ZDHHC20

protein-coding

zinc finger DHHC-type palmitoyltransferase 20, the group of Zinc fingers DHHC-type

Gene summary

Enables protein-cysteine S-palmitoyltransferase activity and zinc ion binding activity. Involved in DNA damage response and peptidyl-L-cysteine S-palmitoylation. Located in Golgi membrane; nucleus; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001330059.2

Inheritance

—

ClinVar variants

U:52B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr13:21,348,784-21,459,370

External References & Databases

Ensembl (ENSG00000180776)

Transcript & Mutation Effects

hg38 • Region Span ~110.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZDHHC20 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330059.2. 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						0
missense			47 clinvar	5 clinvar		52
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	52	5	0	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330059.2	RefSeq	NP_001316988.1	12	MANE Select
ENST00000400590.8	Ensembl	ENSP00000383433.3	12	MANE Select
NM_001286638.2	RefSeq	NP_001273567.1	10	Standard
NM_153251.4	RefSeq	NP_694983.2	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein targeting to membrane
peptidyl-L-cysteine S-palmitoylation
protein palmitoylation

Molecular Function

zinc ion binding
palmitoyltransferase activity
protein-cysteine S-palmitoyltransferase activity

Cellular Component

endoplasmic reticulum
Golgi apparatus
plasma membrane
membrane
integral component of Golgi membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382466
Coding exons: 12
Length: 83247
Individuals with no LoFs: 124633
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 124655
p: 0.0000882

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.25	125	171	0.730	0.00000901	2283
Missense (PolyPhen)		38	62.824	0.60486		892
Synonymous	0.692	55	61.9	0.888	0.00000329	629
Loss of Function	2.43	9	21.0	0.428	9.84e-7	286

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes palmitoylation of Cys residues on target proteins (PubMed:27153536, PubMed:29326245). Catalyzes palmitoylation of Cys residues in the cytoplasmic C-terminus of EGFR, and modulates the duration of EGFR signaling by modulating palmitoylation-dependent EGFR internalization and degradation (PubMed:27153536). Has a preference for acyl-CoA with C16 fatty acid chains (PubMed:29326245). Can also utilize acyl-CoA with C14 and C18 fatty acid chains (PubMed:29326245). {ECO:0000269|PubMed:27153536, ECO:0000269|PubMed:29326245}.;

Intolerance Scores

RVIS EVS: 0.75
RVIS percentile EVS: 86.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.211

Gene Damage Prediction

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