CCDC170

coiled-coil domain containing 170

Basic information

Region (hg38): 6:151494016-151621193

Previous symbols: [ "C6orf97" ]

Links

ENSG00000120262 ∙ NCBI:80129 ∙ ∙ HGNC:21177 ∙ Uniprot:Q8IYT3 ∙ 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 CCDC170 gene.

• Inborn genetic diseases (29 variants)
• not provided (6 variants)
• not specified (1 variants)
• Estrogen resistance syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC170 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		1
missense			28	1	4	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	28	2	5

Variants in CCDC170

This is a list of pathogenic ClinVar variants found in the CCDC170 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-151494140-C-A		not specified	Uncertain significance (Oct 22, 2021)
6-151494178-C-A		not specified	Uncertain significance (Aug 26, 2022)
6-151494178-C-T		not specified	Uncertain significance (Sep 22, 2023)
6-151536319-A-G		not specified	Uncertain significance (Oct 20, 2021)
6-151536351-A-G		not specified	Uncertain significance (May 11, 2022)
6-151538052-A-C		not specified	Uncertain significance (Jan 02, 2024)
6-151538055-T-A		not specified	Uncertain significance (Jan 23, 2024)
6-151538094-A-C		not specified	Uncertain significance (Dec 08, 2023)
6-151538150-C-T		not specified	Uncertain significance (Dec 21, 2021)
6-151538202-T-C		not specified	Uncertain significance (Jan 18, 2023)
6-151538207-A-G		not specified	Uncertain significance (Sep 07, 2022)
6-151544572-A-C		not specified	Uncertain significance (Dec 27, 2023)
6-151544654-C-T		not specified	Uncertain significance (Jan 16, 2024)
6-151548316-C-A		not specified	Uncertain significance (Apr 07, 2023)
6-151548407-C-T		not specified	Uncertain significance (Jun 27, 2023)
6-151548451-G-T		not specified	Uncertain significance (May 04, 2022)
6-151548461-G-A		not specified	Uncertain significance (Jun 09, 2022)
6-151548470-A-G		not specified	Uncertain significance (Dec 03, 2021)
6-151573252-C-G		not specified	Uncertain significance (Dec 20, 2023)
6-151573432-G-A			Conflicting classifications of pathogenicity (Nov 01, 2023)
6-151573463-T-C		not specified	Uncertain significance (Oct 20, 2021)
6-151573470-C-A		not specified	Uncertain significance (Dec 20, 2023)
6-151573472-G-A		not specified	Likely benign (Dec 07, 2021)
6-151585893-T-C		not specified	Uncertain significance (Dec 01, 2022)
6-151585974-G-A			Benign (Jun 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC170	protein_coding	protein_coding	ENST00000239374	11	127164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.61e-24	0.000468	124477	0	334	124811	0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.445	344	368	0.935	0.0000192	4703
Missense in Polyphen		82	82.801	0.99033		1189
Synonymous	0.354	135	140	0.962	0.00000759	1311
Loss of Function	-0.0985	35	34.4	1.02	0.00000189	434

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00272	0.00272
Ashkenazi Jewish	0.000412	0.000397
East Asian	0.00609	0.00608
Finnish	0.00107	0.00107
European (Non-Finnish)	0.000842	0.000839
Middle Eastern	0.00609	0.00608
South Asian	0.00144	0.00144
Other	0.00116	0.00115

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0788

Intolerance Scores

• rvis_EVS: 1.36
• rvis_percentile_EVS: 94.45

Haploinsufficiency Scores

• pHI: 0.0751
• hipred: N
• hipred_score: 0.227

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc170

Gene ontology

• Molecular function: protein binding