CCDC15

coiled-coil domain containing 15

Basic information

Region (hg38): 11:124954121-125041489

Links

ENSG00000149548 ∙ NCBI:80071 ∙ ∙ HGNC:25798 ∙ Uniprot:Q0P6D6 ∙ 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 CCDC15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC15 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				1	1	2
missense			70	4	1	75
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	71	5	2

Variants in CCDC15

This is a list of pathogenic ClinVar variants found in the CCDC15 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-124954748-G-A		not specified	Uncertain significance (Oct 10, 2023)
11-124954762-T-C			Benign (Jun 10, 2018)
11-124954787-G-A		not specified	Uncertain significance (Oct 13, 2021)
11-124954796-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-124954807-C-A		not specified	Uncertain significance (Feb 17, 2023)
11-124954814-G-A		not specified	Uncertain significance (Jan 24, 2024)
11-124954826-C-A		not specified	Uncertain significance (Oct 08, 2024)
11-124954854-C-G		not specified	Uncertain significance (Dec 24, 2024)
11-124954862-G-T		not specified	Uncertain significance (Jan 04, 2024)
11-124954863-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-124959148-G-C		not specified	Uncertain significance (Sep 26, 2024)
11-124959166-C-G		not specified	Uncertain significance (Aug 14, 2024)
11-124959205-C-T		Neurodevelopmental disorder	Uncertain significance (Jun 19, 2024)
11-124959241-C-G		not specified	Uncertain significance (Mar 23, 2023)
11-124959251-A-T		not specified	Uncertain significance (Feb 13, 2024)
11-124959815-G-A		not specified	Uncertain significance (Mar 31, 2024)
11-124959828-G-C			Benign (Jun 10, 2018)
11-124959828-G-T		not specified	Uncertain significance (Apr 08, 2024)
11-124959849-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-124959859-C-G		not specified	Uncertain significance (Oct 05, 2023)
11-124959860-T-G		not specified	Uncertain significance (Aug 26, 2024)
11-124959887-C-T		not specified	Uncertain significance (Apr 17, 2024)
11-124959906-C-T		not specified	Uncertain significance (Oct 11, 2024)
11-124959926-C-G		not specified	Uncertain significance (May 06, 2024)
11-124959930-C-G		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC15	protein_coding	protein_coding	ENST00000344762	15	87369

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.69e-20	0.0723	124596	0	42	124638	0.000169

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.131	420	428	0.982	0.0000201	6251
Missense in Polyphen		106	116.48	0.91002		1941
Synonymous	2.25	119	155	0.769	0.00000741	1669
Loss of Function	1.24	35	43.9	0.797	0.00000221	612

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000958	0.000924
Ashkenazi Jewish	0.00	0.00
East Asian	0.000225	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000105	0.0000973
Middle Eastern	0.000225	0.000223
South Asian	0.000137	0.000131
Other	0.000691	0.000661

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.964
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.02

Haploinsufficiency Scores

• pHI: 0.0396
• hipred: N
• hipred_score: 0.123
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc15

Gene ontology

• Cellular component: centrosome