CNTD1

protein-coding

cyclin N-terminal domain containing 1

Gene summary

Predicted to be involved in reciprocal meiotic recombination and regulation of meiotic cell cycle. Predicted to act upstream of or within spermatogenesis. Predicted to be located in chromosome. Predicted to be active in site of double-strand break. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CNTD

MANE transcript

NM_173478.3

Inheritance

—

ClinVar variants

U:34B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr17:42,798,800-42,811,587

External References & Databases

Ensembl (ENSG00000176563)

Transcript & Mutation Effects

hg38 • Region Span ~12.8 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 CNTD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 37

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173478.3. 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			34 clinvar	4 clinvar		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	4	0	38

Loading ClinVar variants...

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_173478.3	RefSeq	NP_775749.2	7	MANE Select
ENST00000588408.6	Ensembl	ENSP00000465204.1	7	MANE Select
NM_001330222.2	RefSeq	NP_001317151.1	5	Standard
ENST00000585355.5	Ensembl	ENSP00000465999.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

reciprocal meiotic recombination
spermatogenesis

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000588408
Coding exons: 7
Length: 12796
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125747
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.837	145	176	0.823	0.00000892	2131
Missense (PolyPhen)		21	40.788	0.51485		545
Synonymous	1.42	57	72.3	0.788	0.00000395	675
Loss of Function	2.41	7	18.0	0.389	0.00000104	186

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00080	0.00040	rare
East Asian	0.00027	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.583
RVIS EVS: 0.26
RVIS percentile EVS: 70.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0429

Gene Damage Prediction

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