VASN

vasorin

Basic information

Region (hg38): 16:4371848-4383538

Previous symbols: [ "SLITL2" ]

Links

ENSG00000168140

∙ NCBI:114990 ∙ OMIM:608843 ∙ HGNC:18517 ∙ Uniprot:Q6EMK4 ∙ 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 VASN gene.

not_specified (150 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VASN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138440.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			138 clinvar	12 clinvar		150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	138	12	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VASN	protein_coding	protein_coding	ENST00000304735	1	11681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.672	0.327	124611	0	14	124625	0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.295	411	428	0.960	0.0000310	4089
Missense in Polyphen		102	121.31	0.8408		1394
Synonymous	-1.44	237	211	1.13	0.0000153	1599
Loss of Function	2.72	2	12.3	0.163	6.95e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000324	0.0000324
Ashkenazi Jewish	0.000102	0.000100
East Asian	0.0000556	0.0000545
Finnish	0.000118	0.0000929
European (Non-Finnish)	0.0000692	0.0000624
Middle Eastern	0.0000556	0.0000545
South Asian	0.0000665	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May act as an inhibitor of TGF-beta signaling. {ECO:0000269|PubMed:15247411}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

loftool: 0.104
rvis_EVS: 0.05
rvis_percentile_EVS: 57.48

Haploinsufficiency Scores

pHI: 0.328
hipred: N
hipred_score: 0.322
ghis: 0.518

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Vasn
Phenotype: liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype;

Gene ontology

Biological process: negative regulation of epithelial to mesenchymal transition;negative regulation of transforming growth factor beta receptor signaling pathway;cellular response to hypoxia;cellular response to redox state
Cellular component: extracellular space;mitochondrion;lysosomal membrane;plasma membrane;cell surface;integral component of membrane;extracellular matrix;extracellular exosome
Molecular function: protein binding;cadherin binding;transforming growth factor beta binding