ICA1L

Chr 2

islet cell autoantigen 1 like

Also known as: ALS2CR14, ALS2CR15

NCBI Gene: 130026ENSG00000163596UniProt: Q8NDH6OMIM: 621083

The protein is predicted to enable protein domain specific binding and regulate cellular transport, with predicted activity in the Golgi apparatus and involvement in spermatid development. Currently, no definitive disease associations have been established for mutations in this gene. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.64), suggesting some intolerance to complete protein loss.

OMIMResearchSummary from RefSeq
MultiplemechanismLOEUF 0.64
Clinical Summary— ICA1L
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
28 unique Pathogenic / Likely Pathogenic· 53 VUS of 97 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.64LOEUF
pLI 0.001
Z-score 2.97
OE 0.38 (0.23–0.64)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.92Z-score
OE missense 0.83 (0.74–0.94)
203 obs / 243.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.38 (0.23–0.64)
0≤0.351.4
Missense OE0.83 (0.74–0.94)
0≤0.61.4
Synonymous OE0.92
0≤1.21.6
LoF obs/exp: 10 / 26.5Missense obs/exp: 203 / 243.3Syn Z: 0.60
DN
0.75top 25%
GOF
0.6736th %ile
LOF
0.2874th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

97 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic27
Likely Pathogenic1
VUS53
Likely Benign5
27
Pathogenic
1
Likely Pathogenic
53
VUS
5
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
27
0
27
Likely Pathogenic
0
0
1
0
1
VUS
0
48
5
0
53
Likely Benign
0
5
0
0
5
Benign
0
0
0
0
0
Total05333086

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ICA1L · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients