CCDC142

coiled-coil domain containing 142

Basic information

Region (hg38): 2:74471986-74483408

Links

ENSG00000135637 ∙ NCBI:84865 ∙ ∙ HGNC:25889 ∙ Uniprot:Q17RM4 ∙ 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 CCDC142 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC142 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			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	4	0

Variants in CCDC142

This is a list of pathogenic ClinVar variants found in the CCDC142 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74472123-C-G		not specified	Uncertain significance (Sep 14, 2023)
2-74472154-T-G		not specified	Uncertain significance (Nov 07, 2022)
2-74472168-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-74472214-T-C		not specified	Uncertain significance (Feb 12, 2024)
2-74472229-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-74472415-A-G		not specified	Uncertain significance (Dec 02, 2022)
2-74472432-G-A		not specified	Uncertain significance (Aug 29, 2022)
2-74472436-G-C		not specified	Uncertain significance (Nov 29, 2021)
2-74472456-G-C		not specified	Uncertain significance (Oct 12, 2022)
2-74472617-T-G		not specified	Uncertain significance (May 23, 2023)
2-74474574-G-C		not specified	Uncertain significance (Nov 16, 2021)
2-74474583-G-A		not specified	Uncertain significance (May 17, 2023)
2-74474601-C-T		not specified	Uncertain significance (Aug 30, 2021)
2-74474658-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-74474710-G-C		not specified	Uncertain significance (Jun 24, 2022)
2-74474712-G-T		not specified	Uncertain significance (Apr 26, 2023)
2-74474715-G-A		not specified	Uncertain significance (Apr 19, 2023)
2-74474752-T-G		not specified	Uncertain significance (Jun 10, 2024)
2-74474796-C-T		not specified	Uncertain significance (May 09, 2023)
2-74474958-G-T		not specified	Uncertain significance (May 27, 2022)
2-74474965-C-G		not specified	Uncertain significance (Feb 21, 2024)
2-74475011-A-G		not specified	Likely benign (Nov 07, 2022)
2-74475026-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-74475104-G-A		not specified	Uncertain significance (Nov 27, 2023)
2-74475104-G-C		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC142	protein_coding	protein_coding	ENST00000290418	9	11423

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.33e-13	0.795	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.787	368	413	0.891	0.0000207	4645
Missense in Polyphen		108	133.46	0.80921		1608
Synonymous	-0.469	195	187	1.04	0.00000920	1655
Loss of Function	1.81	25	36.8	0.679	0.00000176	361

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00127	0.00127
Ashkenazi Jewish	0.00	0.00
East Asian	0.000554	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000384	0.000369
Middle Eastern	0.000554	0.000544
South Asian	0.000295	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.450
• rvis_EVS: 1.2
• rvis_percentile_EVS: 93.01

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.403
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.804

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc142