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.

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.

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			70	5		75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	5	1

Variants in VASN

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

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

Position	Type	Phenotype	Significance	ClinVar
16-4380938-G-C		not specified	Uncertain significance (Dec 11, 2023)
16-4380944-G-A		not specified	Uncertain significance (Jul 09, 2021)
16-4380956-G-A		not specified	Uncertain significance (Dec 28, 2023)
16-4380999-G-A		not specified	Uncertain significance (Oct 02, 2023)
16-4381008-C-A		not specified	Uncertain significance (Nov 03, 2023)
16-4381079-G-A		not specified	Uncertain significance (Apr 29, 2024)
16-4381130-C-A		not specified	Uncertain significance (Dec 15, 2022)
16-4381142-G-T		not specified	Uncertain significance (May 26, 2024)
16-4381175-G-A		not specified	Uncertain significance (Jan 20, 2023)
16-4381179-A-T		not specified	Uncertain significance (Dec 02, 2022)
16-4381250-C-T		not specified	Uncertain significance (Jan 22, 2024)
16-4381256-G-C		not specified	Uncertain significance (Nov 08, 2022)
16-4381280-C-T		not specified	Uncertain significance (Dec 08, 2023)
16-4381286-C-T		not specified	Uncertain significance (Jul 08, 2022)
16-4381287-G-A		not specified	Likely benign (Sep 22, 2022)
16-4381289-C-T		not specified	Uncertain significance (Aug 19, 2021)
16-4381319-G-A		not specified	Uncertain significance (Jun 30, 2023)
16-4381322-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-4381346-G-A		not specified	Uncertain significance (Jan 20, 2023)
16-4381354-G-T		not specified	Uncertain significance (Mar 01, 2024)
16-4381371-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-4381385-C-T		not specified	Uncertain significance (Dec 17, 2023)
16-4381415-A-C		not specified	Uncertain significance (Jun 03, 2022)
16-4381442-C-G		not specified	Uncertain significance (Oct 26, 2022)
16-4381479-G-T		not specified	Uncertain significance (Nov 09, 2021)

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