CCDC170

protein-coding

coiled-coil domain containing 170

Gene summary

The function of this gene and its encoded protein is not known. Several genome-wide association studies have implicated the region around this gene to be involved in breast cancer and bone mineral density, but no link to this specific gene has been found. [provided by RefSeq, May 2010]

Previous symbols:

C6orf97

MANE transcript

NM_025059.4

Inheritance

—

ClinVar variants

U:99B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr6:151,494,017-151,621,193

External References & Databases

Ensembl (ENSG00000120262)

Transcript & Mutation Effects

hg38 • Region Span ~127.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC170 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025059.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			97 clinvar	2 clinvar	3 clinvar	102
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	99	3	3	105

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025059.4	RefSeq	NP_079335.2	11	MANE Select
ENST00000239374.8	Ensembl	ENSP00000239374.6	11	MANE Select
ENST00000867015.1	Ensembl	ENSP00000537074.1	11	Standard
ENST00000867015.2	Ensembl	ENSP00000537074.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000239374
Coding exons: 11
Length: 127164
Individuals with no LoFs: 124477
Homozygous LoFs: 0
Heterozygous LoFs: 334
Defined: 124811
p: 0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.445	344	368	0.935	0.0000192	4703
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0022	0.0022	notable
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.0061	0.0061	notable
Finnish	0.0011	0.0011	notable
European (Non-Finnish)	0.00084	0.00084	rare
South Asian	0.0014	0.0014	notable
Other	0.0012	0.0012	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0788

Intolerance Scores

RVIS EVS: 1.36
RVIS percentile EVS: 94.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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