ICA1L
protein-codingislet cell autoantigen 1 like, the group of AH domain containing
Gene summary
Predicted to enable membrane curvature sensor activity. Predicted to be involved in membrane bending and regulation of secretion. Predicted to act upstream of or within spermatid development. Predicted to be located in acrosomal vesicle. Predicted to be active in secretory granule membrane. [provided by Alliance of Genome Resources, Jun 2026]
- ALS2CR15
- ALS2CR14
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~98.6 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 ICA1L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001288622.3. 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 | 0 | |||||
| missense | 51 | 5 | 56 | |||
| 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_001275551.1 | 12 | MANE Select | |
| Ensembl | ENSP00000351047.2 | 12 | MANE Select | |
| RefSeq | NP_001275552.1 | 12 | Standard | |
| RefSeq | NP_001275553.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- spermatid development
Molecular Function
- protein binding
- protein domain specific binding
Cellular Component
- acrosomal vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000392237
- Coding exons
- 12
- Length
- 96019
- Individuals with no LoFs
- 125469
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 278
- Defined
- 125748
- p
- 0.00111
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.918 | 203 | 243 | 0.834 | 0.0000119 | 3192 |
| Missense (PolyPhen) | 75 | 95.563 | 0.78482 | 1305 | ||
| Synonymous | 0.599 | 80 | 87.1 | 0.918 | 0.00000442 | 873 |
| Loss of Function | 2.97 | 10 | 26.5 | 0.377 | 0.00000125 | 328 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00074 | 0.00061 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.000057 | 0.000054 | rare |
| Finnish | 0.0049 | 0.0048 | notable |
| European (Non-Finnish) | 0.0011 | 0.00098 | notable |
| South Asian | 0.0011 | 0.0011 | notable |
| Other | 0.00091 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.365
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 75.29
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.215
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |