CCDC159

protein-coding

coiled-coil domain containing 159

Gene summary

Predicted to be involved in spermatid development. Predicted to act upstream of or within several processes, including regulation of phosphatase activity; single fertilization; and sperm flagellum assembly. Predicted to be located in sperm head-tail coupling apparatus. [provided by Alliance of Genome Resources, Apr 2025]

MANE transcript

NM_001080503.3

Inheritance

—

ClinVar variants

U:55B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr19:11,344,684-11,354,944

External References & Databases

Ensembl (ENSG00000183401)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 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 CCDC159 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 49

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080503.3. 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			48 clinvar	2 clinvar		50
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	55	2	0	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080503.3	RefSeq	NP_001073972.2	11	MANE Select
ENST00000458408.6	Ensembl	ENSP00000402239.1	11	MANE Select
ENST00000586451.5	Ensembl	ENSP00000465560.1	4	Standard
ENST00000587531.5	Ensembl	ENSP00000466882.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000588790
Coding exons: 11
Length: 10261
Individuals with no LoFs: 124696
Homozygous LoFs: 0
Heterozygous LoFs: 91
Defined: 124787
p: 0.000365

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.486	143	160	0.892	0.00000919	1927
Missense (PolyPhen)		37	44.798	0.82592		642
Synonymous	1.14	49	60.3	0.812	0.00000348	515
Loss of Function	1.93	12	21.7	0.554	0.00000113	246

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0037	0.0033	notable
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000055	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00010	0.000098	rare
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.738
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.283

Gene Damage Prediction

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