CCDC70

coiled-coil domain containing 70

Basic information

Region (hg38): 13:51861969-51866232

Links

ENSG00000123171 ∙ NCBI:83446 ∙ ∙ HGNC:25303 ∙ Uniprot:Q6NSX1 ∙ 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 CCDC70 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC70 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	22	2	0

Variants in CCDC70

This is a list of pathogenic ClinVar variants found in the CCDC70 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-51865388-C-T		not specified	Uncertain significance (Aug 02, 2021)
13-51865398-G-A		not specified	Uncertain significance (Sep 27, 2021)
13-51865424-A-C		not specified	Uncertain significance (Dec 15, 2022)
13-51865424-A-G		not specified	Uncertain significance (Aug 14, 2023)
13-51865425-A-G		not specified	Uncertain significance (Dec 15, 2023)
13-51865467-C-T		not specified	Likely benign (Dec 14, 2023)
13-51865484-A-T		not specified	Uncertain significance (Aug 11, 2022)
13-51865487-C-T		not specified	Uncertain significance (Oct 12, 2021)
13-51865502-A-G		not specified	Uncertain significance (Apr 04, 2024)
13-51865526-G-T		not specified	Uncertain significance (Nov 01, 2022)
13-51865546-A-C		not specified	Uncertain significance (Jan 24, 2024)
13-51865593-T-G		not specified	Uncertain significance (Jun 03, 2022)
13-51865698-T-G		not specified	Uncertain significance (Feb 05, 2024)
13-51865736-A-G		not specified	Likely benign (Jan 29, 2024)
13-51865755-G-A		not specified	Uncertain significance (Aug 17, 2022)
13-51865774-T-A		not specified	Uncertain significance (Oct 04, 2022)
13-51865796-A-T		not specified	Uncertain significance (Apr 29, 2024)
13-51865818-G-A		not specified	Uncertain significance (Mar 01, 2024)
13-51865823-C-T		not specified	Uncertain significance (Mar 07, 2023)
13-51865874-G-C		not specified	Uncertain significance (Jan 05, 2022)
13-51865890-T-C		not specified	Uncertain significance (Jun 10, 2022)
13-51865981-G-T		not specified	Uncertain significance (Oct 26, 2021)
13-51865986-A-G		not specified	Uncertain significance (Sep 22, 2022)
13-51866033-G-A		not specified	Uncertain significance (Feb 28, 2023)
13-51866048-C-T		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC70	protein_coding	protein_coding	ENST00000242819	1	4250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00924	0.604	125699	0	34	125733	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.971	166	134	1.24	0.00000785	1567
Missense in Polyphen		45	32.884	1.3684		488
Synonymous	-1.11	59	49.1	1.20	0.00000280	394
Loss of Function	0.294	3	3.60	0.833	2.40e-7	34

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000163	0.000163
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0777

Intolerance Scores

• loftool: 0.866
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.0543
• hipred: N
• hipred_score: 0.199
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.534

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc70

Gene ontology

• Cellular component: extracellular region;plasma membrane
• Molecular function: protein binding