VWA5A

von Willebrand factor A domain containing 5A

Basic information

Region (hg38): 11:124115404-124147721

Previous symbols: [ "LOH11CR2A" ]

Links

ENSG00000110002 ∙ NCBI:4013 ∙ OMIM:602929 ∙ HGNC:6658 ∙ Uniprot:O00534 ∙ 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 VWA5A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWA5A 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			41	4		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	4	0

Variants in VWA5A

This is a list of pathogenic ClinVar variants found in the VWA5A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-124117542-C-T		not specified	Uncertain significance (Nov 21, 2023)
11-124117546-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-124117775-C-T		not specified	Uncertain significance (Sep 20, 2023)
11-124117783-G-T		not specified	Likely benign (Aug 08, 2022)
11-124117845-A-T		not specified	Uncertain significance (Mar 17, 2023)
11-124117846-A-G		not specified	Uncertain significance (Dec 08, 2021)
11-124118202-A-G		not specified	Uncertain significance (Dec 21, 2022)
11-124118244-A-T		not specified	Uncertain significance (Mar 20, 2024)
11-124118538-T-G		not specified	Uncertain significance (Jan 08, 2024)
11-124118601-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-124118641-A-G		not specified	Uncertain significance (Jun 29, 2023)
11-124118664-T-A		not specified	Uncertain significance (Sep 16, 2021)
11-124118698-C-T		not specified	Uncertain significance (Jun 17, 2024)
11-124118997-A-T		not specified	Uncertain significance (May 15, 2024)
11-124119051-G-C		not specified	Uncertain significance (Dec 13, 2023)
11-124119053-G-A		not specified	Uncertain significance (Mar 31, 2024)
11-124119062-G-C		not specified	Uncertain significance (Apr 23, 2024)
11-124123062-G-A		not specified	Uncertain significance (May 15, 2023)
11-124123085-A-G		not specified	Uncertain significance (Aug 16, 2021)
11-124123113-G-A		not specified	Uncertain significance (May 15, 2024)
11-124123375-A-T		not specified	Uncertain significance (Jan 03, 2024)
11-124123727-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-124123790-G-A		not specified	Uncertain significance (Dec 20, 2021)
11-124124269-C-A		not specified	Uncertain significance (Jan 26, 2022)
11-124124271-C-T		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VWA5A	protein_coding	protein_coding	ENST00000456829	17	32360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.60e-29	0.0000133	125598	0	150	125748	0.000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.599	466	431	1.08	0.0000220	5169
Missense in Polyphen		109	105.32	1.035		1349
Synonymous	1.10	146	164	0.891	0.00000885	1525
Loss of Function	-0.714	41	36.4	1.13	0.00000179	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000942	0.000873
Ashkenazi Jewish	0.00	0.00
East Asian	0.00158	0.00158
Finnish	0.000418	0.000416
European (Non-Finnish)	0.000566	0.000563
Middle Eastern	0.00158	0.00158
South Asian	0.000858	0.000850
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in tumorigenesis as a tumor suppressor. Altered expression of this protein and disruption of the molecular pathway it is involved in, may contribute directly to or modify tumorigenesis.

Intolerance Scores

• loftool: 0.993
• rvis_EVS: 0.65
• rvis_percentile_EVS: 84.15

Haploinsufficiency Scores

• pHI: 0.0485
• hipred: N
• hipred_score: 0.146
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.151

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vwa5a

Gene ontology

• Cellular component: nucleus;nucleoplasm