CCDC62

protein-coding

coiled-coil domain containing 62

Gene summary

Enables nuclear estrogen receptor binding activity and transcription coactivator activity. Involved in several processes, including cellular response to estradiol stimulus; estrogen receptor signaling pathway; and positive regulation of transcription by RNA polymerase II. Located in acrosomal vesicle and nucleoplasm. Implicated in spermatogenic failure 67. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_201435.5

Inheritance

ClinVar variants

P:2U:99B:9

Top phenotype

Spermatogenic failure 67

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr12:122,774,526-122,827,528

External References & Databases

Ensembl (ENSG00000130783)

Transcript & Mutation Effects

hg38 • Region Span ~53.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Spermatogenic failure 67AR

Manifestation: Genitourinary

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 31985809

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC62 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 97

Spermatogenic failure 67Total: 3

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_201435.5. 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				1 clinvar	2 clinvar	3
missense			97 clinvar	5 clinvar	1 clinvar	103
nonsense	1 clinvar		1 clinvar			2
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	1	99	6	3	110

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_201435.5	RefSeq	NP_958843.2	12	MANE Select
ENST00000253079.11	Ensembl	ENSP00000253079.6	12	MANE Select
ENST00000341952.8	Ensembl	ENSP00000341471.4	12	Standard
ENST00000392440.3	Ensembl	ENSP00000376235.3	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

blastocyst hatching
positive regulation of transcription by RNA polymerase II
cellular response to estradiol stimulus

Molecular Function

protein binding
estrogen receptor binding
nuclear receptor transcription coactivator activity

Cellular Component

nucleus
nucleoplasm
cytoplasm
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253079
Coding exons: 12
Length: 53202
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 101
Defined: 125748
p: 0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.21	293	358	0.820	0.0000188	4530
Missense (PolyPhen)		99	133.79	0.73999		1698
Synonymous	0.442	135	142	0.953	0.00000843	1219
Loss of Function	1.16	28	35.5	0.790	0.00000173	454

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00086	0.00086	rare
Latino/Admixed American	0.00036	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0010	0.0010	notable
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00031	0.00031	rare
South Asian	0.00036	0.00033	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Nuclear receptor coactivator that can enhance preferentially estrogen receptors ESR1 and ESR2 transactivation. Modulates also progesterone/PGR, glucocorticoid/NR3C1 and androgen/AR receptors transactivation, although at lower level; little effect on vitamin D receptor/VDR. {ECO:0000269|PubMed:19126643}.;

Recessive Scores

pRec: 0.146

Intolerance Scores

LoFtool: 0.918
RVIS EVS: 0.58
RVIS percentile EVS: 82.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0902

Gene Damage Prediction

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