CCDC153

coiled-coil domain containing 153

Basic information

Region (hg38): 11:119190249-119196769

Links

ENSG00000248712 ∙ NCBI:283152 ∙ ∙ HGNC:27446 ∙ Uniprot:Q494R4 ∙ 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 CCDC153 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC153 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in CCDC153

This is a list of pathogenic ClinVar variants found in the CCDC153 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-119190335-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-119190335-G-T		not specified	Uncertain significance (Jun 21, 2022)
11-119190337-G-T		not specified	Uncertain significance (Nov 18, 2023)
11-119190377-C-T		not specified	Uncertain significance (Apr 17, 2024)
11-119190780-C-T		not specified	Uncertain significance (Dec 03, 2021)
11-119190787-C-T		not specified	Likely benign (Sep 15, 2021)
11-119190811-G-A		not specified	Uncertain significance (Jul 12, 2023)
11-119190823-C-G		not specified	Uncertain significance (Dec 21, 2021)
11-119193162-C-G		not specified	Uncertain significance (Jun 29, 2022)
11-119193235-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-119193865-G-A		not specified	Uncertain significance (Nov 30, 2021)
11-119194977-C-T		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC153	protein_coding	protein_coding	ENST00000503566	6	7133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000165	0.684	125625	1	120	125746	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.582	106	124	0.853	0.00000729	1356
Missense in Polyphen		19	28.115	0.6758		364
Synonymous	0.788	38	44.7	0.850	0.00000216	410
Loss of Function	0.986	9	12.8	0.703	8.09e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00584	0.00580
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.789
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.53

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.153

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc153

Gene ontology

• Molecular function: protein binding