VWC2

gene
On this page

Also known as PSST739UNQ739

Summary

VWC2 (von Willebrand factor C domain containing 2, HGNC:30200) is a protein-coding gene on chromosome 7p12.2, encoding Brorin (Q2TAL6). BMP antagonist which may play a role in neural development.

This gene encodes a secreted bone morphogenic protein antagonist. The encoded protein is possibly involved in neural function and development and may have a role in cell adhesion.

Source: NCBI Gene 375567 — RefSeq curated summary.

At a glance

  • GWAS associations: 11
  • Clinical variants (ClinVar): 61 total
  • MANE Select transcript: NM_198570

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30200
Approved symbolVWC2
Namevon Willebrand factor C domain containing 2
Location7p12.2
Locus typegene with protein product
StatusApproved
AliasesPSST739, UNQ739
Ensembl geneENSG00000188730
Ensembl biotypeprotein_coding
OMIM611108
Entrez375567

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000340652, ENST00000855725, ENST00000855726, ENST00000855727, ENST00000855728, ENST00000855729, ENST00000855730, ENST00000855731

RefSeq mRNA: 1 — MANE Select: NM_198570 NM_198570

CCDS: CCDS5508

Canonical transcript exons

ENST00000340652 — 4 exons

ExonStartEnd
ENSE000013647044977363849774113
ENSE000013674274980271149802840
ENSE000013873584991203449921950
ENSE000013903084977533349776131

Expression profiles

Bgee: expression breadth broad, 96 present calls, max score 80.55.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4097 / max 48.2534, expressed in 128 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
786090.2556106
786100.083253
786110.053230
786120.01765

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cerebellar cortexUBERON:000212980.55gold quality
cerebellar hemisphereUBERON:000224580.54gold quality
right hemisphere of cerebellumUBERON:001489080.24gold quality
cerebellumUBERON:000203779.85gold quality
heart left ventricleUBERON:000208471.59gold quality
apex of heartUBERON:000209871.57gold quality
cardiac ventricleUBERON:000208270.85gold quality
right atrium auricular regionUBERON:000663170.64gold quality
left ovaryUBERON:000211970.23gold quality
cerebellar vermisUBERON:000472069.64gold quality
prefrontal cortexUBERON:000045169.49gold quality
cardiac atriumUBERON:000208169.26gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047367.96silver quality
heartUBERON:000094866.03gold quality
anterior cingulate cortexUBERON:000983565.61gold quality
primary visual cortexUBERON:000243665.56gold quality
Brodmann (1909) area 9UBERON:001354065.26gold quality
amygdalaUBERON:000187664.65gold quality
ovaryUBERON:000099264.53gold quality
dorsolateral prefrontal cortexUBERON:000983464.13gold quality
right ovaryUBERON:000211863.56gold quality
neocortexUBERON:000195063.51gold quality
right frontal lobeUBERON:000281063.45gold quality
frontal cortexUBERON:000187063.12gold quality
hypothalamusUBERON:000189862.63gold quality
cortical plateUBERON:000534361.11gold quality
cerebral cortexUBERON:000095660.51gold quality
occipital lobeUBERON:000202159.53gold quality
brainUBERON:000095558.81gold quality
Brodmann (1909) area 23UBERON:001355458.05silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-35yes72.90
E-HCAD-25yes43.01
E-ANND-3yes5.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

186 targeting VWC2, 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-126-5P100.0072.713180
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-5692A100.0074.406850
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-656-3P100.0072.152788
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-453499.9966.581907
HSA-MIR-318599.9968.121959
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-570-3P99.9672.414910
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-211099.9666.681930
HSA-MIR-808299.9567.271170
HSA-MIR-651-3P99.9473.485177
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-552-5P99.9368.561583
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-311999.9271.342390
HSA-MIR-205-3P99.9269.923165
HSA-MIR-568099.9169.833421
HSA-MIR-367199.9073.043897

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriovwc2ENSDARG00000076495
mus_musculusVwc2ENSMUSG00000050830
rattus_norvegicusVwc2ENSRNOG00000049076

Paralogs (19): CHRDL2 (ENSG00000054938), CHRD (ENSG00000090539), CHRDL1 (ENSG00000101938), TECTA (ENSG00000109927), VWF (ENSG00000110799), MUC5B (ENSG00000117983), KCP (ENSG00000135253), ZAN (ENSG00000146839), CRIM1 (ENSG00000150938), BMPER (ENSG00000164619), OTOGL (ENSG00000165899), VWCE (ENSG00000167992), VWC2L (ENSG00000174453), MUC6 (ENSG00000184956), OTOG (ENSG00000188162), MUC2 (ENSG00000198788), MUC19 (ENSG00000205592), MUC5AC (ENSG00000215182), FCGBP (ENSG00000275395)

Protein

Protein identifiers

BrorinQ2TAL6 (reviewed: Q2TAL6)

Alternative names: Brain-specific chordin-like protein, von Willebrand factor C domain-containing protein 2

All UniProt accessions (1): Q2TAL6

UniProt curated annotations — full annotation on UniProt →

Function. BMP antagonist which may play a role in neural development. Promotes cell adhesion.

