CCDC113

coiled-coil domain containing 113

Basic information

Region (hg38): 16:58231156-58283836

Links

ENSG00000103021 ∙ NCBI:29070 ∙ OMIM:616070 ∙ HGNC:25002 ∙ Uniprot:Q9H0I3 ∙ 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 CCDC113 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC113 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	2		10
Total	0	0	41	2	0

Variants in CCDC113

This is a list of pathogenic ClinVar variants found in the CCDC113 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-58250033-G-A		not specified	Uncertain significance (Feb 16, 2023)
16-58252740-G-A		not specified	Uncertain significance (Apr 12, 2022)
16-58252830-A-G		not specified	Uncertain significance (May 16, 2023)
16-58252833-T-G		not specified	Uncertain significance (Mar 31, 2024)
16-58254011-G-T		not specified	Uncertain significance (Jan 12, 2024)
16-58254014-G-A		not specified	Likely benign (Oct 16, 2024)
16-58254014-G-C		not specified	Uncertain significance (Aug 19, 2023)
16-58254023-C-A		not specified	Uncertain significance (Nov 14, 2024)
16-58254029-C-G		not specified	Uncertain significance (Feb 15, 2023)
16-58254040-C-T		not specified	Uncertain significance (Dec 19, 2023)
16-58254116-G-A		not specified	Uncertain significance (Nov 29, 2023)
16-58254118-C-T		not specified	Uncertain significance (Oct 26, 2024)
16-58254134-C-T		not specified	Uncertain significance (Jan 04, 2022)
16-58254139-C-T		not specified	Uncertain significance (Dec 20, 2021)
16-58254140-G-A		not specified	Uncertain significance (Jan 03, 2022)
16-58254153-T-A		not specified	Uncertain significance (Mar 20, 2023)
16-58258369-C-T		not specified	Uncertain significance (Jul 27, 2021)
16-58258408-C-T		not specified	Uncertain significance (Jul 12, 2023)
16-58258444-A-G		not specified	Uncertain significance (Aug 02, 2022)
16-58258476-G-T		not specified	Uncertain significance (Oct 03, 2022)
16-58258492-T-C		not specified	Uncertain significance (Jan 23, 2024)
16-58258516-G-A		not specified	Uncertain significance (Jul 12, 2023)
16-58258519-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-58259875-C-A		not specified	Uncertain significance (Nov 24, 2024)
16-58259876-G-A		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC113	protein_coding	protein_coding	ENST00000219299	9	52680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.32e-16	0.00968	125344	1	403	125748	0.00161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.164	210	217	0.969	0.0000127	2475
Missense in Polyphen		61	57.353	1.0636		753
Synonymous	-0.0512	80	79.4	1.01	0.00000461	694
Loss of Function	-0.0332	23	22.8	1.01	0.00000138	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0117	0.0116
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00239	0.00239
Finnish	0.00134	0.00134
European (Non-Finnish)	0.000853	0.000800
Middle Eastern	0.00239	0.00239
South Asian	0.000916	0.000915
Other	0.00135	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of centriolar satellites contributing to primary cilium formation. {ECO:0000269|PubMed:25074808}.

Recessive Scores

• pRec: 0.0802

Intolerance Scores

• loftool: 0.975
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.0517
• hipred: N
• hipred_score: 0.167
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.293

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc113

Gene ontology

• Biological process: cilium assembly
• Cellular component: nucleoplasm;cytosol;protein-containing complex;centriolar satellite
• Molecular function: protein binding