CNPPD1

protein-coding

cyclin Pas1/PHO80 domain containing 1

Gene summary

Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be located in membrane. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C2orf24

MANE transcript

NM_015680.6

Inheritance

—

ClinVar variants

U:74B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr2:219,171,897-219,178,106

External References & Databases

Ensembl (ENSG00000115649)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 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 CNPPD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 75

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015680.6. 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			70 clinvar	6 clinvar		76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	74	6	0	80

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015680.6	RefSeq	NP_056495.4	8	MANE Select
ENST00000360507.10	Ensembl	ENSP00000353698.5	8	MANE Select
NM_001321389.2	RefSeq	NP_001308318.2	8	Standard
NM_001321390.2	RefSeq	NP_001308319.2	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of cyclin-dependent protein serine/threonine kinase activity

Molecular Function

protein kinase binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409789
Coding exons: 8
Length: 6210
Individuals with no LoFs: 125681
Homozygous LoFs: 0
Heterozygous LoFs: 67
Defined: 125748
p: 0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.145	233	239	0.974	0.0000134	2596
Missense (PolyPhen)		71	62.81	1.1304		721
Synonymous	-0.0577	101	100	1.01	0.00000543	878
Loss of Function	1.36	16	23.1	0.694	0.00000125	222

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00033	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0016	0.0016	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.15
RVIS percentile EVS: 92.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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