000638749, ENST00000639448, ENST00000640565, ENST00000689690
RefSeq mRNA: 30 — MANE Select: NM_014575
NM_001197107, NM_001197108, NM_001197109, NM_001394282, NM_001394283, NM_001394284, NM_001394285, NM_001394286, NM_001394287, NM_001394288, NM_001394289, NM_001394290, NM_001394291, NM_001394293, NM_001394294, NM_001394295, NM_001394296, NM_001414415, NM_001414416, NM_001414417, NM_001414418, NM_001414419, NM_001414420, NM_001414421, NM_001414422, NM_001414423, NM_001414424, NM_001414425, NM_001414426, NM_014575
CCDS: CCDS3186, CCDS56292, CCDS56293, CCDS56294, CCDS93418, CCDS93419
Canonical transcript exons
ENST00000638749 — 8 exons
| Exon | Start | End |
|---|---|---|
| ENSE00002216381 | 159896723 | 159897359 |
| ENSE00003803208 | 159273244 | 159273883 |
| ENSE00004473136 | 159764443 | 159765138 |
| ENSE00004475110 | 159888820 | 159888943 |
| ENSE00004475117 | 159886207 | 159886324 |
| ENSE00004475160 | 159887708 | 159887905 |
| ENSE00004475165 | 159866163 | 159866281 |
| ENSE00004475169 | 159892097 | 159892190 |
Expression profiles
Bgee: expression breadth ubiquitous, 133 present calls, max score 97.68.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.2287 / max 1411.1280, expressed in 1446 samples.
FANTOM5 promoters (28 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 39545 | 8.5892 | 483 |
| 39541 | 5.2460 | 1269 |
| 39538 | 1.7921 | 862 |
| 39543 | 1.6689 | 328 |
| 39547 | 1.3413 | 296 |
| 39546 | 1.2330 | 269 |
| 39536 | 0.9091 | 468 |
| 39548 | 0.7508 | 237 |
| 39562 | 0.6784 | 178 |
| 39531 | 0.6004 | 78 |
Top tissues by expression
134 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| ventricular zone | UBERON:0003053 | 97.68 | gold quality |
| prefrontal cortex | UBERON:0000451 | 96.42 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 96.18 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 95.77 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 95.53 | gold quality |
| frontal cortex | UBERON:0001870 | 95.52 | gold quality |
| temporal lobe | UBERON:0001871 | 95.34 | gold quality |
| amygdala | UBERON:0001876 | 95.30 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 95.24 | gold quality |
| cerebral cortex | UBERON:0000956 | 95.23 | gold quality |
| Ammon’s horn | UBERON:0001954 | 95.13 | gold quality |
| gastrocnemius | UBERON:0001388 | 95.10 | gold quality |
| ganglionic eminence | UBERON:0004023 | 94.78 | gold quality |
| corpus callosum | UBERON:0002336 | 94.67 | gold quality |
| muscle of leg | UBERON:0001383 | 94.58 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 94.50 | gold quality |
| primary visual cortex | UBERON:0002436 | 94.36 | gold quality |
| substantia nigra | UBERON:0002038 | 94.14 | gold quality |
| right frontal lobe | UBERON:0002810 | 94.14 | gold quality |
| putamen | UBERON:0001874 | 93.92 | gold quality |
| skeletal muscle tissue | UBERON:0001134 | 93.77 | gold quality |
| caudate nucleus | UBERON:0001873 | 93.49 | gold quality |
| brain | UBERON:0000955 | 93.04 | gold quality |
| nucleus accumbens | UBERON:0001882 | 93.04 | gold quality |
| hindlimb stylopod muscle | UBERON:0004252 | 92.99 | gold quality |
| hypothalamus | UBERON:0001898 | 92.72 | gold quality |
| heart left ventricle | UBERON:0002084 | 92.41 | gold quality |
| cortical plate | UBERON:0005343 | 92.37 | gold quality |
| cerebellum | UBERON:0002037 | 92.03 | gold quality |
