VWCE

protein-coding

von Willebrand factor C and EGF domains, the group of Cysteine rich transmembrane BMP regulators

Gene summary

Predicted to enable calcium ion binding activity. Predicted to be involved in cellular response to virus. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152718.2

Inheritance

—

ClinVar variants

P:1U:137B:14

Top phenotype

Short stature

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr11:61,258,286-61,295,316

External References & Databases

Ensembl (ENSG00000167992)

Transcript & Mutation Effects

hg38 • Region Span ~37.0 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 VWCE variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 4

Short statureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152718.2. 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	1 clinvar	2
missense			136 clinvar	10 clinvar	2 clinvar	148
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	137	11	3	152

Highest pathogenic variant AF is 0.000008055491

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 76 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152718.2	RefSeq	NP_689931.2	20	MANE Select
ENST00000335613.10	Ensembl	ENSP00000334186.5	20	MANE Select
ENST00000301770.10	Ensembl	ENSP00000301770.6	7	Standard
ENST00000535599.1	Ensembl	ENSP00000441565.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular response to virus

Molecular Function

molecular_function
calcium ion binding

Cellular Component

extracellular region
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335613
Coding exons: 20
Length: 37135
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 125748
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.902	479	538	0.891	0.0000306	6027
Missense (PolyPhen)		143	192.26	0.74377		2249
Synonymous	0.751	213	227	0.937	0.0000143	2045
Loss of Function	2.66	26	45.3	0.574	0.00000265	474

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00061	0.00060	rare
Finnish	0.00021	0.00018	rare
European (Non-Finnish)	0.00030	0.00026	rare
South Asian	0.00023	0.00023	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a regulatory element in the beta-catenin signaling pathway and a target for chemoprevention of hapatocellular carcinoma. {ECO:0000269|PubMed:16496348}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.823
RVIS EVS: -0.9
RVIS percentile EVS: 10.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0914

Gene Damage Prediction

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