ZDHHC2

protein-coding

zinc finger DHHC-type palmitoyltransferase 2, the group of Zinc fingers DHHC-type

Gene summary

Enables protein homodimerization activity and protein-cysteine S-palmitoyltransferase activity. Involved in several processes, including peptidyl-L-cysteine S-palmitoylation; protein localization to membrane raft; and synapse assembly. Located in Golgi apparatus; endoplasmic reticulum membrane; and plasma membrane. Is active in postsynaptic recycling endosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016353.5

Inheritance

—

ClinVar variants

U:68B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr8:17,156,482-17,224,799

External References & Databases

Ensembl (ENSG00000104219)

Transcript & Mutation Effects

hg38 • Region Span ~68.3 kb

Loading mutation effect viewer...

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 ZDHHC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016353.5. 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			1 clinvar	2 clinvar		3
missense			59 clinvar	2 clinvar		61
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	68	4	0	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016353.5	RefSeq	NP_057437.1	12	MANE Select
ENST00000262096.13	Ensembl	ENSP00000262096.8	12	MANE Select
NM_001362988.2	RefSeq	NP_001349917.1	13	Standard
NM_001362989.2	RefSeq	NP_001349918.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Surfactant metabolism
Metabolism of proteins

Biological Process

protein targeting to membrane
peptidyl-L-cysteine S-palmitoylation
protein palmitoylation
cellular protein metabolic process

Molecular Function

palmitoyltransferase activity
protein-cysteine S-palmitoyltransferase activity

Cellular Component

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262096
Coding exons: 12
Length: 68771
Individuals with no LoFs: 124581
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 124635
p: 0.000217

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.296	178	167	1.06	0.00000790	2393
Missense (PolyPhen)		66	66.142	0.99785		1003
Synonymous	-2.17	79	58.0	1.36	0.00000288	642
Loss of Function	2.67	9	22.8	0.395	0.00000127	283

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00045	0.00043	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.0012	0.0011	notable
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Palmitoyltransferase specific for GAP43 and DLG4/PSD95. {ECO:0000250}.;

Recessive Scores

pRec: 0.0886

Intolerance Scores

LoFtool: 0.695
RVIS EVS: -0.05
RVIS percentile EVS: 50.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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