CCDC116

coiled-coil domain containing 116

Basic information

Region (hg38): 22:21632716-21637329

Links

ENSG00000161180 ∙ NCBI:164592 ∙ ∙ HGNC:26688 ∙ Uniprot:Q8IYX3 ∙ 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 CCDC116 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC116 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	3	4
missense			51	7	4	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	51	8	7

Variants in CCDC116

This is a list of pathogenic ClinVar variants found in the CCDC116 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-21633195-G-A		not specified	Uncertain significance (Dec 16, 2021)
22-21634014-C-T			Benign (May 08, 2018)
22-21634022-G-T		not specified	Uncertain significance (Dec 15, 2023)
22-21634036-G-T		not specified	Uncertain significance (Mar 21, 2023)
22-21634058-C-T		not specified	Uncertain significance (Sep 20, 2024)
22-21634076-G-C		not specified	Uncertain significance (Jun 28, 2024)
22-21634079-C-T		not specified	Uncertain significance (Apr 28, 2022)
22-21634109-A-C		not specified	Uncertain significance (Jul 11, 2023)
22-21634182-C-T		not specified	Uncertain significance (Oct 13, 2023)
22-21634188-G-T		not specified	Uncertain significance (Mar 25, 2024)
22-21634254-C-A		not specified	Uncertain significance (Nov 18, 2022)
22-21634274-G-T		not specified	Uncertain significance (Jul 25, 2023)
22-21634289-C-A		not specified	Uncertain significance (Nov 23, 2024)
22-21634316-C-T		not specified	Uncertain significance (Sep 09, 2024)
22-21634320-C-T		not specified	Likely benign (Dec 03, 2021)
22-21634329-G-A		not specified	Uncertain significance (Aug 08, 2022)
22-21634346-G-A		not specified	Uncertain significance (Sep 02, 2024)
22-21634359-G-A		not specified	Uncertain significance (Feb 07, 2023)
22-21634364-C-T		not specified	Uncertain significance (Jan 28, 2025)
22-21634371-C-T		not specified	Uncertain significance (Mar 17, 2023)
22-21634448-G-A		not specified	Uncertain significance (Feb 20, 2025)
22-21634463-C-T		not specified	Uncertain significance (May 10, 2024)
22-21634471-G-A			Benign (Aug 17, 2017)
22-21634545-G-T		not specified	Uncertain significance (Oct 01, 2024)
22-21634569-G-T		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC116	protein_coding	protein_coding	ENST00000292779	4	4612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000393	0.614	125668	0	77	125745	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.101	376	382	0.985	0.0000245	3967
Missense in Polyphen		82	102.35	0.80118		1218
Synonymous	0.592	149	158	0.940	0.00000958	1280
Loss of Function	0.920	10	13.7	0.732	7.57e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000877	0.0000877
Ashkenazi Jewish	0.00	0.00
East Asian	0.00196	0.00196
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.00196	0.00196
South Asian	0.000265	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.872
• rvis_EVS: 2.63
• rvis_percentile_EVS: 98.8

Haploinsufficiency Scores

• pHI: 0.0869
• hipred: N
• hipred_score: 0.123
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc116

Gene ontology

• Cellular component: cytoplasm;centrosome
• Molecular function: protein binding