Subunit / interactions. Peripherally associated with AMPAR complex. AMPAR complex consists of an inner core made of 4 pore-forming GluA/GRIA proteins (GRIA1, GRIA2, GRIA3 and GRIA4) and 4 major auxiliary subunits arranged in a twofold symmetry. One of the two pairs of distinct binding sites is occupied either by CNIH2, CNIH3 or CACNG2, CACNG3. The other harbors CACNG2, CACNG3, CACNG4, CACNG8 or GSG1L. This inner core of AMPAR complex is complemented by outer core constituents binding directly to the GluA/GRIA proteins at sites distinct from the interaction sites of the inner core constituents. Outer core constituents include at least PRRT1, PRRT2, CKAMP44/SHISA9, FRRS1L and NRN1. The proteins of the inner and outer core serve as a platform for other, more peripherally associated AMPAR constituents, including VWC2. Alone or in combination, these auxiliary subunits control the gating and pharmacology of the AMPAR complex and profoundly impact their biogenesis and protein processing.

Subcellular location. Secreted. Extracellular space. Extracellular matrix. Basement membrane. Synapse.

RefSeq proteins (1): NP_940972* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001007VWF_domDomain
IPR042979VWC2/VWC2LFamily
IPR057856VWC2L_CDomain
IPR059152VWC2L_NDomain

Pfam: PF23331, PF23333, PF23334

UniProt features (10 total): domain 2, compositionally biased region 2, signal peptide 1, chain 1, region of interest 1, short sequence motif 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2TAL6-F169.080.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 144 (showing top): GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_POSITIVE_REGULATION_OF_NEURON_DIFFERENTIATION, TATTATA_MIR374, GOBP_NEUROGENESIS, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_REGULATION_OF_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, GOBP_NEGATIVE_REGULATION_OF_BMP_SIGNALING_PATHWAY, GOBP_RESPONSE_TO_BMP, GOBP_REGULATION_OF_CELL_SUBSTRATE_ADHESION, GOBP_RESPONSE_TO_GROWTH_FACTOR, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE

GO Biological Process (4): positive regulation of cell-substrate adhesion (GO:0010811), negative regulation of BMP signaling pathway (GO:0030514), positive regulation of neuron differentiation (GO:0045666), neurotransmitter receptor localization to postsynaptic specialization membrane (GO:0099645)

GO Molecular Function (2): molecular_function (GO:0003674), protein binding (GO:0005515)

GO Cellular Component (9): basement membrane (GO:0005604), interstitial matrix (GO:0005614), obsolete extracellular space (GO:0005615), AMPA glutamate receptor complex (GO:0032281), extrinsic component of postsynaptic membrane (GO:0098890), glutamatergic synapse (GO:0098978), extracellular region (GO:0005576), extracellular matrix (GO:0031012), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
extracellular matrix2
regulation of cell-substrate adhesion1
cell-substrate adhesion1
positive regulation of cell adhesion1
BMP signaling pathway1
regulation of BMP signaling pathway1
negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway1
negative regulation of cellular response to growth factor stimulus1
neuron differentiation1
positive regulation of cell differentiation1
regulation of neuron differentiation1
protein-containing complex localization1
receptor localization to synapse1
regulation of postsynaptic membrane neurotransmitter receptor levels1
protein localization to postsynaptic specialization membrane1
binding1
ionotropic glutamate receptor complex1
postsynaptic membrane1
extrinsic component of synaptic membrane1
synapse1
cellular anatomical structure1
external encapsulating structure1
cell junction1

Protein interactions and networks

STRING

958 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
VWC2CHRDQ9H2X0819
VWC2NRN1Q9NPD7622
VWC2BMP6P22004620
VWC2VWCEQ96DN2601
VWC2NOGQ13253591
VWC2CCDC175P0C221591
VWC2PRR35P0CG20575
VWC2GSG1LQ6UXU4527
VWC2KBTBD12Q3ZCT8521
VWC2BMP2P12643511
VWC2CLVS2Q5SYC1506
VWC2RRP36Q96EU6492
VWC2ZPBPQ9BS86487
VWC2BMPERQ8N8U9478
VWC2TOGARAM1Q9Y4F4463

