CCDC6

coiled-coil domain containing 6

Basic information

Region (hg38): 10:59788746-59906556

Previous symbols: [ "TST1", "D10S170" ]

Links

ENSG00000108091 ∙ NCBI:8030 ∙ OMIM:601985 ∙ HGNC:18782 ∙ Uniprot:Q16204 ∙ 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 CCDC6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC6 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					2	2
missense			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	3

Variants in CCDC6

This is a list of pathogenic ClinVar variants found in the CCDC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-59793005-G-A			Benign (Jan 01, 2024)
10-59793085-A-T		not specified	Uncertain significance (Sep 13, 2023)
10-59793098-C-T		not specified	Uncertain significance (Jan 31, 2024)
10-59804429-T-G		not specified	Uncertain significance (Nov 07, 2022)
10-59807031-C-G		not specified	Uncertain significance (Apr 20, 2023)
10-59807033-C-G		not specified	Uncertain significance (Sep 16, 2022)
10-59812639-T-G		not specified	Uncertain significance (Jan 30, 2024)
10-59812660-C-A		not specified	Uncertain significance (Apr 01, 2024)
10-59812757-G-A		not specified	Uncertain significance (Sep 07, 2022)
10-59812766-A-G		not specified	Uncertain significance (Dec 22, 2023)
10-59812767-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-59814722-A-G			Benign (Aug 02, 2017)
10-59814748-C-T		not specified	Uncertain significance (May 24, 2024)
10-59832583-A-C		not specified	Uncertain significance (Dec 22, 2023)
10-59832645-A-G			Benign (Aug 02, 2017)
10-59906283-C-T		not specified	Uncertain significance (Oct 05, 2023)
10-59906307-C-T		not specified	Uncertain significance (Jul 29, 2023)
10-59906331-C-T		not specified	Uncertain significance (Jun 29, 2023)
10-59906385-C-A		not specified	Uncertain significance (Nov 03, 2022)
10-59906388-C-T		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC6	protein_coding	protein_coding	ENST00000263102	9	117894

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.577	0.423	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.81	144	275	0.523	0.0000151	3087
Missense in Polyphen		15	77.374	0.19386		1010
Synonymous	0.815	102	113	0.902	0.00000660	914
Loss of Function	3.64	5	24.4	0.205	0.00000129	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000754	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000364	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving CCDC6 is found in papillary thyroid carcinomas (PTCs). Inversion inv(10)(q11.2;q21) generates the RET/CCDC6 (PTC1) oncogene. {ECO:0000269|PubMed:2406025}.
• Pathway: Pathways in cancer - Homo sapiens (human);Thyroid cancer - Homo sapiens (human);Retinoblastoma (RB) in Cancer;Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.167

Intolerance Scores

• loftool: 0.178
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.437
• hipred: Y
• hipred_score: 0.748
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.691

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc6

Gene ontology

• Biological process: cytoskeleton organization;biological_process
• Cellular component: cytosol;cytoskeleton
• Molecular function: structural constituent of cytoskeleton;protein binding;SH3 domain binding