VSNL1

visinin like 1, the group of EF-hand domain containing

Basic information

Region (hg38): 2:17539126-17657018

Links

ENSG00000163032 ∙ NCBI:7447 ∙ OMIM:600817 ∙ HGNC:12722 ∙ Uniprot:P62760 ∙ 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 VSNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSNL1 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	4	0	0

Variants in VSNL1

This is a list of pathogenic ClinVar variants found in the VSNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-17581965-AGGTGATGCAGCAACAGCAGTTGTGTAATTTGCAAAAGAAGAAGTAGCCGTACAGTGAAGTCACTGAAAATGAGGTACCTCCTCTACATCTTGAAATATCAGTGGGAGTTCACTAGAGAACCAACGTGTAGCTAATGAGAACTGCCCTCAGAGCAAAAGGAGCAGCAAAAGGAAACACAGAGAGGTTTGGCATGATATTAGGAAGTTGTAGCATAGGTGAGAACATGGGGAGAGAGGAAACTAAAGAGGTGCCAGGAGGGGTGAGGGGAAGGAGGAAGGTGGGAGGCTGGAGGGAAAGTGTAGGCCCAAGTGAGCAGGTCTGGGAAGCCATGCTCACAGTTGGAATTCAGAGTGAGGATAATGAGAGACCACTGAAGGGTTTAAGCAGGGCAGTGACATGATTGGGTTTTGTGTTTTAGAAAGGTCATTCCAGCTATGATAGTATGGAAGATGGAATTCAGGAGGGTAAGACTTTAGATGGAGAAGCAAGTTAGGAAGCTATTGTACTACTCAAAGTGATAGGATAATGGCTTGAACCAAAGTAGTGGCAACAGAGAAAAGTAGATGGAATCAAGAGTTAGAAAGTAGAATCTACCAACTTCTTAACTTGTTGATAGGTTTACATACAGAAACACGAAATAGAGAAGTTCAGAATGATGCCCAGACTCTGCATGGAACCTTGTGAAGATGGCGGGCCACTTACTCGGAGAGGAACAAAGAATAAAAGGATGTTTTAGGGGAAAAAGGAGGACAAATTCATGTTTGCATAGTATGTTGAGTTTGATGTGGTGGTAGAATACAATGGTGGAAATGTCTAGCAGGCAGATGAATACATTATCTAGTATTCCCAAATTTTTCTTTAGGACCTCCCCTAAAGACCTGGAAAGACCTGTCCTAAAGAAAAATTTGGGAATCATATGATAATACTGAGTAAAAGTTTGCTGAATAAATGAATGAATTGACTCATTTTCAGCATCATGTTTCCTTCAACTAGAACATTTTACTTCTATAAAGCCACCTTCATACGAGAATTTCAAAGTTGTTTTTAAGACTAACCAACATGAATTAAAGTATCTTTTTAGAATTACTGTAGAGATAACAACTTAGGAACATGGTGAGTGCAAATGGCTCTCAGAGAGGAAAGAGTACCAGCCTAAGAGTCAGAAGATGAGTGAGTTGGAACTTGTCTACTATTGGTGGACACTGGTACATGCCACTCACCCCCTCCACCAAATATTCAAGTTCTCTGAATGCAAAGACAGGGGTTGCATTCCTGATGATCAATGCCTAACCCTGTGACAGGGAATGTGCAGGTGAAGCGGGACACTCCAGGTCTGCTCTTCTCTCTCGGCAGCTCCCTGCTGTTCTCAGATAAGGGCCACAGTCCCTCCCCACTGGGACTTGGCAGCACAACCTAGAACACAATCTGTTGGACAGAAGGCTGTGATTATTAATGAAAGCATTTCCTCTGTTACCTCACAGAACTAAGTGAGGTTCTAACACTGCCAAAGATGGCCCATTTCCTTTCATAGAAACCAATTCTCAGAAACACATAGGATGGTCAGAGACAGTACACATAGGGAAGTAAAAATAAGGTGCAGAAAAGTGGGTGGCTGCTTGAAACACTCCCAGATGAAAGGTTACCAGCTATTAATCAGCTCACACTTCTGTTCAGTGGGTGAGCAAGAAATTGGATGGAAACTTCACTCAATGGTTGATGCTTAGTTGGGGCTGTGAGGTCCTCAGATGACTTTCCTCAGTCAGGTCGGATATGATGCACTTTTATGTAAAGGAAGGAGAGTCAACAAGGCCACAGCAAAATTCCCTATGTTTCACAATTTGTGTACGTCTGTTTACATGTGCCAGGCTCGGTGCCATGTATTGAGGTTAGGATGACTCCTGCTGTCTAGGCCTGAATCTTGAACAGTCCCCCTCTCCATCATTTGGAGCAGCCCAGTTGGCTGGGTCCTGTGATGAGGATAATAATAGTTACTGTTTTTTGGACACCTGCCTCATGGAAGGCACTGTTGGAAAAAAGTCAGCATTATCTCATTTATCCTCACAACAACCCTTTGAGCAAATAACATTATTTTATTTGAAAAATGGGGAGATTGGGGTTCCAGTG-A		See cases	Uncertain significance (Mar 03, 2022)
2-17592082-A-G		not specified	Uncertain significance (Dec 30, 2023)
2-17649434-A-G		not specified	Uncertain significance (Jan 09, 2024)
2-17649600-G-A		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSNL1	protein_coding	protein_coding	ENST00000406397	3	117893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.457	0.537	125743	0	2	125745	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	31	106	0.291	0.00000551	1300
Missense in Polyphen		14	46.95	0.29819		555
Synonymous	0.112	42	42.9	0.978	0.00000261	330
Loss of Function	2.33	2	9.94	0.201	7.78e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates (in vitro) the inhibition of rhodopsin phosphorylation in a calcium-dependent manner. {ECO:0000250}.
• Pathway: miR-targeted genes in muscle cell - TarBase (Consensus)

Intolerance Scores

• loftool: 0.189
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.451
• hipred: Y
• hipred_score: 0.728
• ghis: 0.649

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vsnl1

Gene ontology

• Biological process: positive regulation of insulin secretion involved in cellular response to glucose stimulus;positive regulation of exocytosis;negative regulation of insulin secretion
• Cellular component: cytosol;membrane
• Molecular function: calcium ion binding;protein binding