| cerebellar cortex | UBERON:0002129 | 91.99 | gold quality |
Single-cell (SCXA)
Detected in 5 experiment(s), a significant marker in 3.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-8271 | yes | 16.72 |
| E-MTAB-9067 | yes | 10.99 |
| E-ANND-3 | yes | 6.37 |
| E-ENAD-27 | no | 4.46 |
| E-MTAB-9543 | no | 1.22 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
39 targeting SCHIP1, 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-4262 | 100.00 | 73.26 | 3931 |
| HSA-MIR-181D-5P | 99.99 | 73.04 | 2997 |
| HSA-MIR-181A-5P | 99.99 | 72.96 | 2995 |
| HSA-MIR-181B-5P | 99.99 | 72.97 | 2996 |
| HSA-MIR-181C-5P | 99.99 | 72.95 | 2996 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-1468-3P | 99.96 | 72.74 | 3797 |
| HSA-MIR-141-3P | 99.94 | 72.79 | 2421 |
| HSA-MIR-200A-3P | 99.94 | 72.68 | 2420 |
| HSA-MIR-7-1-3P | 99.91 | 71.53 | 4384 |
| HSA-MIR-7-2-3P | 99.91 | 71.40 | 4394 |
| HSA-MIR-10527-5P | 99.91 | 72.28 | 3754 |
| HSA-MIR-5582-3P | 99.86 | 72.48 | 4221 |
| HSA-MIR-548AR-3P | 99.85 | 71.26 | 3889 |
| HSA-MIR-548AZ-3P | 99.82 | 70.56 | 3549 |
| HSA-MIR-548BC | 99.82 | 70.61 | 3524 |
| HSA-MIR-548E-3P | 99.82 | 70.59 | 3514 |
| HSA-MIR-548F-3P | 99.82 | 70.59 | 3540 |
| HSA-MIR-139-5P | 99.80 | 69.50 | 1399 |
| HSA-MIR-4668-5P | 99.79 | 70.58 | 3782 |
| HSA-MIR-548A-3P | 99.76 | 70.58 | 3524 |
| HSA-MIR-4753-5P | 99.54 | 68.51 | 1356 |
| HSA-MIR-409-3P | 99.50 | 66.33 | 1192 |
| HSA-MIR-653-5P | 99.46 | 67.35 | 1300 |
| HSA-MIR-520F-5P | 99.34 | 70.40 | 1632 |
| HSA-MIR-130A-5P | 99.33 | 70.26 | 2623 |
| HSA-MIR-10522-5P | 99.26 | 68.50 | 2087 |
| HSA-MIR-3191-5P | 99.24 | 66.52 | 1722 |
| HSA-MIR-3675-3P | 99.09 | 67.70 | 968 |
| HSA-MIR-140-3P | 99.04 | 67.69 | 1324 |
Literature-anchored findings (GeneRIF, showing 4)
- chromosome 3 mapping by in situ hybridization and somatic cell hybrids (PMID:11701967)
- Schip1 associates with the cortical actin cytoskeleton network and modulates its dynamics in response to PDGF signaling via interaction with the Nherf2/ezrin complex. (PMID:25807495)
- SNPs within genes SCHIP1 and PDE8A were associated with measures of facial size in both the GWAS and replication cohorts and passed a stringent genomewide significance threshold adjusted for multiple testing of 34 correlated traits. For both SCHIP1 and PDE8A, we demonstrated clear expression in the developing mouse face by both whole-mount in situ hybridization and RNA-seq (PMID:27560698)
- This is the first report of a SCHIP1/IQCJ-SCHIP1 point mutation in humans associated with a neurological-developmental phenotype (PMID:28787085)
Cross-species orthologs
6 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | schip1 | ENSDARG00000035175 |
| danio_rerio | SCHIP1 | ENSDARG00000038981 |
| mus_musculus | Schip1 | ENSMUSG00000027777 |
| rattus_norvegicus | Schip1 | ENSRNOG00000009276 |
| drosophila_melanogaster | Schip1 | FBGN0032221 |
| caenorhabditis_elegans | WBGENE00018074 |
Protein
Protein identifiers
Schwannomin-interacting protein 1 — P0DPB3 (reviewed: P0DPB3)
All UniProt accessions (8): P0DPB3, A0A1W2PQT1, A0A1W2PR78, A0A1W2PR91, A0A8I5KTZ3, C9J366, C9JWG6, F8WDG0
UniProt curated annotations — full annotation on UniProt →
Subunit / interactions. Homooligomer (via coiled coil domain). Interacts with NF2; the interaction is direct. Interacts with ANK3.
