CCDC106

coiled-coil domain containing 106

Basic information

Region (hg38): 19:55641062-55653161

Links

ENSG00000173581 ∙ NCBI:29903 ∙ OMIM:613478 ∙ HGNC:30181 ∙ Uniprot:Q9BWC9 ∙ 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 CCDC106 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC106 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in CCDC106

This is a list of pathogenic ClinVar variants found in the CCDC106 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55642584-G-C		not specified	Uncertain significance (Feb 10, 2022)
19-55642599-A-C		not specified	Uncertain significance (Jul 27, 2023)
19-55642615-C-G		not specified	Uncertain significance (Oct 08, 2024)
19-55642648-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-55642692-C-T		not specified	Uncertain significance (Aug 06, 2021)
19-55642707-G-A		not specified	Uncertain significance (Nov 27, 2023)
19-55642731-G-C		not specified	Uncertain significance (Jan 08, 2025)
19-55642752-C-A			Benign (Jul 13, 2018)
19-55642789-G-A		not specified	Uncertain significance (Aug 10, 2024)
19-55642801-C-A		not specified	Uncertain significance (Dec 03, 2024)
19-55642856-C-G		not specified	Uncertain significance (Jul 16, 2024)
19-55642888-A-G		not specified	Uncertain significance (Feb 25, 2025)
19-55642944-G-A		not specified	Uncertain significance (Apr 06, 2024)
19-55642963-G-A		not specified	Uncertain significance (Mar 28, 2023)
19-55642981-G-A		not specified	Uncertain significance (Aug 21, 2023)
19-55644639-C-T		not specified	Uncertain significance (May 03, 2023)
19-55644641-C-T		not specified	Uncertain significance (Oct 17, 2023)
19-55644644-C-T		not specified	Uncertain significance (Dec 19, 2023)
19-55644645-G-A		not specified	Uncertain significance (Apr 20, 2023)
19-55644681-C-G		not specified	Uncertain significance (Nov 03, 2023)
19-55644702-C-T		not specified	Uncertain significance (Feb 09, 2025)
19-55644710-C-T		not specified	Uncertain significance (May 18, 2022)
19-55644720-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-55644868-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-55644917-G-A		not specified	Uncertain significance (Aug 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC106	protein_coding	protein_coding	ENST00000586790	5	12100

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0272	0.926	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	131	193	0.678	0.0000140	1810
Missense in Polyphen		37	90.537	0.40867		851
Synonymous	-1.85	106	84.3	1.26	0.00000614	565
Loss of Function	1.71	4	9.75	0.410	4.13e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes the degradation of p53/TP53 protein and inhibits its transactivity. {ECO:0000269|PubMed:20159018}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.151
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.740
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.865

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc106

Gene ontology

• Cellular component: nucleus;cytosol
• Molecular function: protein binding