CCDC62

coiled-coil domain containing 62

Basic information

Region (hg38): 12:122774525-122827528

Links

ENSG00000130783 ∙ NCBI:84660 ∙ OMIM:613481 ∙ HGNC:30723 ∙ Uniprot:Q6P9F0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 67	AR	General	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	Genitourinary	31985809

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC62 gene.

• Inborn genetic diseases (24 variants)
• not provided (3 variants)
• Spermatogenic failure 67 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC62 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			24		1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	25	0	3

Variants in CCDC62

This is a list of pathogenic ClinVar variants found in the CCDC62 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-122774686-G-A		not specified	Likely benign (Jan 23, 2024)
12-122774692-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-122774701-C-T		not specified	Uncertain significance (Jul 30, 2023)
12-122774705-A-T		not specified	Uncertain significance (Aug 16, 2022)
12-122777496-C-T			Benign (Nov 01, 2022)
12-122777555-T-C		not specified	Uncertain significance (Apr 04, 2023)
12-122777573-G-A		not specified	Uncertain significance (Feb 16, 2023)
12-122777593-A-G		not specified	Uncertain significance (Jan 04, 2024)
12-122777638-C-T		not specified	Uncertain significance (May 28, 2023)
12-122777653-A-G		not specified	Uncertain significance (Jan 03, 2024)
12-122777665-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-122781319-G-C		Spermatogenic failure 67	Uncertain significance (Mar 01, 2022)
12-122785730-A-C		not specified	Uncertain significance (Dec 21, 2023)
12-122785732-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-122785764-C-T		Spermatogenic failure 67	Pathogenic (Mar 21, 2022)
12-122785801-C-G		not specified	Uncertain significance (Jul 14, 2021)
12-122785815-C-A		not specified	Uncertain significance (Jun 02, 2023)
12-122788786-A-G		not specified	Uncertain significance (Nov 28, 2023)
12-122788801-C-T		not specified	Uncertain significance (Jul 06, 2021)
12-122788834-G-A		not specified	Uncertain significance (Jun 06, 2023)
12-122792022-G-A		not specified	Uncertain significance (Jan 11, 2023)
12-122797331-A-G		not specified	Uncertain significance (Jan 25, 2023)
12-122797345-G-T		not specified	Uncertain significance (Dec 18, 2023)
12-122798161-A-T			Benign (Mar 29, 2018)
12-122798172-A-G		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC62	protein_coding	protein_coding	ENST00000253079	12	53202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.39e-16	0.155	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	293	358	0.820	0.0000188	4530
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00122	0.00122
Ashkenazi Jewish	0.00	0.00
East Asian	0.00103	0.00103
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000310	0.000308
Middle Eastern	0.00103	0.00103
South Asian	0.000362	0.000327
Other	0.000662	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc62
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: blastocyst hatching;positive regulation of transcription by RNA polymerase II;cellular response to estradiol stimulus
• Cellular component: nucleus;nucleoplasm;cytoplasm;plasma membrane
• Molecular function: protein binding;estrogen receptor binding;nuclear receptor transcription coactivator activity