VSIG10L

V-set and immunoglobulin domain containing 10 like, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 19:51331536-51342139

Links

ENSG00000186806 ∙ NCBI:147645 ∙ OMIM:617740 ∙ HGNC:27111 ∙ Uniprot:Q86VR7 ∙ 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 VSIG10L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSIG10L 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			52	1	2	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	52	2	3

Variants in VSIG10L

This is a list of pathogenic ClinVar variants found in the VSIG10L region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51333800-C-G		not specified	Uncertain significance (Dec 15, 2023)
19-51333890-G-A			Likely benign (Mar 14, 2018)
19-51334278-C-T		not specified	Uncertain significance (Jan 08, 2024)
19-51334289-T-A		not specified	Uncertain significance (Oct 30, 2023)
19-51334311-G-A			Benign (Jul 06, 2018)
19-51337244-G-A		not specified	Uncertain significance (Feb 11, 2022)
19-51337244-G-C		not specified	Uncertain significance (Apr 26, 2024)
19-51337271-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-51337279-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-51337300-C-T		not specified	Uncertain significance (Dec 08, 2021)
19-51337493-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-51337507-T-C		not specified	Uncertain significance (Aug 02, 2021)
19-51338009-G-C		not specified	Uncertain significance (May 31, 2023)
19-51338023-T-C		not specified	Uncertain significance (Jun 17, 2024)
19-51338035-G-A		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
19-51338058-C-T			Benign (Jul 06, 2018)
19-51338088-C-G		not specified	Uncertain significance (Apr 12, 2022)
19-51338145-A-G		not specified	Uncertain significance (Nov 29, 2021)
19-51338176-C-A		not specified	Uncertain significance (Mar 07, 2024)
19-51338183-A-C		not specified	Uncertain significance (Mar 27, 2023)
19-51338184-T-C		not specified	Uncertain significance (Mar 15, 2024)
19-51338205-G-T		not specified	Uncertain significance (Aug 02, 2021)
19-51338960-G-A		not specified	Uncertain significance (Jan 18, 2022)
19-51339022-G-A		not specified	Uncertain significance (Jan 07, 2022)
19-51339028-C-A		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSIG10L	protein_coding	protein_coding	ENST00000335624	10	10589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-8	0.778	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	279	406	0.688	0.0000220	5354
Missense in Polyphen		78	98.432	0.79242		1281
Synonymous	2.40	142	183	0.774	0.0000102	2025
Loss of Function	1.47	16	23.7	0.674	0.00000118	308

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vsig10l

Gene ontology

• Cellular component: nucleus;nucleoplasm;integral component of membrane