ICA1L

islet cell autoantigen 1 like, the group of AH domain containing

Basic information

Region (hg38): 2:202773150-202871766

Previous symbols: [ "ALS2CR15", "ALS2CR14" ]

Links

ENSG00000163596 ∙ NCBI:130026 ∙ ∙ HGNC:14442 ∙ Uniprot:Q8NDH6 ∙ 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 ICA1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICA1L 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						0
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in ICA1L

This is a list of pathogenic ClinVar variants found in the ICA1L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-202779577-G-T		not specified	Uncertain significance (Feb 28, 2023)
2-202779634-T-A		not specified	Uncertain significance (Feb 14, 2024)
2-202788886-C-T		not specified	Likely benign (May 25, 2022)
2-202788899-C-T		not specified	Uncertain significance (Jan 26, 2023)
2-202788908-C-G		not specified	Uncertain significance (Jun 02, 2024)
2-202788934-G-A		not specified	Uncertain significance (Aug 02, 2021)
2-202788947-T-C		not specified	Uncertain significance (Sep 26, 2024)
2-202788947-T-G		not specified	Uncertain significance (Apr 20, 2024)
2-202788955-C-G		not specified	Uncertain significance (Aug 14, 2024)
2-202788986-C-G		not specified	Uncertain significance (Aug 08, 2022)
2-202788988-C-T		not specified	Uncertain significance (Oct 29, 2024)
2-202788994-C-G		not specified	Uncertain significance (Sep 06, 2024)
2-202789060-A-G		not specified	Uncertain significance (Nov 08, 2022)
2-202811761-A-T		not specified	Uncertain significance (Nov 22, 2023)
2-202814711-T-C		not specified	Uncertain significance (Aug 27, 2024)
2-202814771-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-202815915-A-G		not specified	Uncertain significance (Dec 08, 2023)
2-202815933-G-A		not specified	Uncertain significance (Sep 08, 2024)
2-202815949-A-G		not specified	Uncertain significance (Feb 22, 2025)
2-202815981-G-A		not specified	Uncertain significance (Dec 10, 2024)
2-202815988-T-C		not specified	Likely benign (Dec 01, 2022)
2-202816008-C-G		not specified	Uncertain significance (Dec 23, 2023)
2-202817516-C-T		not specified	Uncertain significance (Mar 04, 2025)
2-202819746-T-A		not specified	Uncertain significance (Feb 13, 2024)
2-202819873-C-A		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICA1L	protein_coding	protein_coding	ENST00000392237	12	96019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000779	0.999	125469	1	278	125748	0.00111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.918	203	243	0.834	0.0000119	3192
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000924	0.000922
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000571	0.0000544
Finnish	0.00489	0.00477
European (Non-Finnish)	0.00105	0.000976
Middle Eastern	0.0000571	0.0000544
South Asian	0.00111	0.00111
Other	0.000910	0.000815

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.365
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.308
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ica1l
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: spermatid development
• Cellular component: acrosomal vesicle
• Molecular function: protein binding;protein domain specific binding