CCDC159

coiled-coil domain containing 159

Basic information

Region (hg38): 19:11344684-11354944

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.

• not_specified (48 variants)

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. These statistics are base on transcript: NM_001080503.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			46	2		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	2	0

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