ZDHHC12

protein-coding

zinc finger DHHC-type palmitoyltransferase 12, the group of Zinc fingers DHHC-type

Gene summary

Enables protein-cysteine S-palmitoyltransferase activity. Involved in gephyrin clustering involved in postsynaptic density assembly and negative regulation of NLRP3 inflammasome complex assembly. Located in Golgi apparatus and endoplasmic reticulum. Is active in dendritic spine. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032799.5

Inheritance

—

ClinVar variants

U:60B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr9:128,720,870-128,724,127

External References & Databases

Ensembl (ENSG00000160446)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 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 ZDHHC12 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 56

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032799.5. 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	1 clinvar		2
missense			57 clinvar			57
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	60	1	0	61

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032799.5	RefSeq	NP_116188.3	5	MANE Select
ENST00000372663.9	Ensembl	ENSP00000361748.4	5	MANE Select
NM_001318015.2	RefSeq	NP_001304944.2	5	Standard
NM_001318016.2	RefSeq	NP_001304945.1	5	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

palmitoyltransferase activity
protein-cysteine S-palmitoyltransferase activity

Cellular Component

endoplasmic reticulum
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372663
Coding exons: 5
Length: 3259
Individuals with no LoFs: 125655
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125709
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.340	143	155	0.923	0.00000948	1641
Missense (PolyPhen)		62	63.632	0.97435		706
Synonymous	0.518	62	67.4	0.920	0.00000372	581
Loss of Function	1.45	7	12.5	0.558	6.21e-7	124

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00035	0.00031	rare
Latino/Admixed American	0.00045	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00025	0.00024	rare
South Asian	0.000068	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.557
RVIS EVS: 0.69
RVIS percentile EVS: 85.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.701

Gene Damage Prediction

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