SCHIP1

gene
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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

FieldValue
HGNC IDHGNC:15678
Approved symbolSCHIP1
Nameschwannomin interacting protein 1
Location3q25.33
Locus typegene with protein product
StatusApproved
AliasesSCHIP-1
Ensembl geneENSG00000151967
Ensembl biotypeprotein_coding
OMIM619206
Entrez29970

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

ExonStartEnd
ENSE00002216381159896723159897359
ENSE00003803208159273244159273883
ENSE00004473136159764443159765138
ENSE00004475110159888820159888943
ENSE00004475117159886207159886324
ENSE00004475160159887708159887905
ENSE00004475165159866163159866281
ENSE00004475169159892097159892190

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 IDTPM avgSamples expressed
395458.5892483
395415.24601269
395381.7921862
395431.6689328
395471.3413296
395461.2330269
395360.9091468
395480.7508237
395620.6784178
395310.600478

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305397.68gold quality
prefrontal cortexUBERON:000045196.42gold quality
Brodmann (1909) area 9UBERON:001354096.18gold quality
superior frontal gyrusUBERON:000266195.77gold quality
C1 segment of cervical spinal cordUBERON:000646995.53gold quality
frontal cortexUBERON:000187095.52gold quality
temporal lobeUBERON:000187195.34gold quality
amygdalaUBERON:000187695.30gold quality
dorsolateral prefrontal cortexUBERON:000983495.24gold quality
cerebral cortexUBERON:000095695.23gold quality
Ammon’s hornUBERON:000195495.13gold quality
gastrocnemiusUBERON:000138895.10gold quality
ganglionic eminenceUBERON:000402394.78gold quality
corpus callosumUBERON:000233694.67gold quality
muscle of legUBERON:000138394.58gold quality
anterior cingulate cortexUBERON:000983594.50gold quality
primary visual cortexUBERON:000243694.36gold quality
substantia nigraUBERON:000203894.14gold quality
right frontal lobeUBERON:000281094.14gold quality
putamenUBERON:000187493.92gold quality
skeletal muscle tissueUBERON:000113493.77gold quality
caudate nucleusUBERON:000187393.49gold quality
brainUBERON:000095593.04gold quality
nucleus accumbensUBERON:000188293.04gold quality
hindlimb stylopod muscleUBERON:000425292.99gold quality
hypothalamusUBERON:000189892.72gold quality
heart left ventricleUBERON:000208492.41gold quality
cortical plateUBERON:000534392.37gold quality
cerebellumUBERON:000203792.03gold quality
cerebellar cortexUBERON:000212991.99gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-8271yes16.72
E-MTAB-9067yes10.99
E-ANND-3yes6.37
E-ENAD-27no4.46
E-MTAB-9543no1.22

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):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4262100.0073.263931
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-477599.9875.006394
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-139-5P99.8069.501399
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-409-3P99.5066.331192
HSA-MIR-653-5P99.4667.351300
HSA-MIR-520F-5P99.3470.401632
HSA-MIR-130A-5P99.3370.262623
HSA-MIR-10522-5P99.2668.502087
HSA-MIR-3191-5P99.2466.521722
HSA-MIR-3675-3P99.0967.70968
HSA-MIR-140-3P99.0467.691324

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

OrganismSymbolGene ID
danio_rerioschip1ENSDARG00000035175
danio_rerioSCHIP1ENSDARG00000038981
mus_musculusSchip1ENSMUSG00000027777
rattus_norvegicusSchip1ENSRNOG00000009276
drosophila_melanogasterSchip1FBGN0032221
caenorhabditis_elegansWBGENE00018074

Protein

Protein identifiers

Schwannomin-interacting protein 1P0DPB3 (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 IDNamesCanonical?
P0DPB3-1SCHIP1-1, SCHIP-1, SCHIP-1ayes
P0DPB3-2SCHIP1-2, SCHIP-1-D241/253
P0DPB3-3SCHIP1-3, SCHIP-1-D22/253
P0DPB3-4SCHIP1-4
B3KU38-1IQCJ-SCHIP1-1
B3KU38-2IQCJ-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)

IDNameType
IPR015649SCHIP_1_CDomain
IPR039045SCHIP_1Family

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)

ModelpLDDTFraction very-high
AF-P0DPB3-F161.130.15

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:

