CCDC158

protein-coding

coiled-coil domain containing 158

Gene summary

Enables clathrin binding activity. Involved in receptor-mediated endocytosis. Located in clathrin-coated vesicle and early endosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001394954.1

Inheritance

ClinVar variants

U:177B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr4:76,312,997-76,421,868

External References & Databases

Ensembl (ENSG00000163749)

Transcript & Mutation Effects

hg38 • Region Span ~108.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

renal tubule disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0021568

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC158 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 173

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394954.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			172 clinvar	4 clinvar		176
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	177	4	0	181

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394954.1	RefSeq	NP_001381883.1	23	MANE Select
ENST00000682701.1	Ensembl	ENSP00000507278.1	23	MANE Select
NM_001042784.1	RefSeq	NP_001036249.1	23	Standard
ENST00000388914.7	Ensembl	ENSP00000373566.2	23	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000388914
Coding exons: 23
Length: 108868
Individuals with no LoFs: 124547
Homozygous LoFs: 0
Heterozygous LoFs: 250
Defined: 124797
p: 0.00100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.229	593	578	1.03	0.0000310	7327
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0016	notable
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0013	0.0013	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.0010	0.0010	notable
South Asian	0.0014	0.0014	notable
Other	0.0010	0.00099	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.973
RVIS EVS: 0.15
RVIS percentile EVS: 63.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.757

Gene Damage Prediction

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