Subcellular location. Cytoplasm.
Tissue specificity. Preferentially expressed in brain, skeletal muscles and heart. Also expressed in detected in pancreas, kidney, liver, lung, and placenta.
Similarity. Belongs to the SCHIP1 family.
Isoforms (6)
| UniProt ID | Names | Canonical? |
|---|---|---|
| P0DPB3-1 | SCHIP1-1, SCHIP-1, SCHIP-1a | yes |
| P0DPB3-2 | SCHIP1-2, SCHIP-1-D241/253 | |
| P0DPB3-3 | SCHIP1-3, SCHIP-1-D22/253 | |
| P0DPB3-4 | SCHIP1-4 | |
| B3KU38-1 | IQCJ-SCHIP1-1 | |
| B3KU38-2 | IQCJ-SCHIP1-2 |
RefSeq proteins (30): NP_001184036, NP_001184037, NP_001184038, NP_001381211, NP_001381212, NP_001381213, NP_001381214, NP_001381215, NP_001381216, NP_001381217, NP_001381218, NP_001381219, NP_001381220, NP_001381222, NP_001381223, NP_001381224, NP_001381225, NP_001401344, NP_001401345, NP_001401346, NP_001401347, NP_001401348, NP_001401349, NP_001401350, NP_001401351, NP_001401352, NP_001401353, NP_001401354, NP_001401355, NP_055390* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR015649 | SCHIP_1_C | Domain |
| IPR039045 | SCHIP_1 | Family |
Pfam: PF10148
UniProt features (23 total): compositionally biased region 9, region of interest 4, splice variant 4, sequence variant 2, chain 1, modified residue 1, sequence conflict 1, coiled-coil region 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-P0DPB3-F1 | 61.13 | 0.15 |
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): 117
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 207 (showing top):
MODULE_52, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MULLIGHAN_NPM1_SIGNATURE_3_UP, ACTACCT_MIR196A_MIR196B, BROWNE_HCMV_INFECTION_6HR_DN, YAGI_AML_WITH_INV_16_TRANSLOCATION, GENTILE_RESPONSE_CLUSTER_D3, GOBP_HIPPO_SIGNALING, GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN, MODULE_66, MODULE_118, FOSTER_TOLERANT_MACROPHAGE_UP, SCHMAHL_PDGF_SIGNALING, HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP, HFH4_01
GO Biological Process (12): positive regulation of hippo signaling (GO:0035332), luteinization (GO:0001553), kidney development (GO:0001822), estrogen metabolic process (GO:0008210), female gonad development (GO:0008585), post-embryonic development (GO:0009791), fibroblast migration (GO:0010761), platelet-derived growth factor receptor signaling pathway (GO:0048008), skeletal system morphogenesis (GO:0048705), smooth muscle tissue development (GO:0048745), roof of mouth development (GO:0060021), face morphogenesis (GO:0060325)
GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)
GO Cellular Component (6): cytoplasm (GO:0005737), plasma membrane (GO:0005886), cell junction (GO:0030054), nucleoplasm (GO:0005654), cytosol (GO:0005829), nuclear body (GO:0016604)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 4 |
| hippo signaling | 1 |
| regulation of hippo signaling | 1 |
| positive regulation of intracellular signal transduction | 1 |
| female gonad development | 1 |
| ovulation cycle process | 1 |
| animal organ development | 1 |
| renal system development | 1 |
| steroid metabolic process | 1 |
| hormone metabolic process | 1 |
| gonad development | 1 |
| development of primary female sexual characteristics | 1 |
| multicellular organism development | 1 |
| multicellular organismal process | 1 |
| ameboidal-type cell migration | 1 |