CategoryTerms
cellular anatomical structure4
hippo signaling1
regulation of hippo signaling1
positive regulation of intracellular signal transduction1
female gonad development1
ovulation cycle process1
animal organ development1
renal system development1
steroid metabolic process1
hormone metabolic process1
gonad development1
development of primary female sexual characteristics1
multicellular organism development1
multicellular organismal process1
ameboidal-type cell migration1
cell surface receptor protein tyrosine kinase signaling pathway1
skeletal system development1
animal organ morphogenesis1
muscle tissue development1
anatomical structure development1
anatomical structure morphogenesis1
head morphogenesis1
face development1
protein binding1
binding1
intracellular anatomical structure1
membrane1
cell periphery1
nuclear lumen1
cytoplasm1
nucleoplasm1
intracellular membraneless organelle1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

60 interactions, top by confidence:

ABTypeScore
SCHIP1SCOCpsi-mi:“MI:0915”(physical association)0.690
SCOCSCHIP1psi-mi:“MI:0915”(physical association)0.690
SCHIP1SCHIP1psi-mi:“MI:0915”(physical association)0.590
SCHIP1PSMD4psi-mi:“MI:0915”(physical association)0.520
SCHIP1NF2psi-mi:“MI:0915”(physical association)0.400
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
SCOCSSNA1psi-mi:“MI:0914”(association)0.350
SCHIP1VWA8psi-mi:“MI:0914”(association)0.350
FGFR4SH3PXD2Bpsi-mi:“MI:2364”(proximity)0.270
SCHIP1ARFGEF1psi-mi:“MI:0915”(physical association)0.000
SCHIP1SCHIP1psi-mi:“MI:0915”(physical association)0.000
SCHIP1TRHDEpsi-mi:“MI:0915”(physical association)0.000
STRNSCHIP1psi-mi:“MI:0915”(physical association)0.000
DCAF6SCHIP1psi-mi:“MI:0915”(physical association)0.000
SENP6SCHIP1psi-mi:“MI:0915”(physical association)0.000
ZC3H13SCHIP1psi-mi:“MI:0915”(physical association)0.000
FTH1SCHIP1psi-mi:“MI:0915”(physical association)0.000
USP11SCHIP1psi-mi:“MI:0915”(physical association)0.000
NAP1L1SCHIP1psi-mi:“MI:0915”(physical association)0.000
SCHIP1PSMD4psi-mi:“MI:0915”(physical association)0.000
AHSA1SCHIP1psi-mi:“MI:0915”(physical association)0.000
NCAM2SCHIP1psi-mi:“MI:0915”(physical association)0.000
SCHIP1MAP1Bpsi-mi:“MI:0915”(physical association)0.000
SCHIP1PBRM1psi-mi:“MI:0915”(physical association)0.000
SLC8A1SCHIP1psi-mi:“MI:0915”(physical association)0.000
PTMSSCHIP1psi-mi:“MI:0915”(physical association)0.000
SCHIP1SLF2psi-mi:“MI:0915”(physical association)0.000
SCHIP1HERC1psi-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):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance8
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3243 predictions. Top by Δscore:

VariantEffectΔscore
3:159287880:A:Tdonor_gain0.9900
3:159619202:A:AGacceptor_gain0.9900
3:159619202:AAT:Aacceptor_gain0.9900
3:159619202:AATG:Aacceptor_gain0.9900
3:159664158:A:Tdonor_gain0.9900
3:159764437:CCCTA:Cacceptor_loss0.9900
3:159764438:CCTA:Cacceptor_loss0.9900
3:159764441:A:AGacceptor_gain0.9900
3:159764441:A:Tacceptor_loss0.9900
3:159764441:AG:Aacceptor_gain0.9900
3:159764442:G:GGacceptor_gain0.9900
3:159764442:GG:Gacceptor_gain0.9900
3:159765097:G:GTdonor_gain0.9900
3:159765139:G:GGdonor_gain0.9900
3:159273882:GT:Gdonor_gain0.9800
3:159273884:G:GGdonor_gain0.9800
3:159287845:C:CGdonor_gain0.9800
3:159462816:TAGA:Tacceptor_gain0.9800
3:159619203:A:Gacceptor_gain0.9800
3:159619204:T:TAacceptor_gain0.9800
3:159764442:GGA:Gacceptor_gain0.9800
3:159764442:GGATT:Gacceptor_gain0.9800
3:159273880:CAGT:Cdonor_gain0.9700
3:159422645:G:GGdonor_gain0.9700
3:159462815:TTAGA:Tacceptor_gain0.9700
3:159462817:AGATA:Aacceptor_gain0.9700
3:159489981:GGGC:Gdonor_gain0.9700
3:159551738:T:Gacceptor_gain0.9700
3:159764442:GGAT:Gacceptor_gain0.9700
3:159422640:GTACA:Gdonor_gain0.9600

