CCAR1

protein-coding

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

Gene summary

Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in positive regulation of cell migration and positive regulation of cell population proliferation. Acts upstream of or within positive regulation of apoptotic process. Located in Golgi apparatus; nuclear envelope lumen; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018237.4

Inheritance

—

ClinVar variants

U:92B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr10:68,721,012-68,792,377

External References & Databases

Ensembl (ENSG00000060339)

Transcript & Mutation Effects

hg38 • Region Span ~71.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCAR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018237.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			84 clinvar	1 clinvar		85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	92	1	0	93

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018237.4	RefSeq	NP_060707.2	24	MANE Select
ENST00000265872.11	Ensembl	ENSP00000265872.6	24	MANE Select
NM_001282959.2	RefSeq	NP_001269888.1	23	Standard
NM_001282960.2	RefSeq	NP_001269889.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

mRNA splicing, via spliceosome
regulation of transcription, DNA-templated
apoptotic process
cell cycle
positive regulation of cell population proliferation

Molecular Function

RNA polymerase II distal enhancer sequence-specific DNA binding
transcription coactivator activity
transcription corepressor activity
RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265872
Coding exons: 24
Length: 71366
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125746
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.64	353	605	0.584	0.0000323	7540
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.000082	0.000079	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.159

Intolerance Scores

LoFtool: 0.584
RVIS EVS: -1.09
RVIS percentile EVS: 7.11

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.816

Gene Damage Prediction

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