| cell surface receptor protein tyrosine kinase signaling pathway | 1 |
| skeletal system development | 1 |
| animal organ morphogenesis | 1 |
| muscle tissue development | 1 |
| anatomical structure development | 1 |
| anatomical structure morphogenesis | 1 |
| head morphogenesis | 1 |
| face development | 1 |
| protein binding | 1 |
| binding | 1 |
| intracellular anatomical structure | 1 |
| membrane | 1 |
| cell periphery | 1 |
| nuclear lumen | 1 |
| cytoplasm | 1 |
| nucleoplasm | 1 |
| intracellular membraneless organelle | 1 |
Protein interactions and networks
STRING
0 interactions, top by confidence (×1000):
IntAct
60 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SCHIP1 | SCOC | psi-mi:“MI:0915”(physical association) | 0.690 |
| SCOC | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.690 |
| SCHIP1 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.590 |
| SCHIP1 | PSMD4 | psi-mi:“MI:0915”(physical association) | 0.520 |
| SCHIP1 | NF2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| Xpo1 | IFT56 | psi-mi:“MI:0914”(association) | 0.350 |
| SCOC | SSNA1 | psi-mi:“MI:0914”(association) | 0.350 |
| SCHIP1 | VWA8 | psi-mi:“MI:0914”(association) | 0.350 |
| FGFR4 | SH3PXD2B | psi-mi:“MI:2364”(proximity) | 0.270 |
| SCHIP1 | ARFGEF1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCHIP1 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCHIP1 | TRHDE | psi-mi:“MI:0915”(physical association) | 0.000 |
| STRN | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| DCAF6 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SENP6 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| ZC3H13 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| FTH1 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| USP11 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| NAP1L1 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCHIP1 | PSMD4 | psi-mi:“MI:0915”(physical association) | 0.000 |
| AHSA1 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| NCAM2 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCHIP1 | MAP1B | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCHIP1 | PBRM1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SLC8A1 | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PTMS | SCHIP1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCHIP1 | SLF2 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SCHIP1 | HERC1 | psi-mi:“MI:0915”(physical association) | 0.000 |
ESM2 similar proteins: A0A088MLT8, A2AQ25, B3KU38, B5DF41, E9PSK7, O15079, O35274, P0DPB3, P0DPB4, P12755, P49140, P85299, Q0D2I5, Q14DQ1, Q1LY51, Q3B7M3, Q3SYW5, Q4KMA0, Q4R3X1, Q50H33, Q5F3L9, Q5FVG6, Q5RD40, Q5XKK7, Q60698, Q6ZNC4, Q6ZUS6, Q6ZWB6, Q80U23, Q80U62, Q80XA6, Q812A5, Q86YI8, Q8BXL9, Q8K2W6, Q8ND83, Q8NFH8, Q8QFX1, Q8TEK3, Q924W7
Diamond homologs: A0A088MLT8, A8DYY6, B3KU38, P0DPB3, P0DPB4, Q1A5X6, Q8BPW0
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
9 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 8 |
| Likely benign | 0 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
3243 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 3:159287880:A:T | donor_gain | 0.9900 |
| 3:159619202:A:AG | acceptor_gain | 0.9900 |
| 3:159619202:AAT:A | acceptor_gain | 0.9900 |
| 3:159619202:AATG:A | acceptor_gain | 0.9900 |
| 3:159664158:A:T | donor_gain | 0.9900 |
