VWC2

protein-coding

von Willebrand factor C domain containing 2, the group of Chordin family

Gene summary

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.[provided by RefSeq, Oct 2009]

MANE transcript

NM_198570.5

Inheritance

—

ClinVar variants

U:55B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr7:49,773,638-49,921,950

External References & Databases

Ensembl (ENSG00000188730)

Transcript & Mutation Effects

hg38 • Region Span ~148.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VWC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198570.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			54 clinvar	1 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	3	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198570.5	RefSeq	NP_940972.2	3	MANE Select
ENST00000340652.5	Ensembl	ENSP00000341819.3	3	MANE Select
ENST00000855725.1	Ensembl	ENSP00000525784.1	3	Standard
ENST00000855725.2	Ensembl	ENSP00000525784.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of cell-substrate adhesion
negative regulation of BMP signaling pathway
positive regulation of neuron differentiation

Molecular Function

molecular_function

Cellular Component

basement membrane
interstitial matrix
extracellular space
cell junction
AMPA glutamate receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340652
Coding exons: 3
Length: 148290
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	112	174	0.643	0.00000899	2063
Missense (PolyPhen)		23	70.819	0.32477		756
Synonymous	0.801	70	79.1	0.885	0.00000454	638
Loss of Function	3.06	0	10.9	0.00	4.65e-7	136

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: BMP antagonist which may play a role in neural development. Promotes cell adhesion (By similarity). {ECO:0000250}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0923

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium