IGSF6

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

Basic information

Region (hg38): 16:21639550-21652608

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.

• not_specified (42 variants)

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. These statistics are base on transcript: NM_000005849.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			40	2		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	2	0

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