CCDC30

coiled-coil domain containing 30

Basic information

Region (hg38): 1:42463220-42657190

Links

ENSG00000186409 ∙ NCBI:728621 ∙ ∙ HGNC:26103 ∙ Uniprot:Q5VVM6 ∙ 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 CCDC30 gene.

• Inborn genetic diseases (28 variants)
• not provided (2 variants)
• Cardiomyopathy, dilated, 2c (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC30 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			25	3		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1			1	2
Total	0	1	25	4	1

Highest pathogenic variant AF is 0.000118

Variants in CCDC30

This is a list of pathogenic ClinVar variants found in the CCDC30 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-42473143-ATACT-A		Cardiomyopathy, dilated, 2c	Likely pathogenic (Apr 30, 2021)
1-42473350-C-G			Benign (May 14, 2021)
1-42536542-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-42539195-A-G		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
1-42539225-A-G		not specified	Likely benign (Nov 28, 2023)
1-42539238-A-C		not specified	Uncertain significance (Sep 13, 2023)
1-42539296-G-A		not specified	Uncertain significance (Aug 19, 2023)
1-42545415-G-T		not specified	Uncertain significance (Apr 25, 2023)
1-42545435-C-A		not specified	Likely benign (Dec 01, 2022)
1-42545461-G-A		not specified	Likely benign (Jan 03, 2024)
1-42545489-C-A		not specified	Uncertain significance (Feb 27, 2023)
1-42545555-G-A		not specified	Uncertain significance (May 06, 2022)
1-42545564-A-T		not specified	Uncertain significance (Dec 16, 2023)
1-42556167-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-42556197-A-G		not specified	Uncertain significance (May 09, 2023)
1-42556332-A-G		not specified	Uncertain significance (Jun 05, 2023)
1-42556356-T-G		not specified	Uncertain significance (Oct 03, 2022)
1-42566377-A-T		not specified	Uncertain significance (Nov 06, 2023)
1-42577115-A-C		not specified	Uncertain significance (Dec 11, 2023)
1-42577164-T-A		not specified	Uncertain significance (Feb 13, 2024)
1-42581376-G-A		not specified	Likely benign (Apr 07, 2023)
1-42581396-A-G		not specified	Uncertain significance (Apr 07, 2022)
1-42589344-A-C		not specified	Uncertain significance (May 05, 2023)
1-42589386-A-G		not specified	Uncertain significance (Mar 06, 2023)
1-42589481-G-A		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC30	protein_coding	protein_coding	ENST00000428554	15	191335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-17	0.698	125672	0	74	125746	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	318	367	0.867	0.0000175	5182
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000767	0.000762
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000165	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000356	0.000352
Middle Eastern	0.000165	0.000163
South Asian	0.000431	0.000425
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.969
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.26

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.145
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0154

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc30