CAAP1

protein-coding

caspase activity and apoptosis inhibitor 1

Gene summary

Involved in negative regulation of apoptotic process. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf82

MANE transcript

NM_024828.4

Inheritance

—

ClinVar variants

U:54B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr9:26,840,685-26,892,803

External References & Databases

Ensembl (ENSG00000120159)

Transcript & Mutation Effects

hg38 • Region Span ~52.1 kb

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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 CAAP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 53

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024828.4. 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			1 clinvar			1
missense			51 clinvar	3 clinvar		54
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	54	3	0	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024828.4	RefSeq	NP_079104.3	6	MANE Select
ENST00000333916.8	Ensembl	ENSP00000369431.3	6	MANE Select
NM_001167575.2	RefSeq	NP_001161047.1	5	Standard
ENST00000483493.6	Ensembl	ENSP00000427916.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic process
negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333916
Coding exons: 6
Length: 52120
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125659
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.475	207	189	1.10	0.00000862	2363
Missense (PolyPhen)		38	50.501	0.75245		735
Synonymous	-1.99	95	73.3	1.30	0.00000386	673
Loss of Function	2.95	2	13.8	0.145	5.80e-7	199

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000065	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Anti-apoptotic protein that modulates a caspase-10 dependent mitochondrial caspase-3/9 feedback amplification loop. {ECO:0000269|PubMed:21980415}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

RVIS EVS: 0.24
RVIS percentile EVS: 69.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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