CCDC7

coiled-coil domain containing 7

Basic information

Region (hg38): 10:32446139-32882874

Previous symbols: [ "C10orf68" ]

Links

ENSG00000216937 ∙ NCBI:79741 ∙ OMIM:619444 ∙ HGNC:26533 ∙ Uniprot:Q96M83 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC7 gene.

• Inborn genetic diseases (26 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC7 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in CCDC7

This is a list of pathogenic ClinVar variants found in the CCDC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-32451666-G-T		not specified	Uncertain significance (Jul 27, 2022)
10-32451667-A-G		not specified	Likely benign (Jul 27, 2022)
10-32451677-A-G		not specified	Uncertain significance (Dec 08, 2023)
10-32451709-A-C		not specified	Uncertain significance (Sep 19, 2022)
10-32451740-C-G		not specified	Uncertain significance (Feb 28, 2023)
10-32451884-A-G		not specified	Uncertain significance (Jan 08, 2024)
10-32453369-A-G		not specified	Uncertain significance (Jun 06, 2023)
10-32456288-C-T		not specified	Uncertain significance (Jun 08, 2022)
10-32456312-A-C		not specified	Likely benign (Nov 08, 2022)
10-32471127-A-G		not specified	Uncertain significance (Aug 30, 2022)
10-32471178-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-32471205-G-A		not specified	Uncertain significance (Oct 29, 2021)
10-32473999-A-G		not specified	Uncertain significance (Jun 29, 2023)
10-32474005-G-T		not specified	Uncertain significance (Oct 14, 2021)
10-32491958-T-C		not specified	Uncertain significance (Oct 13, 2021)
10-32518437-G-T		not specified	Uncertain significance (Jun 29, 2023)
10-32518453-C-T		not specified	Uncertain significance (Feb 07, 2023)
10-32544266-G-C		not specified	Uncertain significance (Sep 12, 2023)
10-32689116-A-G		not specified	Uncertain significance (Nov 12, 2021)
10-32694929-G-A		not specified	Uncertain significance (Aug 13, 2021)
10-32711637-G-A		not specified	Likely benign (Sep 17, 2021)
10-32711724-C-T		not specified	Uncertain significance (Oct 12, 2021)
10-32729388-G-C		not specified	Uncertain significance (Aug 12, 2021)
10-32729412-G-A		not specified	Uncertain significance (Sep 01, 2021)
10-32805090-G-T		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC7	protein_coding	protein_coding	ENST00000362006	17	128425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.29e-12	0.716	104773	1163	19781	125717	0.0871

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.346	209	224	0.935	0.0000106	3185
Missense in Polyphen		53	56.644	0.93566		862
Synonymous	-0.847	87	77.5	1.12	0.00000375	825
Loss of Function	1.64	23	33.2	0.693	0.00000177	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0998	0.0989
Ashkenazi Jewish	0.120	0.115
East Asian	0.168	0.159
Finnish	0.0908	0.0896
European (Non-Finnish)	0.0930	0.0891
Middle Eastern	0.168	0.159
South Asian	0.0919	0.0830
Other	0.0965	0.0897

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in tumorigenesis. {ECO:0000250|UniProtKB:Q9D541}.

Recessive Scores

• pRec: 0.0724

Intolerance Scores

• loftool: 0.986
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.44

Haploinsufficiency Scores

• pHI: 0.0786
• hipred: N
• hipred_score: 0.123
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.483

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc7b