ZDHHC13

protein-coding

zinc finger DHHC-type palmitoyltransferase 13, the group of Zinc fingers DHHC-type|Ankyrin repeat domain containing

Gene summary

Predicted to enable magnesium ion transmembrane transporter activity and palmitoyltransferase activity. Involved in positive regulation of canonical NF-kappaB signal transduction. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_019028.3

Inheritance

—

ClinVar variants

U:92B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr11:19,117,099-19,176,422

External References & Databases

Ensembl (ENSG00000177054)

Transcript & Mutation Effects

hg38 • