IGSF5
protein-codingimmunoglobulin superfamily member 5, the group of Ig-like cell adhesion molecule family|I-set domain containing
Gene summary
Predicted to enable PDZ domain binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be located in apical plasma membrane. Predicted to be active in bicellular tight junction and cell surface. [provided by Alliance of Genome Resources, Apr 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~56.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to IGSF5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080444.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 50 | 4 | 54 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 52 | 5 | 0 | 57 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073913.1 | 9 | MANE Select | |
| Ensembl | ENSP00000369962.4 | 9 | MANE Select | |
| Ensembl | ENSP00000811138.1 | 9 | Standard | |
| RefSeq | XP_047296655.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tight junction - Homo sapiens (human)
- Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human)
Biological Process
- cell-cell adhesion
Cellular Component
- bicellular tight junction
- cell surface
- integral component of membrane
- apical plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000380588
- Coding exons
- 9
- Length
- 56690
- Individuals with no LoFs
- 125594
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 153
- Defined
- 125747
- p
- 0.000609
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.253 | 231 | 242 | 0.954 | 0.0000145 | 2640 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0025 | 0.0023 | notable |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0.0019 | 0.0019 | notable |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00036 | 0.00034 | rare |
| South Asian | 0.0011 | 0.0011 | notable |
| Other | 0.00069 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.0877
Intolerance Scores
- LoFtool
- 0.957
- RVIS EVS
- 1.69
- RVIS percentile EVS
- 96.41
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0411
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |