ZDHHC19

protein-coding

zinc finger DHHC-type palmitoyltransferase 19, the group of Zinc fingers DHHC-type

Gene summary

Enables protein-cysteine S-palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation and positive regulation of aggrephagy. Located in Golgi membrane; endoplasmic reticulum; and perinucleolar compartment. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001039617.2

Inheritance

—

ClinVar variants

U:50B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr3:196,197,452-196,211,437

External References & Databases

Ensembl (ENSG00000163958)

Transcript & Mutation Effects

hg38 • Region Span ~14.0 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 ZDHHC19 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039617.2. 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			50 clinvar	5 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	6	0	56

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039617.2	RefSeq	NP_001034706.1	7	MANE Select
ENST00000296326.8	Ensembl	ENSP00000296326.3	7	MANE Select
ENST00000397544.6	Ensembl	ENSP00000380678.2	7	Standard
ENST00000438232.5	Ensembl	ENSP00000393710.1	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
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296326
Coding exons: 7
Length: 13989
Individuals with no LoFs: 124823
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 124859
p: 0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.17	138	182	0.757	0.0000104	1980
Missense (PolyPhen)		41	54.497	0.75234		644
Synonymous	-0.0518	79	78.4	1.01	0.00000483	645
Loss of Function	2.13	6	14.9	0.404	8.06e-7	149

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00013	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00028	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00036	0.00036	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0878

Intolerance Scores

LoFtool: 0.628
RVIS EVS: 1.02
RVIS percentile EVS: 90.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.612

Gene Damage Prediction

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