CCDC25

coiled-coil domain containing 25

Basic information

Region (hg38): 8:27733316-27772653

Links

ENSG00000147419 ∙ NCBI:55246 ∙ OMIM:619100 ∙ HGNC:25591 ∙ Uniprot:Q86WR0 ∙ 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 CCDC25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC25 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in CCDC25

This is a list of pathogenic ClinVar variants found in the CCDC25 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-27736238-T-C		not specified	Uncertain significance (Feb 14, 2023)
8-27740485-A-G		not specified	Uncertain significance (Dec 27, 2023)
8-27748095-C-T		not specified	Uncertain significance (Mar 19, 2024)
8-27748204-G-A		not specified	Uncertain significance (Oct 26, 2022)
8-27748205-G-C		not specified	Uncertain significance (Mar 31, 2024)
8-27748209-C-T		not specified	Uncertain significance (May 27, 2022)
8-27748221-G-A		not specified	Uncertain significance (Dec 16, 2023)
8-27748517-A-G		not specified	Uncertain significance (Nov 30, 2022)
8-27748562-G-A		not specified	Uncertain significance (Apr 15, 2024)
8-27748583-T-C		not specified	Uncertain significance (Jun 26, 2024)
8-27752518-T-A		not specified	Uncertain significance (Nov 24, 2024)
8-27752537-G-C		not specified	Uncertain significance (Nov 24, 2024)
8-27762433-C-A		not specified	Uncertain significance (Nov 19, 2022)
8-27765231-T-C		not specified	Uncertain significance (Jul 09, 2024)
8-27765242-G-T		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC25	protein_coding	protein_coding	ENST00000356537	9	39336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00912	0.980	125718	0	11	125729	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	65	111	0.585	0.00000559	1402
Missense in Polyphen		11	27.525	0.39964		386
Synonymous	0.725	32	37.7	0.850	0.00000207	322
Loss of Function	2.24	6	15.5	0.387	8.07e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000256	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0719

Intolerance Scores

• loftool: 0.498
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.0952
• hipred: N
• hipred_score: 0.319
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.692

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc25

Gene ontology

• Molecular function: protein binding