INCA1

inhibitor of CDK, cyclin A1 interacting protein 1

Basic information

Region (hg38): 17:4988130-4997610

Links

ENSG00000196388 ∙ NCBI:388324 ∙ OMIM:617374 ∙ HGNC:32224 ∙ Uniprot:Q0VD86 ∙ 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 INCA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INCA1 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			15	2		17
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	15	2	0

Variants in INCA1

This is a list of pathogenic ClinVar variants found in the INCA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4988439-G-A		not specified	Uncertain significance (Jan 16, 2024)
17-4988511-C-T		not specified	Uncertain significance (Oct 03, 2022)
17-4988526-T-C		not specified	Likely benign (Apr 28, 2022)
17-4988533-G-A		not specified	Uncertain significance (Mar 02, 2023)
17-4988535-C-G		not specified	Uncertain significance (Aug 07, 2023)
17-4988840-T-A		not specified	Uncertain significance (Dec 12, 2023)
17-4988844-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-4988858-T-C		not specified	Uncertain significance (Feb 06, 2023)
17-4988888-C-T		not specified	Likely benign (Aug 12, 2021)
17-4988916-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-4989542-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-4989547-C-G		not specified	Uncertain significance (May 24, 2024)
17-4989591-G-A		not specified	Uncertain significance (Apr 08, 2024)
17-4989599-C-G		not specified	Uncertain significance (Dec 06, 2024)
17-4989901-G-T		not specified	Uncertain significance (Mar 29, 2023)
17-4990169-G-C		not specified	Uncertain significance (Dec 21, 2023)
17-4990195-G-A		not specified	Uncertain significance (Sep 20, 2023)
17-4990233-G-C		not specified	Uncertain significance (May 09, 2023)
17-4990234-G-C		not specified	Uncertain significance (Dec 28, 2022)
17-4990249-T-C		not specified	Uncertain significance (Apr 05, 2023)
17-4990268-G-A			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INCA1	protein_coding	protein_coding	ENST00000396829	6	9481

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.50e-11	0.0153	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.229	127	134	0.944	0.00000691	1531
Missense in Polyphen		29	36.291	0.79911		403
Synonymous	0.384	45	48.4	0.930	0.00000240	465
Loss of Function	-0.736	15	12.2	1.23	6.17e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00135
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.000458	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to CDK2-bound cyclins and inhibits the kinase activity of CDK2; binding to cyclins is critical for its function as CDK inhibitor (PubMed:21540187). Inhibits cell growth and cell proliferation and may play a role in cell cycle control (By similarity). Required for ING5-mediated regulation of S-phase progression, enhancement of Fas-induced apoptosis and inhibition of cell growth (By similarity). {ECO:0000250|UniProtKB:Q6PKN7, ECO:0000269|PubMed:21540187}.

Intolerance Scores

• loftool: 0.265
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.438
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inca1
• Phenotype: cellular phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of cell population proliferation;negative regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear body
• Molecular function: cyclin-dependent protein serine/threonine kinase inhibitor activity;protein binding;cyclin binding;protein-containing complex binding