IntAct

178 interactions, top by confidence:

ABTypeScore
VWC2ZNF696psi-mi:“MI:0915”(physical association)0.670
KRTAP5-9VWC2psi-mi:“MI:0915”(physical association)0.560
OTX1VWC2psi-mi:“MI:0915”(physical association)0.560
POU4F2VWC2psi-mi:“MI:0915”(physical association)0.560
VWC2LCE2Cpsi-mi:“MI:0915”(physical association)0.560
VWC2KRTAP2-4psi-mi:“MI:0915”(physical association)0.560
CYSRT1VWC2psi-mi:“MI:0915”(physical association)0.560
VWC2UBQLN2psi-mi:“MI:0915”(physical association)0.560
HOXA1VWC2psi-mi:“MI:0915”(physical association)0.560
KRTAP10-8VWC2psi-mi:“MI:0915”(physical association)0.560
VWC2ADAMTSL4psi-mi:“MI:0915”(physical association)0.560
VWC2UBQLN1psi-mi:“MI:0915”(physical association)0.560
VWC2CRY2psi-mi:“MI:0915”(physical association)0.560
VWC2SCNM1psi-mi:“MI:0915”(physical association)0.560
VWC2LCE2Dpsi-mi:“MI:0915”(physical association)0.560
VWC2LCE3Apsi-mi:“MI:0915”(physical association)0.560
HPCAL1VWC2psi-mi:“MI:0915”(physical association)0.560
VWC2LCE3Dpsi-mi:“MI:0915”(physical association)0.560
VWC2SGTBpsi-mi:“MI:0915”(physical association)0.560
VWC2LCE1Fpsi-mi:“MI:0915”(physical association)0.560
VWC2SHFLpsi-mi:“MI:0915”(physical association)0.560
VWC2CNNM3psi-mi:“MI:0915”(physical association)0.560
VWC2LCE1Cpsi-mi:“MI:0915”(physical association)0.560
VWC2FAM90A1psi-mi:“MI:0915”(physical association)0.560
VWC2FUCA2psi-mi:“MI:0915”(physical association)0.560
VWC2KRTAP13-2psi-mi:“MI:0915”(physical association)0.560
VWC2LCE3Epsi-mi:“MI:0915”(physical association)0.560
VWC2ZNF417psi-mi:“MI:0915”(physical association)0.560
VWC2CATSPER1psi-mi:“MI:0915”(physical association)0.560
VWC2KRTAP13-3psi-mi:“MI:0915”(physical association)0.560

BioGRID (63): VWC2 (Affinity Capture-MS), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid), VWC2 (Two-hybrid)

ESM2 similar proteins: A0A1W2PP97, A6NLX4, A6QNY1, P0DJK0, P12838, P13207, P22389, P22749, P23943, P29473, P29474, P55056, P70313, P79209, P97270, P98162, Q1RMT9, Q28969, Q2TAL6, Q2VPJ9, Q4TUC0, Q566C8, Q5BIR3, Q5JTB6, Q5NRP8, Q5RCS3, Q5SPX3, Q5XIX0, Q62600, Q64322, Q7TMJ8, Q7TPD7, Q7TSF4, Q80TT8, Q867D0, Q8BZT7, Q8C8N3, Q8K1T4, Q8K4Z2, Q8MJW9

Diamond homologs: A0A1D5NSM8, A1A5Y0, A2AVA0, A2RUV0, A2VCU8, A5A8Y8, A6QR11, B3EWY9, B5DFC9, G3I6Z6, O75095, O88322, P07996, P0C6B8, P10493, P12105, P14585, P21783, P35441, P35448, P35555, P35556, P41990, P46531, P82279, P98133, Q01705, Q07008, Q14112, Q20911, Q28178, Q2PC93, Q2TAL6, Q2VWQ2, Q3U515, Q4LDE5, Q5R3Z7, Q5RBP1, Q61220, Q61554

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 57 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
Formation of the cornified envelope920.3×1e-08
Keratinization1420.0×1e-13

GO biological processes:

GO termPartnersFoldFDR
keratinization940.5×2e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance55
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1488 predictions. Top by Δscore:

