CCDC152

coiled-coil domain containing 152

Basic information

Region (hg38): 5:42756817-42802439

Links

ENSG00000198865 ∙ NCBI:100129792 ∙ ∙ HGNC:34438 ∙ Uniprot:Q4G0S7 ∙ 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 CCDC152 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC152 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						0
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	15	1	1

Variants in CCDC152

This is a list of pathogenic ClinVar variants found in the CCDC152 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-42759144-G-A		not specified	Uncertain significance (Jun 17, 2022)
5-42759197-C-A		not specified	Uncertain significance (Aug 18, 2023)
5-42762455-A-G		not specified	Uncertain significance (Dec 09, 2023)
5-42762459-A-G		not specified	Likely benign (Aug 02, 2022)
5-42762537-C-T		not specified	Uncertain significance (May 18, 2022)
5-42779458-G-A		not specified	Uncertain significance (Nov 29, 2021)
5-42779473-T-C		not specified	Uncertain significance (Dec 03, 2021)
5-42779483-T-A		not specified	Uncertain significance (May 26, 2022)
5-42783493-C-A		not specified	Uncertain significance (Aug 05, 2021)
5-42783575-A-C		not specified	Uncertain significance (May 23, 2023)
5-42799432-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-42799696-T-C		not specified	Uncertain significance (Aug 17, 2022)
5-42799708-G-A		not specified	Uncertain significance (Aug 02, 2022)
5-42799716-A-G		not specified	Uncertain significance (Aug 22, 2023)
5-42799764-A-G		not specified	Uncertain significance (Aug 02, 2022)
5-42800763-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-42800785-T-C		not specified	Uncertain significance (Dec 13, 2023)
5-42800806-T-G		not specified	Uncertain significance (May 25, 2022)
5-42800976-G-C		not specified	Uncertain significance (Apr 07, 2022)
5-42800982-A-G		not specified	Likely benign (Sep 16, 2021)
5-42801176-T-C			Benign (May 31, 2018)
5-42801259-G-A		not specified	Uncertain significance (Nov 22, 2021)
5-42801261-G-A		not specified	Uncertain significance (May 31, 2023)
5-42801304-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC152	protein_coding	protein_coding	ENST00000361970	8	45560

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000382	0.625	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	63	95.5	0.660	0.00000484	1704
Missense in Polyphen		15	22.246	0.67427		467
Synonymous	1.80	17	29.4	0.579	0.00000135	394
Loss of Function	0.810	8	10.9	0.735	4.62e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.3
• rvis_percentile_EVS: 71.81

Haploinsufficiency Scores

• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc152