CCDC117

coiled-coil domain containing 117

Basic information

Region (hg38): 22:28772673-28789301

Links

ENSG00000159873 ∙ NCBI:150275 ∙ ∙ HGNC:26599 ∙ Uniprot:Q8IWD4 ∙ 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 CCDC117 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC117 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in CCDC117

This is a list of pathogenic ClinVar variants found in the CCDC117 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-28772943-T-C		not specified	Uncertain significance (Dec 14, 2021)
22-28772969-G-C		not specified	Likely benign (Feb 22, 2023)
22-28772979-C-T		not specified	Uncertain significance (Dec 06, 2022)
22-28773000-C-T		not specified	Uncertain significance (Jan 09, 2024)
22-28773004-G-C		not specified	Uncertain significance (Dec 03, 2021)
22-28773006-A-G		not specified	Uncertain significance (Dec 21, 2023)
22-28773013-C-G		not specified	Likely benign (Mar 01, 2024)
22-28773018-A-C		not specified	Uncertain significance (Aug 09, 2021)
22-28773730-C-T		not specified	Uncertain significance (Dec 28, 2023)
22-28781030-G-T		not specified	Uncertain significance (Jun 30, 2022)
22-28781088-A-G		not specified	Uncertain significance (Feb 23, 2023)
22-28781100-A-T		not specified	Uncertain significance (Feb 08, 2023)
22-28781114-A-G		not specified	Uncertain significance (Jul 19, 2022)
22-28781161-G-T		not specified	Uncertain significance (Oct 04, 2022)
22-28781168-G-A		not specified	Uncertain significance (Aug 29, 2022)
22-28783576-C-G		not specified	Uncertain significance (Jan 03, 2024)
22-28783600-A-G		not specified	Uncertain significance (Nov 08, 2021)
22-28786159-T-A		not specified	Uncertain significance (Dec 18, 2023)
22-28786247-C-T		not specified	Likely benign (Jan 18, 2023)
22-28786274-T-C		not specified	Uncertain significance (Nov 08, 2022)
22-28786298-C-G		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC117	protein_coding	protein_coding	ENST00000249064	5	16622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.788	0.211	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.225	125	118	1.06	0.00000553	1835
Missense in Polyphen		31	30.04	1.032		480
Synonymous	0.881	31	37.9	0.818	0.00000171	554
Loss of Function	2.55	1	9.48	0.105	5.27e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.394
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.245
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc117

Gene ontology

• Molecular function: protein binding