CCDC42

coiled-coil domain containing 42

Basic information

Region (hg38): 17:8729934-8745219

Links

ENSG00000161973 ∙ NCBI:146849 ∙ ∙ HGNC:26528 ∙ Uniprot:Q96M95 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC42 gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC42 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						0
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in CCDC42

This is a list of pathogenic ClinVar variants found in the CCDC42 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-8730168-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-8730185-C-T		not specified	Uncertain significance (Feb 27, 2024)
17-8735165-C-G		not specified	Uncertain significance (Mar 24, 2023)
17-8735181-G-A		not specified	Uncertain significance (Jan 18, 2022)
17-8735191-T-C		not specified	Uncertain significance (Aug 19, 2023)
17-8735194-T-C		not specified	Uncertain significance (Dec 14, 2023)
17-8735406-C-T		not specified	Uncertain significance (May 27, 2022)
17-8735469-T-C		not specified	Uncertain significance (Nov 04, 2022)
17-8735484-A-G		not specified	Uncertain significance (Jun 29, 2022)
17-8735487-T-C		not specified	Uncertain significance (Nov 27, 2023)
17-8735491-G-A		not specified	Uncertain significance (Jan 27, 2022)
17-8735499-C-T		not specified	Uncertain significance (Feb 06, 2023)
17-8735608-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-8741475-T-C		not specified	Uncertain significance (Oct 25, 2022)
17-8741496-T-C		not specified	Uncertain significance (Aug 23, 2021)
17-8741556-A-G		not specified	Uncertain significance (Jan 23, 2024)
17-8741566-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-8741581-T-C		not specified	Uncertain significance (May 23, 2023)
17-8741647-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-8741655-C-T		not specified	Uncertain significance (Nov 08, 2022)
17-8743681-C-T		not specified	Uncertain significance (Dec 13, 2023)
17-8743688-C-G		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC42	protein_coding	protein_coding	ENST00000293845	7	15286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000362	0.821	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.661	176	202	0.869	0.0000133	2099
Missense in Polyphen		81	94.677	0.85554		1068
Synonymous	0.804	69	78.0	0.884	0.00000478	571
Loss of Function	1.36	11	17.1	0.644	8.12e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000729	0.000727
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000256	0.000255
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00180	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for sperm development. {ECO:0000250|UniProtKB:Q5SV66}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.916
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.21

Haploinsufficiency Scores

• pHI: 0.0933
• hipred: N
• hipred_score: 0.208

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.667

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc42
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: spermatid development
• Molecular function: protein binding