CCDC38

protein-coding

coiled-coil domain containing 38

Gene summary

Predicted to enable ubiquitin-modified histone reader activity. Predicted to be involved in acrosome assembly and sperm flagellum assembly. Located in centrosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_182496.3

Inheritance

—

ClinVar variants

U:91B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr12:95,867,048-95,942,635

External References & Databases

Ensembl (ENSG00000165972)

Transcript & Mutation Effects

hg38 • Region Span ~75.6 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 CCDC38 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 94

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182496.3. 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				2 clinvar		2
missense			87 clinvar	8 clinvar		95
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	91	10	0	101

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182496.3	RefSeq	NP_872302.2	15	MANE Select
ENST00000344280.8	Ensembl	ENSP00000345470.3	15	MANE Select
ENST00000546386.1	Ensembl	ENSP00000448644.1	2	Standard
ENST00000546386.2	Ensembl	ENSP00000448644.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

cytoplasm
centrosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344280
Coding exons: 15
Length: 75927
Individuals with no LoFs: 125490
Homozygous LoFs: 0
Heterozygous LoFs: 258
Defined: 125748
p: 0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.150	275	282	0.975	0.0000141	3724
Missense (PolyPhen)		85	83.77	1.0147		1198
Synonymous	-0.752	107	97.6	1.10	0.00000495	975
Loss of Function	1.27	24	31.7	0.756	0.00000150	420

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0042	0.0041	notable
Finnish	0.00069	0.00069	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.00053	0.00052	rare
Other	0.0015	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.974
RVIS EVS: 0.45
RVIS percentile EVS: 77.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.119

Gene Damage Prediction

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