VASH2

vasohibin 2

Basic information

Region (hg38): 1:212950520-212992037

Links

ENSG00000143494 ∙ NCBI:79805 ∙ OMIM:610471 ∙ HGNC:25723 ∙ Uniprot:Q86V25 ∙ 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 VASH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VASH2 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				1		1
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in VASH2

This is a list of pathogenic ClinVar variants found in the VASH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-212951627-C-A		not specified	Uncertain significance (Oct 26, 2022)
1-212951681-G-C		not specified	Uncertain significance (Apr 04, 2024)
1-212951723-C-T		not specified	Uncertain significance (Feb 17, 2024)
1-212961172-A-G		not specified	Likely benign (May 18, 2023)
1-212961215-A-C		not specified	Uncertain significance (Dec 06, 2022)
1-212961227-C-A		not specified	Uncertain significance (Jan 16, 2024)
1-212972656-C-T		not specified	Uncertain significance (Jul 19, 2023)
1-212972668-C-G		not specified	Uncertain significance (Nov 09, 2021)
1-212972749-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-212972767-A-G		not specified	Uncertain significance (Jun 07, 2023)
1-212972799-C-T			Likely benign (Jul 01, 2022)
1-212972821-A-C		not specified	Uncertain significance (Nov 27, 2023)
1-212972825-T-C		not specified	Uncertain significance (May 30, 2024)
1-212972836-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-212972845-G-A		not specified	Uncertain significance (May 03, 2023)
1-212972847-G-C		not specified	Uncertain significance (May 03, 2023)
1-212972942-C-A		not specified	Uncertain significance (Jun 07, 2023)
1-212974000-C-T		not specified	Uncertain significance (Jan 10, 2023)
1-212974003-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-212974057-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-212988520-T-C		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VASH2	protein_coding	protein_coding	ENST00000366965	5	41518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.242	0.752	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.747	156	185	0.845	0.00000990	2020
Missense in Polyphen		55	68.426	0.80379		754
Synonymous	0.562	68	74.2	0.917	0.00000402	604
Loss of Function	2.37	3	11.8	0.255	5.82e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine carboxypeptidase that removes the C-terminal tyrosine residue of alpha-tubulin, thereby regulating microtubule dynamics and function (PubMed:29146869). Acts as an activator of angiogenesis: expressed in infiltrating mononuclear cells in the sprouting front to promote angiogenesis (PubMed:19204325). {ECO:0000269|PubMed:19204325, ECO:0000269|PubMed:29146869}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.0719
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.433
• hipred: Y
• hipred_score: 0.749
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vash2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: syncytium formation by plasma membrane fusion;positive regulation of endothelial cell proliferation;proteolysis;positive regulation of angiogenesis;labyrinthine layer blood vessel development;cell-cell fusion
• Cellular component: extracellular region;cytoplasm
• Molecular function: actin binding;metallocarboxypeptidase activity;protein binding