CCDC42

protein-coding

coiled-coil domain containing 42

Gene summary

Predicted to be involved in spermatid development. Predicted to act upstream of or within acrosome assembly; centrosome cycle; and cilium assembly. Predicted to be located in several cellular components, including microtubule cytoskeleton; sperm head-tail coupling apparatus; and sperm principal piece. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_144681.3

Inheritance

—

ClinVar variants

U:46B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr17:8,729,935-8,745,219

External References & Databases

Ensembl (ENSG00000161973)

Transcript & Mutation Effects

hg38 • Region Span ~15.3 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 CCDC42 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144681.3. 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			45 clinvar	3 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	46	3	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144681.3	RefSeq	NP_653282.2	7	MANE Select
ENST00000293845.8	Ensembl	ENSP00000293845.3	7	MANE Select
NM_001158261.2	RefSeq	NP_001151733.1	6	Standard
ENST00000539522.2	Ensembl	ENSP00000444359.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatid development

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293845
Coding exons: 7
Length: 15286
Individuals with no LoFs: 125674
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 125748
p: 0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.661	176	202	0.869	0.0000133	2099
Missense (PolyPhen)		81	94.677	0.85554		1068
Synonymous	0.804	69	78.0	0.884	0.00000478	571
Loss of Function	1.36	11	17.1	0.644	8.12e-7	192

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.000098	0.000098	rare
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for sperm development. {ECO:0000250|UniProtKB:Q5SV66}.;

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.916
RVIS EVS: 0.73
RVIS percentile EVS: 86.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.667

Gene Damage Prediction

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