IGSF5

immunoglobulin superfamily member 5, the group of Ig-like cell adhesion molecule family|I-set domain containing

Basic information

Region (hg38): 21:39745182-39802081

Links

ENSG00000183067 ∙ NCBI:150084 ∙ OMIM:610638 ∙ HGNC:5952 ∙ Uniprot:Q9NSI5 ∙ 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 IGSF5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF5 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	0

Variants in IGSF5

This is a list of pathogenic ClinVar variants found in the IGSF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-39765568-C-A		not specified	Uncertain significance (May 30, 2023)
21-39765576-G-A		not specified	Uncertain significance (May 16, 2024)
21-39765592-G-T		not specified	Uncertain significance (Jun 16, 2024)
21-39765604-G-A		not specified	Uncertain significance (Aug 09, 2021)
21-39765622-C-T		not specified	Uncertain significance (May 11, 2022)
21-39765639-A-C		not specified	Uncertain significance (Mar 15, 2024)
21-39765675-G-A		not specified	Likely benign (Nov 17, 2022)
21-39765708-C-T		not specified	Uncertain significance (Dec 12, 2022)
21-39765762-A-T		not specified	Uncertain significance (Mar 15, 2024)
21-39765766-A-G		not specified	Uncertain significance (Aug 13, 2021)
21-39765771-G-A		not specified	Uncertain significance (May 04, 2022)
21-39765835-C-T		not specified	Uncertain significance (Nov 15, 2021)
21-39765840-C-G		not specified	Uncertain significance (Sep 17, 2021)
21-39770957-G-A		not specified	Likely benign (Feb 09, 2022)
21-39771143-G-A		not specified	Uncertain significance (Apr 12, 2023)
21-39771150-C-T		not specified	Uncertain significance (Aug 12, 2021)
21-39771170-C-T		not specified	Uncertain significance (Apr 01, 2024)
21-39779117-G-A		not specified	Uncertain significance (Jan 26, 2022)
21-39779135-C-T		not specified	Uncertain significance (May 23, 2023)
21-39779204-C-T		not specified	Uncertain significance (Nov 10, 2022)
21-39779205-G-A			Likely benign (Feb 11, 2021)
21-39779210-C-T		not specified	Uncertain significance (Apr 13, 2022)
21-39779227-C-CGCTGCT			Likely benign (Mar 01, 2023)
21-39779246-G-A		not specified	Uncertain significance (Apr 07, 2022)
21-39779287-T-C		not specified	Uncertain significance (Nov 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF5	protein_coding	protein_coding	ENST00000380588	9	56690

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.63e-17	0.00143	125594	0	153	125747	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	231	242	0.954	0.0000145	2640
Missense in Polyphen		43	56.223	0.76481		663
Synonymous	1.13	76	89.6	0.849	0.00000555	803
Loss of Function	-0.790	23	19.3	1.19	8.98e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00289	0.00269
Ashkenazi Jewish	0.00191	0.00189
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000362	0.000343
Middle Eastern	0.000381	0.000381
South Asian	0.00113	0.00108
Other	0.000693	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Provides, together with MAGI1, an adhesion machinery at tight junctions, which may regulate the permeability of kidney glomerulus and small intestinal epithelial cells. Mediates calcium-independent homophilic cell adhesion. In testis, it may function as a cell adhesion molecule rather than a tight-junction protein. It may participate in the adhesion between spermatogonia- spermatogonia, spermatogonia-Sertoli cells, and Sertoli cells- Sertoli cells (By similarity). {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0877

Intolerance Scores

• loftool: 0.957
• rvis_EVS: 1.69
• rvis_percentile_EVS: 96.41

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.147

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0411

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igsf5
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell-cell adhesion
• Cellular component: bicellular tight junction;cell surface;integral component of membrane;apical plasma membrane