CCDC125

protein-coding

coiled-coil domain containing 125

Gene summary

Enables identical protein binding activity. Involved in activation of GTPase activity; negative regulation of Rho protein signal transduction; and negative regulation of cell motility. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_176816.5

Inheritance

—

ClinVar variants

U:60B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr5:69,280,175-69,332,809

External References & Databases

Ensembl (ENSG00000183323)

Transcript & Mutation Effects

hg38 • Region Span ~52.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC125 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_176816.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			57 clinvar	3 clinvar		60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	60	3	0	63

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_176816.5	RefSeq	NP_789786.2	11	MANE Select
ENST00000396496.7	Ensembl	ENSP00000379754.2	11	MANE Select
NM_001297696.2	RefSeq	NP_001284625.1	9	Standard
NM_001297697.2	RefSeq	NP_001284626.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of Rho protein signal transduction
activation of GTPase activity
negative regulation of cell motility

Molecular Function

molecular_function

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396496
Coding exons: 11
Length: 52635
Individuals with no LoFs: 121667
Homozygous LoFs: 31
Heterozygous LoFs: 4049
Defined: 125747
p: 0.0164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.353	247	263	0.939	0.0000129	3419
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0049	0.0048	notable
Latino/Admixed American	0.013	0.013	notable
Ashkenazi Jewish	0.0097	0.0098	notable
East Asian	0.00038	0.00038	rare
Finnish	0.032	0.032	notable
European (Non-Finnish)	0.023	0.023	notable
South Asian	0.0036	0.0036	notable
Other	0.019	0.019	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0609

Gene Damage Prediction

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