| 3:159764437:CCCTA:C | acceptor_loss | 0.9900 |
| 3:159764438:CCTA:C | acceptor_loss | 0.9900 |
| 3:159764441:A:AG | acceptor_gain | 0.9900 |
| 3:159764441:A:T | acceptor_loss | 0.9900 |
| 3:159764441:AG:A | acceptor_gain | 0.9900 |
| 3:159764442:G:GG | acceptor_gain | 0.9900 |
| 3:159764442:GG:G | acceptor_gain | 0.9900 |
| 3:159765097:G:GT | donor_gain | 0.9900 |
| 3:159765139:G:GG | donor_gain | 0.9900 |
| 3:159273882:GT:G | donor_gain | 0.9800 |
| 3:159273884:G:GG | donor_gain | 0.9800 |
| 3:159287845:C:CG | donor_gain | 0.9800 |
| 3:159462816:TAGA:T | acceptor_gain | 0.9800 |
| 3:159619203:A:G | acceptor_gain | 0.9800 |
| 3:159619204:T:TA | acceptor_gain | 0.9800 |
| 3:159764442:GGA:G | acceptor_gain | 0.9800 |
| 3:159764442:GGATT:G | acceptor_gain | 0.9800 |
| 3:159273880:CAGT:C | donor_gain | 0.9700 |
| 3:159422645:G:GG | donor_gain | 0.9700 |
| 3:159462815:TTAGA:T | acceptor_gain | 0.9700 |
| 3:159462817:AGATA:A | acceptor_gain | 0.9700 |
| 3:159489981:GGGC:G | donor_gain | 0.9700 |
| 3:159551738:T:G | acceptor_gain | 0.9700 |
| 3:159764442:GGAT:G | acceptor_gain | 0.9700 |
| 3:159422640:GTACA:G | donor_gain | 0.9600 |
AlphaMissense
3263 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 3:159866188:T:A | I338N | 1.000 |
| 3:159866191:G:C | R339T | 1.000 |
| 3:159866192:A:C | R339S | 1.000 |
| 3:159866192:A:T | R339S | 1.000 |
| 3:159866200:T:C | L342S | 1.000 |
| 3:159886209:T:C | L370P | 1.000 |
| 3:159886227:T:C | L376S | 1.000 |
| 3:159886227:T:G | L376W | 1.000 |
| 3:159886233:T:A | I378K | 1.000 |
| 3:159886233:T:C | I378T | 1.000 |
| 3:159886233:T:G | I378R | 1.000 |
| 3:159886235:T:C | C379R | 1.000 |
| 3:159886236:G:A | C379Y | 1.000 |
| 3:159886237:C:G | C379W | 1.000 |
| 3:159886238:T:C | F380L | 1.000 |
| 3:159886239:T:C | F380S | 1.000 |
| 3:159886239:T:G | F380C | 1.000 |
| 3:159886240:T:A | F380L | 1.000 |
| 3:159886240:T:G | F380L | 1.000 |
| 3:159887802:T:C | L440S | 1.000 |
| 3:159887807:G:C | A442P | 1.000 |
| 3:159887813:G:C | A444P | 1.000 |
| 3:159887814:C:A | A444D | 1.000 |
| 3:159887822:G:C | A447P | 1.000 |
| 3:159887826:T:C | L448P | 1.000 |
| 3:159887828:G:C | A449P | 1.000 |
| 3:159887834:G:C | A451P | 1.000 |
| 3:159887835:C:A | A451D | 1.000 |
| 3:159887846:G:C | A455P | 1.000 |
| 3:159887847:C:A | A455D | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000002930 (3:159449555 G>A), RS1000010671 (3:159435969 C>A), RS1000026687 (3:159455329 C>A,G,T), RS1000028369 (3:159827601 C>G,T), RS1000030019 (3:159294394 C>T), RS1000033975 (3:159287622 G>A), RS1000040552 (3:159429068 G>T), RS1000048395 (3:159737896 C>T), RS1000064249 (3:159852977 G>A,C), RS1000064810 (3:159715016 A>C), RS1000066137 (3:159655135 CT>C), RS1000067235 (3:159495213 C>A), RS1000067305 (3:159596737 G>A), RS1000072448 (3:159681897 G>A,C,T), RS1000081586 (3:159742118 C>T)
Disease associations
OMIM: gene MIM:619206 | 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
23 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000157_2 | Celiac disease | 1.000000e-09 |
| GCST000337_16 | Quantitative traits | 8.000000e-07 |
| GCST001850_13 | Major depressive disorder | 1.000000e-06 |
| GCST003129_8 | Primary biliary cholangitis | 1.000000e-23 |
| GCST004571_18 | Iron status biomarkers (total iron binding capacity) | 5.000000e-07 |
