CCDC125

coiled-coil domain containing 125

Basic information

Region (hg38): 5:69280175-69332809

Links

ENSG00000183323 ∙ NCBI:202243 ∙ OMIM:613781 ∙ HGNC:28924 ∙ Uniprot:Q86Z20 ∙ 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 CCDC125 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC125 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in CCDC125

This is a list of pathogenic ClinVar variants found in the CCDC125 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-69282845-T-C		not specified	Uncertain significance (Sep 23, 2023)
5-69282889-C-A		not specified	Uncertain significance (Oct 02, 2023)
5-69282974-C-T		not specified	Uncertain significance (Apr 12, 2024)
5-69282976-C-T		not specified	Uncertain significance (Oct 04, 2022)
5-69282991-C-G		not specified	Uncertain significance (Aug 16, 2022)
5-69285435-C-T		not specified	Uncertain significance (Feb 28, 2024)
5-69292235-T-A		not specified	Uncertain significance (Nov 18, 2023)
5-69292269-G-C		not specified	Uncertain significance (Jul 13, 2021)
5-69292280-C-T		not specified	Uncertain significance (Nov 18, 2022)
5-69292285-T-G		not specified	Uncertain significance (Apr 01, 2024)
5-69294849-A-G		not specified	Uncertain significance (Feb 13, 2024)
5-69294896-G-A		not specified	Uncertain significance (Feb 10, 2022)
5-69300014-C-G		not specified	Uncertain significance (Jun 22, 2021)
5-69300044-T-C		not specified	Uncertain significance (Nov 29, 2021)
5-69306867-A-T		not specified	Uncertain significance (May 05, 2023)
5-69307966-G-C		not specified	Likely benign (Jan 08, 2024)
5-69307977-T-C		not specified	Likely benign (Feb 28, 2024)
5-69307992-C-T		not specified	Uncertain significance (Aug 30, 2022)
5-69311145-C-G		not specified	Uncertain significance (Feb 22, 2023)
5-69313986-T-A		not specified	Uncertain significance (Aug 02, 2021)
5-69320278-T-C		not specified	Uncertain significance (Mar 25, 2024)
5-69320282-G-A		not specified	Uncertain significance (Jan 04, 2022)
5-69320398-G-A		not specified	Uncertain significance (Aug 16, 2022)
5-69320404-T-A		not specified	Uncertain significance (Aug 24, 2022)
5-69320429-C-T		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC125	protein_coding	protein_coding	ENST00000396496	11	52635

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.59e-10	0.716	121667	31	4049	125747	0.0164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.353	247	263	0.939	0.0000129	3419
Missense in Polyphen		83	94.694	0.8765		1350
Synonymous	1.58	72	91.2	0.789	0.00000492	858
Loss of Function	1.45	18	26.0	0.692	0.00000109	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0177	0.0177
Ashkenazi Jewish	0.00974	0.00977
East Asian	0.000382	0.000381
Finnish	0.0318	0.0316
European (Non-Finnish)	0.0227	0.0227
Middle Eastern	0.000382	0.000381
South Asian	0.00363	0.00363
Other	0.0186	0.0186

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of cell migration. {ECO:0000269|PubMed:19787194}.

Intolerance Scores

• loftool: 0.923
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.14

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.145
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0609

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc125

Gene ontology

• Biological process: negative regulation of Rho protein signal transduction;activation of GTPase activity;negative regulation of cell motility
• Cellular component: cytoplasm
• Molecular function: molecular_function