ZDHHC4

protein-coding

zinc finger DHHC-type palmitoyltransferase 4, the group of Zinc fingers DHHC-type

Gene summary

Enables palmitoyltransferase activity. Involved in positive regulation of innate immune response and protein localization to plasma membrane. Located in Golgi apparatus and endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001134389.2

Inheritance

—

ClinVar variants

U:55B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr7:6,577,434-6,589,374

External References & Databases

Ensembl (ENSG00000136247)

Transcript & Mutation Effects

hg38 • Region Span ~11.9 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 ZDHHC4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001134389.2. 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			2 clinvar			2
missense			48 clinvar	8 clinvar		56
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	55	8	0	63

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 108 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001134389.2	RefSeq	NP_001127861.1	6	MANE Select
ENST00000335965.11	Ensembl	ENSP00000337475.6	6	MANE Select
NM_001134387.2	RefSeq	NP_001127859.1	6	Standard
NM_001134388.2	RefSeq	NP_001127860.1	6	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

Molecular Function

protein-cysteine S-palmitoyltransferase activity

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396706
Coding exons: 6
Length: 11941
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125748
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0564	195	193	1.01	0.0000107	2241
Missense (PolyPhen)		62	57.716	1.0742		739
Synonymous	-0.634	88	80.8	1.09	0.00000494	685
Loss of Function	0.122	13	13.5	0.964	6.34e-7	163

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00087	0.00087	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00029	0.00029	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0717

Intolerance Scores

LoFtool: 0.997
RVIS EVS: 0.78
RVIS percentile EVS: 87.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.148

Gene Damage Prediction

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