CCDC107

protein-coding

coiled-coil domain containing 107

Gene summary

This gene encodes a membrane protein which contains a coiled-coil domain in the central region. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2013]

MANE transcript

NM_174923.3

Inheritance

—

ClinVar variants

U:63B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.09

Max pathogenic AF

—

Genomic locus

chr9:35,658,290-35,661,511

External References & Databases

Ensembl (ENSG00000159884)

Transcript & Mutation Effects

hg38 • Region Span ~3.2 kb

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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 CCDC107 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 62

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174923.3. 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			3 clinvar	3 clinvar		6
missense			56 clinvar	4 clinvar		60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	63	7	0	70

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174923.3	RefSeq	NP_777583.2	5	MANE Select
ENST00000426546.7	Ensembl	ENSP00000414964.2	5	MANE Select
NM_001195200.2	RefSeq	NP_001182129.1	6	Standard
NM_001195201.2	RefSeq	NP_001182130.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000426546
Coding exons: 5
Length: 3208
Individuals with no LoFs: 125606
Homozygous LoFs: 0
Heterozygous LoFs: 142
Defined: 125748
p: 0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.194	139	146	0.955	0.00000760	1760
Missense (PolyPhen)		52	55.933	0.92968		715
Synonymous	0.250	62	64.6	0.960	0.00000365	610
Loss of Function	-0.290	12	11.0	1.09	4.70e-7	127

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0055	0.0055	notable
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00036	0.00036	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0482

Intolerance Scores

LoFtool: 0.865
RVIS EVS: 0.17
RVIS percentile EVS: 65.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.217

Gene Damage Prediction

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