ZDHHC3

protein-coding

zinc finger DHHC-type palmitoyltransferase 3, the group of Zinc fingers DHHC-type

Gene summary

Enables palmitoyltransferase activity. Involved in several processes, including TRAIL-activated apoptotic signaling pathway; protein localization to photoreceptor outer segment; and regulation of signal transduction. Located in membrane. Is active in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001135179.2

Inheritance

—

ClinVar variants

U:30

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr3:44,915,257-44,976,185

External References & Databases

Ensembl (ENSG00000163812)

Transcript & Mutation Effects

hg38 • Region Span ~60.9 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 ZDHHC3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 28

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001135179.2. 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			1 clinvar			1
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	30	0	0	30

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 89 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001135179.2	RefSeq	NP_001128651.1	6	MANE Select
ENST00000424952.7	Ensembl	ENSP00000395502.2	6	MANE Select
NM_001330761.2	RefSeq	NP_001317690.1	7	Standard
NM_001349376.2	RefSeq	NP_001336305.1	7	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
localization within membrane
protein localization to photoreceptor outer segment

Molecular Function

palmitoyltransferase activity
protein-cysteine S-palmitoyltransferase activity

Cellular Component

Golgi membrane
endoplasmic reticulum
Golgi apparatus
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296127
Coding exons: 7
Length: 60929
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.08	112	193	0.580	0.0000109	2170
Missense (PolyPhen)		26	64.005	0.40622		757
Synonymous	0.494	68	73.4	0.927	0.00000465	609
Loss of Function	2.69	6	18.5	0.324	0.00000112	186

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000070	0.000070	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Palmitoyltransferase with broad specificity (PubMed:21926431, PubMed:23034182). Palmitoylates GABA receptors on their gamma subunit (GABRG1, GABRG2 and GABRG3), which regulates synaptic clustering and/or cell surface stability (By similarity). Palmitoylates glutamate receptors GRIA1 and GRIA2, which leads to their retention in Golgi. May also palmitoylate DLG4, DNAJC5 and SNAP25 (By similarity). {ECO:0000250|UniProtKB:Q8R173, ECO:0000269|PubMed:21926431, ECO:0000269|PubMed:23034182}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.708
RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.692

Gene Damage Prediction

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