CCDC30

Gene

coiled-coil domain containing 30

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

MANE transcript

NM_001395517.1

Inheritance

—

ClinVar variants

U:99B:7

Top phenotype

Cardiomyopathy, dilated, 2c

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr1:42,463,221-42,657,190

External References & Databases

Ensembl (ENSG00000186409)

Transcript & Mutation Effects

hg38 • Region Span ~194.0 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 CCDC30 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 97

not providedTotal: 2

Cardiomyopathy, dilated, 2cTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395517.1. 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	1 clinvar		4
missense			90 clinvar	6 clinvar		96
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	99	7	0	106

Highest pathogenic variant AF is 0.000024397146

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395517.1	RefSeq	NP_001382446.1	20	MANE Select
ENST00000657597.2	Ensembl	ENSP00000499662.2	20	MANE Select
NM_001080850.4	RefSeq	NP_001074319.1	15	Standard
NM_001355224.2	RefSeq	NP_001342153.1	10	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000428554
Coding exons: 15
Length: 191335
Individuals with no LoFs: 125672
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 125746
p: 0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.906	318	367	0.867	0.0000175	5182
Missense (PolyPhen)		71	89.551	0.79284		1513
Synonymous	1.12	114	130	0.875	0.00000600	1316
Loss of Function	1.96	34	48.8	0.697	0.00000267	585

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00043	0.00042	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.969
RVIS EVS: 0.42
RVIS percentile EVS: 77.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0154

Gene Damage Prediction

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