VariantEffectΔscore
7:49802704:GTTTC:Gacceptor_loss0.9900
7:49802705:TTTCA:Tacceptor_loss0.9900
7:49802706:TTCAG:Tacceptor_loss0.9900
7:49802707:TCAGG:Tacceptor_loss0.9900
7:49802708:CA:Cacceptor_loss0.9900
7:49826200:T:Gacceptor_gain0.9900
7:49826204:T:Aacceptor_gain0.9900
7:49912123:G:GTdonor_gain0.9900
7:49802710:GGT:Gacceptor_gain0.9800
7:49826191:T:TAacceptor_gain0.9800
7:49826199:A:AGacceptor_gain0.9800
7:49912177:C:Tdonor_gain0.9800
7:49776129:GTG:Gdonor_gain0.9700
7:49826202:ACT:Aacceptor_gain0.9700
7:49910474:T:Gdonor_gain0.9700
7:49776077:G:GTdonor_gain0.9600
7:49776128:CGTGG:Cdonor_loss0.9600
7:49776130:TGGT:Tdonor_loss0.9600
7:49776131:GGTAA:Gdonor_loss0.9600
7:49776132:G:GCdonor_loss0.9600
7:49776132:G:GGdonor_gain0.9600
7:49776133:T:TTdonor_loss0.9600
7:49776173:G:GTdonor_gain0.9600
7:49802709:A:AGacceptor_gain0.9600
7:49802710:G:GGacceptor_gain0.9600
7:49776134:A:Cdonor_loss0.9500
7:49793079:T:Gacceptor_gain0.9500
7:49773916:A:Gdonor_gain0.9400
7:49802709:AG:Aacceptor_gain0.9400
7:49802710:GG:Gacceptor_gain0.9400

AlphaMissense

2118 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:49775898:T:AC155S1.000
7:49775899:G:CC155S1.000
7:49775941:T:GF169C1.000
7:49775973:T:AC180S1.000
7:49775974:G:CC180S1.000
7:49776127:T:GF231C1.000
7:49802789:T:AC259S1.000
7:49802789:T:CC259R1.000
7:49802790:G:CC259S1.000
7:49912042:T:AC279S1.000
7:49912042:T:CC279R1.000
7:49912043:G:CC279S1.000
7:49912044:C:GC279W1.000
7:49912134:G:CW309C1.000
7:49912134:G:TW309C1.000
7:49775898:T:CC155R0.999
7:49775899:G:AC155Y0.999
7:49775900:C:GC155W0.999
7:49775940:T:CF169L0.999
7:49775941:T:CF169S0.999
7:49775942:C:AF169L0.999
7:49775942:C:GF169L0.999
7:49775967:T:CC178R0.999
7:49775973:T:CC180R0.999
7:49775974:G:AC180Y0.999
7:49775975:C:GC180W0.999
7:49775994:T:AC187S0.999
7:49775995:G:CC187S0.999
7:49776009:T:AC192S0.999
7:49776009:T:CC192R0.999

dbSNP variants (sampled 300 via entrez): RS1000018041 (7:49791271 C>G,T), RS1000018716 (7:49882754 T>C), RS1000043554 (7:49776149 G>A,C,T), RS1000057468 (7:49903993 A>G), RS1000062416 (7:49841043 A>C), RS1000077271 (7:49834583 C>G), RS1000142679 (7:49897190 C>T), RS1000146899 (7:49917721 T>C,G), RS1000186590 (7:49869752 C>A), RS1000194769 (7:49897492 A>G), RS1000196201 (7:49833400 A>T), RS1000200385 (7:49853005 C>G), RS1000243555 (7:49866409 G>T), RS1000257157 (7:49847010 C>G,T), RS1000301108 (7:49869948 T>C)

Disease associations

OMIM: gene MIM:611108 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

11 associations (top):

StudyTraitp-value
GCST002707_7Serum thyroid-stimulating hormone levels5.000000e-06
GCST002783_395Body mass index2.000000e-06
GCST002783_482Body mass index4.000000e-06
GCST003264_198Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST004747_20Lung cancer in never smokers4.000000e-06
GCST004904_76Body mass index5.000000e-10
GCST005024_21Pursuit maintenance gain7.000000e-06
GCST006585_810Blood protein levels1.000000e-22
GCST008478_28Neurological blood protein biomarker levels5.000000e-17
GCST012420_13tricyclic pyrone compound response (IC50)9.000000e-06
GCST90000050_57Age at first birth1.000000e-08

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0004713FEV/FVC ratio
EFO:0008433pursuit maintenance gain measurement
EFO:0600033response to mitochondrial complex I inhibitor
EFO:0009101age at first birth measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression, increases methylation2
bisphenol Adecreases methylation1
N-acetyl-4-benzoquinoneimineaffects response to substance1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
CGP 52608affects binding, increases reaction1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
bisphenol Saffects cotreatment, decreases methylation, increases methylation1
MT19c compounddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Catechinaffects cotreatment, decreases expression1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression1
Plant Extractsaffects cotreatment, decreases expression1
Valproic Aciddecreases methylation1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.