CCDC158

coiled-coil domain containing 158

Basic information

Region (hg38): 4:76312997-76421868

Links

ENSG00000163749 ∙ NCBI:339965 ∙ ∙ HGNC:26374 ∙ Uniprot:Q5M9N0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• renal tubule disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC158 gene.

• not_specified (152 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC158 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001394954.1. 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			149	4		153
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	149	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC158	protein_coding	protein_coding	ENST00000388914	23	108868

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-25	0.110	124547	0	250	124797	0.00100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.229	593	578	1.03	0.0000310	7327
Missense in Polyphen		310	323.72	0.95762		4323
Synonymous	-0.0235	196	196	1.00	0.00000916	2034
Loss of Function	1.76	47	62.0	0.759	0.00000333	775

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00285	0.00278
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00132	0.00128
Finnish	0.00	0.00
European (Non-Finnish)	0.00101	0.000998
Middle Eastern	0.00132	0.00128
South Asian	0.00142	0.00137
Other	0.00101	0.000990

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.973
• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.413
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc158