CCAR1

cell division cycle and apoptosis regulator 1, the group of Spliceosomal A complex|MicroRNA protein coding host genes|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 10:68721012-68792377

Links

ENSG00000060339 ∙ NCBI:55749 ∙ OMIM:612569 ∙ HGNC:24236 ∙ Uniprot:Q8IX12 ∙ 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 CCAR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCAR1 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	33	1	0

Variants in CCAR1

This is a list of pathogenic ClinVar variants found in the CCAR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-68736923-A-G		not specified	Uncertain significance (Aug 24, 2023)
10-68742508-G-A		not specified	Uncertain significance (Apr 05, 2023)
10-68747408-C-G		not specified	Uncertain significance (Jun 16, 2024)
10-68747493-G-C		not specified	Uncertain significance (Dec 27, 2023)
10-68749174-C-T		not specified	Uncertain significance (Aug 05, 2023)
10-68749208-G-A		not specified	Uncertain significance (Mar 29, 2024)
10-68749601-G-A		not specified	Uncertain significance (Jun 28, 2022)
10-68749624-C-T		not specified	Uncertain significance (May 08, 2023)
10-68749637-G-T		not specified	Uncertain significance (Mar 20, 2024)
10-68753854-C-T		not specified	Uncertain significance (Apr 17, 2023)
10-68753857-G-T		not specified	Uncertain significance (Oct 14, 2023)
10-68753866-T-C		not specified	Uncertain significance (Jul 20, 2021)
10-68753884-G-A		not specified	Uncertain significance (Jul 13, 2021)
10-68754070-G-A		not specified	Uncertain significance (Sep 28, 2022)
10-68754730-G-C		not specified	Uncertain significance (Jul 19, 2023)
10-68754793-G-A		not specified	Uncertain significance (Apr 28, 2022)
10-68755520-A-T		not specified	Uncertain significance (Sep 26, 2023)
10-68755521-G-A		not specified	Uncertain significance (May 24, 2023)
10-68756465-G-T		not specified	Uncertain significance (Oct 20, 2021)
10-68761124-A-G		not specified	Uncertain significance (Jan 10, 2023)
10-68761162-T-A		not specified	Likely benign (Mar 01, 2023)
10-68765961-C-T		not specified	Uncertain significance (Jan 08, 2024)
10-68771338-A-G		not specified	Uncertain significance (Jul 26, 2022)
10-68771387-C-T		not specified	Uncertain significance (May 05, 2023)
10-68773046-A-C		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCAR1	protein_coding	protein_coding	ENST00000265872	24	71366

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000655	125728	0	18	125746	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.64	353	605	0.584	0.0000323	7540
Missense in Polyphen		81	187.5	0.43201		2022
Synonymous	1.55	177	205	0.862	0.0000101	2086
Loss of Function	6.95	9	73.1	0.123	0.00000425	833

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000819	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with components of the Mediator and p160 coactivator complexes that play a role as intermediaries transducing regulatory signals from upstream transcriptional activator proteins to basal transcription machinery at the core promoter. Recruited to endogenous nuclear receptor target genes in response to the appropriate hormone. Also functions as a p53 coactivator. May thus play an important role in transcriptional regulation (By similarity). May be involved in apoptosis signaling in the presence of the reinoid CD437. Apoptosis induction involves sequestration of 14-3-3 protein(s) and mediated altered expression of multiple cell cycle regulatory genes including MYC, CCNB1 and CDKN1A. Plays a role in cell cycle progression and/or cell proliferation (PubMed:12816952). In association with CALCOCO1 enhances GATA1- and MED1-mediated transcriptional activation from the gamma-globin promoter during erythroid differentiation of K562 erythroleukemia cells (PubMed:24245781). Can act as a both a coactivator and corepressor of AR-mediated transcription. Contributes to chromatin looping and AR transcription complex assembly by stabilizing AR-GATA2 association on chromatin and facilitating MED1 and RNA polymerase II recruitment to AR-binding sites. May play an important role in the growth and tumorigenesis of prostate cancer cells (PubMed:23887938). {ECO:0000250|UniProtKB:Q8CH18, ECO:0000269|PubMed:12816952, ECO:0000269|PubMed:23887938, ECO:0000269|PubMed:24245781}.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.584
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.11

Haploinsufficiency Scores

• pHI: 0.686
• hipred: Y
• hipred_score: 0.639
• ghis: 0.696

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.816

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccar1

Gene ontology

• Biological process: mRNA splicing, via spliceosome;regulation of transcription, DNA-templated;apoptotic process;cell cycle;positive regulation of cell population proliferation;positive regulation of cell migration;negative regulation of nucleic acid-templated transcription;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;perinuclear region of cytoplasm
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;transcription coactivator activity;transcription corepressor activity;RNA binding;protein binding;nuclear receptor transcription coactivator activity