| GCST004572_31 | Iron status biomarkers (transferrin saturation) | 5.000000e-07 |
| GCST004721_15 | Congenital heart disease (maternal effect) | 3.000000e-06 |
| GCST004721_16 | Congenital heart disease (maternal effect) | 7.000000e-06 |
| GCST004723_13 | Conotruncal heart defects (maternal effects) | 8.000000e-06 |
| GCST004723_19 | Conotruncal heart defects (maternal effects) | 3.000000e-06 |
| GCST005523_17 | Celiac disease | 1.000000e-08 |
| GCST005523_18 | Celiac disease | 8.000000e-08 |
| GCST005523_41 | Celiac disease | 3.000000e-27 |
| GCST005533_2 | Limited cutaneous systemic scleroderma | 2.000000e-11 |
| GCST005534_12 | Systemic sclerosis | 9.000000e-06 |
| GCST005534_2 | Systemic sclerosis | 1.000000e-11 |
| GCST005534_9 | Systemic sclerosis | 2.000000e-08 |
| GCST006107_2 | Upper eyelid morphology | 6.000000e-06 |
| GCST006444_2 | Bone mineral density (hip) | 4.000000e-10 |
| GCST007508_5 | Self-reported childhood asthma in adult smokers | 2.000000e-07 |
| GCST008489_16 | Celiac disease | 4.000000e-08 |
| GCST90000032_2 | Myeloproliferative neoplasms | 8.000000e-11 |
| GCST90002381_193 | Eosinophil count | 3.000000e-11 |
EFO canonical traits (5, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0006334 | total iron binding capacity |
| EFO:1001017 | limited scleroderma |
| EFO:0007702 | hip bone mineral density |
| EFO:0004251 | myeloproliferative disorder |
| EFO:0004842 | eosinophil count |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
37 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | affects methylation, increases expression, increases mutagenesis | 3 |
| bisphenol A | decreases expression | 2 |
| Arsenic | affects methylation, increases abundance, increases expression | 2 |
| Valproic Acid | affects expression, decreases methylation | 2 |
| Cyclosporine | decreases expression, increases methylation | 2 |
| pirinixic acid | increases activity, increases expression, affects binding | 1 |
| sodium arsenate | increases expression, increases abundance | 1 |
| trichostatin A | affects cotreatment, decreases expression | 1 |
| afimoxifene | decreases expression, decreases reaction | 1 |
| sodium arsenite | affects expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| aflatoxin B2 | increases methylation | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| entinostat | decreases expression | 1 |
| mesotrione | affects methylation, increases abundance | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| jinfukang | decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| PCI 5002 | affects cotreatment, increases expression | 1 |
| Bortezomib | decreases expression | 1 |
| Temozolomide | increases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Atrazine | decreases expression | 1 |
| Cisplatin | increases expression | 1 |
| Doxorubicin | increases expression | 1 |
| Estrogens | decreases expression, decreases reaction | 1 |
| Herbicides | affects methylation, increases abundance | 1 |
| Methapyrilene | increases methylation | 1 |
| Mitoxantrone | affects response to substance | 1 |
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
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): celiac disease, complex neurodevelopmental disorder, conotruncal heart malformations, primary biliary cholangitis, systemic sclerosis