CCDC34

coiled-coil domain containing 34

Basic information

Region (hg38): 11:27330827-27363234

Links

ENSG00000109881 ∙ NCBI:91057 ∙ OMIM:612324 ∙ HGNC:25079 ∙ Uniprot:Q96HJ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 76 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 76	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	34348960

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC34 gene.

• not_specified (34 variants)
• Spermatogenic_failure_76 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC34 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030771.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			32	2		34
nonsense						0
start loss						0
frameshift	2					2
splice donor/acceptor (+/-2bp)						0
Total	2	0	32	2	0

Highest pathogenic variant AF is 0.00003421096

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC34	protein_coding	protein_coding	ENST00000328697	6	33042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000501	0.871	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.263	200	190	1.05	0.00000928	2451
Missense in Polyphen		55	55.804	0.98559		832
Synonymous	0.452	63	67.7	0.930	0.00000318	649
Loss of Function	1.49	11	17.8	0.618	7.51e-7	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000579	0.000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000326	0.000326
South Asian	0.0000348	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving CCDC34 is found in a patient with hamartoma of the retinal pigment epithelium and retina. Translocation t(11;18) (p13;p11.2). {ECO:0000269|PubMed:11173847}.

Recessive Scores

• pRec: 0.0956

Intolerance Scores

• loftool: 0.842
• rvis_EVS: 1.11
• rvis_percentile_EVS: 91.99

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.123
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc34