ZDHHC1

protein-coding

zinc finger DHHC-type containing 1, the group of Zinc fingers DHHC-type

Gene summary

Enables protein-cysteine S-palmitoyltransferase activity. Involved in antiviral innate immune response; positive regulation of NLRP3 inflammasome complex assembly; and positive regulation of defense response to virus by host. Located in Golgi apparatus and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C16orf1

MANE transcript

NM_001323627.2

Inheritance

—

ClinVar variants

U:77B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr16:67,394,152-67,416,833

External References & Databases

Ensembl (ENSG00000159714)

Transcript & Mutation Effects

hg38 • Region Span ~22.7 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 ZDHHC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001323627.2. 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			9 clinvar	2 clinvar	1 clinvar	12
missense			65 clinvar	3 clinvar		68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	77	5	1	83

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001323627.2	RefSeq	NP_001310556.1	11	MANE Select
ENST00000565726.3	Ensembl	ENSP00000459264.2	11	MANE Select
NM_013304.3	RefSeq	NP_037436.1	10	Standard
ENST00000348579.6	Ensembl	ENSP00000340299.2	10	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

DNA binding
palmitoyltransferase activity
protein-cysteine S-palmitoyltransferase activity

Cellular Component

endoplasmic reticulum
Golgi apparatus
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000348579
Coding exons: 10
Length: 22415
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125745
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	247	303	0.816	0.0000201	3068
Missense (PolyPhen)		38	54.531	0.69685		627
Synonymous	0.132	127	129	0.985	0.00000898	1026
Loss of Function	0.958	17	21.8	0.779	0.00000111	229

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.741
RVIS EVS: -0.42
RVIS percentile EVS: 25.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.440

Gene Damage Prediction

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