CCDC159

coiled-coil domain containing 159

Basic information

Region (hg38): 19:11344683-11354944

Links

ENSG00000183401 ∙ NCBI:126075 ∙ ∙ HGNC:26996 ∙ Uniprot:P0C7I6 ∙ 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 CCDC159 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC159 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in CCDC159

This is a list of pathogenic ClinVar variants found in the CCDC159 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11345259-G-T		not specified	Uncertain significance (Jun 09, 2022)
19-11345313-T-C		not specified	Uncertain significance (Feb 28, 2024)
19-11345325-C-G		not specified	Uncertain significance (Aug 08, 2023)
19-11345356-A-G		not specified	Uncertain significance (May 05, 2023)
19-11345388-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-11345539-C-T		not specified	Uncertain significance (Feb 26, 2024)
19-11345581-C-T		not specified	Uncertain significance (May 02, 2024)
19-11345594-C-G		not specified	Uncertain significance (Jul 25, 2023)
19-11345613-C-T		not specified	Uncertain significance (May 07, 2024)
19-11350016-C-A		not specified	Uncertain significance (Jul 15, 2021)
19-11350143-T-G		not specified	Uncertain significance (Feb 07, 2023)
19-11350148-A-T		not specified	Uncertain significance (May 18, 2022)
19-11350823-C-T		not specified	Uncertain significance (Apr 19, 2023)
19-11350828-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-11350829-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-11350835-G-A		not specified	Uncertain significance (Nov 01, 2022)
19-11350853-A-G		not specified	Uncertain significance (Apr 12, 2024)
19-11350873-C-T		not specified	Uncertain significance (May 18, 2022)
19-11350930-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-11350931-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-11350957-C-G		not specified	Uncertain significance (Sep 17, 2021)
19-11350997-G-A		not specified	Uncertain significance (Nov 09, 2023)
19-11351941-G-A		not specified	Uncertain significance (Apr 06, 2023)
19-11352096-T-C		not specified	Uncertain significance (Mar 01, 2024)
19-11352129-G-A		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC159	protein_coding	protein_coding	ENST00000588790	11	10261

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000454	0.962	124696	0	91	124787	0.000365

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.486	143	160	0.892	0.00000919	1927
Missense in Polyphen		37	44.798	0.82592		642
Synonymous	1.14	49	60.3	0.812	0.00000348	515
Loss of Function	1.93	12	21.7	0.554	0.00000113	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00394	0.00361
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000554
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000179	0.000177
Middle Eastern	0.0000556	0.0000554
South Asian	0.000102	0.0000980
Other	0.000507	0.000495

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.738
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc159
• Phenotype: reproductive system phenotype