VWC2L

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

Basic information

Region (hg38): 2:214411053-214578976

Links

ENSG00000174453 ∙ NCBI:402117 ∙ OMIM:619794 ∙ HGNC:37203 ∙ Uniprot:B2RUY7 ∙ 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 VWC2L gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWC2L 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			5			5
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in VWC2L

This is a list of pathogenic ClinVar variants found in the VWC2L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-214414216-C-T		not specified	Uncertain significance (Sep 20, 2023)
2-214414252-C-T		not specified	Uncertain significance (Mar 21, 2023)
2-214414312-A-G		not specified	Uncertain significance (Jan 18, 2023)
2-214414347-G-T		not specified	Uncertain significance (Jan 23, 2024)
2-214414390-G-T		not specified	Uncertain significance (Dec 06, 2022)
2-214436720-T-C		not specified	Uncertain significance (Dec 22, 2023)
2-214575687-C-T		not specified	Uncertain significance (Nov 10, 2022)
2-214575696-C-T		not specified	Uncertain significance (Sep 14, 2023)
2-214575714-T-C		not specified	Uncertain significance (Apr 07, 2022)
2-214575813-C-G		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VWC2L	protein_coding	protein_coding	ENST00000312504	3	167895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.130	0.850	124618	0	5	124623	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	78	127	0.614	0.00000662	1483
Missense in Polyphen		30	69.556	0.43131		799
Synonymous	0.0868	45	45.7	0.984	0.00000278	391
Loss of Function	2.00	3	9.75	0.308	5.75e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000556
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.00000887	0.00000885
Middle Eastern	0.0000558	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in neurogenesis. May play a role in bone differentiation and matrix mineralization. {ECO:0000250}.

Intolerance Scores

• loftool: 0.242
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.604
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vwc2l

Zebrafish Information Network

• Gene name: vwc2l
• Affected structure: telencephalic ventricle
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: negative regulation of BMP signaling pathway;positive regulation of neuron differentiation
• Cellular component: extracellular space;cell junction;AMPA glutamate receptor complex;synapse
• Molecular function: protein binding