VWC2

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

Basic information

Region (hg38): 7:49773638-49921950

Links

ENSG00000188730 ∙ NCBI:375567 ∙ OMIM:611108 ∙ HGNC:30200 ∙ Uniprot:Q2TAL6 ∙ 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 VWC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWC2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in VWC2

This is a list of pathogenic ClinVar variants found in the VWC2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-49775461-T-G		not specified	Uncertain significance (Nov 09, 2023)
7-49775476-G-A		not specified	Uncertain significance (May 21, 2024)
7-49775585-C-A		not specified	Uncertain significance (Oct 20, 2021)
7-49775598-G-T		not specified	Uncertain significance (Feb 06, 2024)
7-49775602-C-A		not specified	Uncertain significance (Apr 08, 2024)
7-49775632-C-A		not specified	Uncertain significance (Sep 01, 2021)
7-49775640-G-A		not specified	Uncertain significance (Apr 30, 2024)
7-49775640-G-C		not specified	Uncertain significance (Oct 06, 2021)
7-49775653-G-C		not specified	Uncertain significance (Jan 13, 2023)
7-49775708-C-A		not specified	Uncertain significance (Jun 29, 2023)
7-49775740-G-T		not specified	Uncertain significance (Mar 26, 2024)
7-49775745-G-A		not specified	Uncertain significance (Dec 27, 2023)
7-49775754-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-49775785-C-T		not specified	Uncertain significance (Jun 11, 2021)
7-49775818-A-G		not specified	Uncertain significance (May 11, 2022)
7-49775821-A-T		not specified	Uncertain significance (Jun 04, 2024)
7-49775845-C-G		not specified	Uncertain significance (Dec 18, 2023)
7-49776013-C-A		not specified	Uncertain significance (Mar 14, 2023)
7-49776030-T-A		not specified	Uncertain significance (Dec 15, 2022)
7-49776054-T-G		not specified	Uncertain significance (Oct 13, 2023)
7-49776091-A-G		not specified	Uncertain significance (Feb 28, 2024)
7-49776100-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-49776115-C-T		not specified	Uncertain significance (Mar 29, 2023)
7-49776126-T-C		not specified	Uncertain significance (Mar 02, 2023)
7-49802711-G-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VWC2	protein_coding	protein_coding	ENST00000340652	3	148290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0291	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	112	174	0.643	0.00000899	2063
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.634
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vwc2

Gene ontology

• Biological process: positive regulation of cell-substrate adhesion;negative regulation of BMP signaling pathway;positive regulation of neuron differentiation
• Cellular component: basement membrane;interstitial matrix;extracellular space;cell junction;AMPA glutamate receptor complex;synapse
• Molecular function: molecular_function