VWCE

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

Basic information

Region (hg38): 11:61258286-61295316

Links

ENSG00000167992 ∙ NCBI:220001 ∙ OMIM:611115 ∙ HGNC:26487 ∙ Uniprot:Q96DN2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VWCE gene.

• not_specified (125 variants)
• not_provided (4 variants)
• Short_stature (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWCE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152718.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			115	10	2	127
nonsense	1					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	115	11	3

Highest pathogenic variant AF is 0.000008055491

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VWCE	protein_coding	protein_coding	ENST00000335613	20	37135

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.05e-12	0.994	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.902	479	538	0.891	0.0000306	6027
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000606	0.000603
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000605	0.000598
Finnish	0.000205	0.000185
European (Non-Finnish)	0.000297	0.000264
Middle Eastern	0.000605	0.000598
South Asian	0.000230	0.000229
Other	0.000495	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.197
• hipred: N
• hipred_score: 0.270
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vwce

Gene ontology

• Biological process: cellular response to virus
• Cellular component: extracellular region;cytoplasm
• Molecular function: molecular_function;calcium ion binding