AlphaMissense

3263 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:159866188:T:AI338N1.000
3:159866191:G:CR339T1.000
3:159866192:A:CR339S1.000
3:159866192:A:TR339S1.000
3:159866200:T:CL342S1.000
3:159886209:T:CL370P1.000
3:159886227:T:CL376S1.000
3:159886227:T:GL376W1.000
3:159886233:T:AI378K1.000
3:159886233:T:CI378T1.000
3:159886233:T:GI378R1.000
3:159886235:T:CC379R1.000
3:159886236:G:AC379Y1.000
3:159886237:C:GC379W1.000
3:159886238:T:CF380L1.000
3:159886239:T:CF380S1.000
3:159886239:T:GF380C1.000
3:159886240:T:AF380L1.000
3:159886240:T:GF380L1.000
3:159887802:T:CL440S1.000
3:159887807:G:CA442P1.000
3:159887813:G:CA444P1.000
3:159887814:C:AA444D1.000
3:159887822:G:CA447P1.000
3:159887826:T:CL448P1.000
3:159887828:G:CA449P1.000
3:159887834:G:CA451P1.000
3:159887835:C:AA451D1.000
3:159887846:G:CA455P1.000
3:159887847:C:AA455D1.000

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

DiseaseClassificationInheritance
complex neurodevelopmental disorderLimitedAutosomal 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):

StudyTraitp-value
GCST000157_2Celiac disease1.000000e-09
GCST000337_16Quantitative traits8.000000e-07
GCST001850_13Major depressive disorder1.000000e-06
GCST003129_8Primary biliary cholangitis1.000000e-23
GCST004571_18Iron status biomarkers (total iron binding capacity)5.000000e-07
GCST004572_31Iron status biomarkers (transferrin saturation)5.000000e-07
GCST004721_15Congenital heart disease (maternal effect)3.000000e-06
GCST004721_16Congenital heart disease (maternal effect)7.000000e-06
GCST004723_13Conotruncal heart defects (maternal effects)8.000000e-06
GCST004723_19Conotruncal heart defects (maternal effects)3.000000e-06
GCST005523_17Celiac disease1.000000e-08
GCST005523_18Celiac disease8.000000e-08
GCST005523_41Celiac disease3.000000e-27
GCST005533_2Limited cutaneous systemic scleroderma2.000000e-11
GCST005534_12Systemic sclerosis9.000000e-06
GCST005534_2Systemic sclerosis1.000000e-11
GCST005534_9Systemic sclerosis2.000000e-08
GCST006107_2Upper eyelid morphology6.000000e-06
GCST006444_2Bone mineral density (hip)4.000000e-10
GCST007508_5Self-reported childhood asthma in adult smokers2.000000e-07
GCST008489_16Celiac disease4.000000e-08
GCST90000032_2Myeloproliferative neoplasms8.000000e-11
GCST90002381_193Eosinophil count3.000000e-11

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0006334total iron binding capacity
EFO:1001017limited scleroderma
EFO:0007702hip bone mineral density
EFO:0004251myeloproliferative disorder
EFO:0004842eosinophil 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.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression, increases mutagenesis3
bisphenol Adecreases expression2
Arsenicaffects methylation, increases abundance, increases expression2
Valproic Acidaffects expression, decreases methylation2
Cyclosporinedecreases expression, increases methylation2
pirinixic acidincreases activity, increases expression, affects binding1
sodium arsenateincreases expression, increases abundance1
trichostatin Aaffects cotreatment, decreases expression1
afimoxifenedecreases expression, decreases reaction1
sodium arseniteaffects expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
CGP 52608affects binding, increases reaction1
entinostatdecreases expression1
mesotrioneaffects methylation, increases abundance1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
(+)-JQ1 compounddecreases expression1
PCI 5002affects cotreatment, increases expression1
Bortezomibdecreases expression1
Temozolomideincreases expression1
Acetaminophendecreases expression1
Atrazinedecreases expression1
Cisplatinincreases expression1
Doxorubicinincreases expression1
Estrogensdecreases expression, decreases reaction1
Herbicidesaffects methylation, increases abundance1
Methapyrileneincreases methylation1
Mitoxantroneaffects response to substance1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT06310681Not specifiedCOMPLETEDPilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049Not specifiedNOT_YET_RECRUITINGCognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder