ICA1

islet cell autoantigen 1, the group of AH domain containing

Basic information

Region (hg38): 7:8113183-8262687

Links

ENSG00000003147 ∙ NCBI:3382 ∙ OMIM:147625 ∙ HGNC:5343 ∙ Uniprot:Q05084 ∙ 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 ICA1 gene.

• Inborn genetic diseases (27 variants)
• not specified (2 variants)
• not provided (2 variants)
• ICA1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICA1 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					2	2
missense			28		1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	0	3

Variants in ICA1

This is a list of pathogenic ClinVar variants found in the ICA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-8113988-C-T		not specified	Uncertain significance (Jan 18, 2022)
7-8127890-A-G		not specified	Uncertain significance (Jul 14, 2021)
7-8127953-G-A		not specified	Uncertain significance (Jun 21, 2021)
7-8128052-G-A		not specified	Uncertain significance (Oct 26, 2021)
7-8128073-C-A		not specified	Uncertain significance (Feb 13, 2023)
7-8128130-G-A		not specified	Uncertain significance (Apr 19, 2023)
7-8128134-C-T		not specified	Uncertain significance (May 11, 2022)
7-8128139-C-T		not specified	Uncertain significance (Nov 29, 2021)
7-8138843-C-G		not specified	Uncertain significance (Sep 15, 2022)
7-8138843-C-T		not specified	Uncertain significance (Nov 27, 2023)
7-8138861-C-T		not specified	Uncertain significance (Dec 06, 2022)
7-8138988-A-T		not specified	Uncertain significance (Sep 13, 2023)
7-8141774-T-C		not specified	Uncertain significance (Sep 22, 2023)
7-8141779-G-A		not specified	Uncertain significance (Sep 26, 2023)
7-8141789-G-A		not specified	Uncertain significance (Apr 13, 2022)
7-8143877-G-T		not specified	Uncertain significance (Oct 03, 2022)
7-8143881-G-A		not specified	Uncertain significance (Feb 15, 2023)
7-8143882-G-A		not specified	Uncertain significance (Jul 19, 2023)
7-8143886-C-G		not specified	Uncertain significance (Aug 09, 2021)
7-8143893-G-A		not specified	Uncertain significance (Dec 22, 2023)
7-8143902-G-A		not specified	Uncertain significance (Dec 27, 2022)
7-8143949-T-G		not specified	Uncertain significance (Aug 12, 2021)
7-8156941-A-G		not specified	Benign (-)
7-8156945-A-G		not specified	Benign (-)
7-8157147-C-A		ICA1-related disorder	Uncertain significance (Jun 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICA1	protein_coding	protein_coding	ENST00000402384	13	149504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000991	0.999	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.492	236	258	0.914	0.0000138	3177
Missense in Polyphen		80	114.09	0.7012		1376
Synonymous	-0.470	107	101	1.06	0.00000620	863
Loss of Function	3.39	11	31.6	0.349	0.00000163	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.000111	0.000109
South Asian	0.000137	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in neurotransmitter secretion. {ECO:0000250}.
• Pathway: Type I diabetes mellitus - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.166
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.5

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.487
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ica1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; immune system phenotype

Gene ontology

• Biological process: neurotransmitter transport;regulation of insulin secretion
• Cellular component: Golgi membrane;cytoplasm;cytosol;cell junction;secretory granule membrane;synaptic vesicle membrane;intracellular membrane-bounded organelle
• Molecular function: molecular_function;protein binding;protein domain specific binding