IGSF6

immunoglobulin superfamily member 6, the group of V-set domain containing

Basic information

Region (hg38): 16:21639549-21652608

Links

ENSG00000140749 ∙ NCBI:10261 ∙ OMIM:606222 ∙ HGNC:5953 ∙ Uniprot:O95976 ∙ 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 IGSF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF6 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in IGSF6

This is a list of pathogenic ClinVar variants found in the IGSF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-21641543-T-A		not specified	Uncertain significance (Apr 20, 2024)
16-21641562-C-A		not specified	Uncertain significance (Dec 06, 2022)
16-21643105-T-C		not specified	Uncertain significance (Jun 02, 2023)
16-21643138-C-T		not specified	Uncertain significance (May 09, 2022)
16-21643152-C-G		not specified	Uncertain significance (Jan 03, 2024)
16-21643583-G-T		not specified	Uncertain significance (Oct 27, 2023)
16-21643585-G-A		not specified	Uncertain significance (May 17, 2023)
16-21644292-T-C		not specified	Uncertain significance (Nov 22, 2023)
16-21644313-C-T		not specified	Uncertain significance (Nov 09, 2023)
16-21644327-A-G		not specified	Uncertain significance (Sep 14, 2022)
16-21644354-G-A		not specified	Uncertain significance (Apr 26, 2024)
16-21647168-T-C		not specified	Uncertain significance (Feb 27, 2023)
16-21647297-T-G		not specified	Uncertain significance (Mar 18, 2024)
16-21647346-C-A		not specified	Uncertain significance (Sep 25, 2023)
16-21647417-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-21647445-C-G		not specified	Uncertain significance (May 14, 2024)
16-21647456-G-A		not specified	Uncertain significance (Jul 16, 2021)
16-21647489-G-A		not specified	Uncertain significance (May 15, 2023)
16-21652537-C-T		not specified	Likely benign (Sep 17, 2021)
16-21652571-C-T		not specified	Uncertain significance (Jul 30, 2023)
16-21652578-G-T		not specified	Uncertain significance (Jul 30, 2023)
16-21652594-C-T		not specified	Likely benign (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF6	protein_coding	protein_coding	ENST00000268389	6	11373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00148	0.886	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.148	129	134	0.964	0.00000766	1551
Missense in Polyphen		35	38.87	0.90043		500
Synonymous	-0.111	56	55.0	1.02	0.00000352	483
Loss of Function	1.38	6	10.9	0.550	4.63e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.000394	0.000392
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.650
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.172
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.337

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igsf6

Gene ontology

• Biological process: immune response;cell surface receptor signaling pathway
• Cellular component: integral component of plasma membrane
• Molecular function: transmembrane signaling receptor activity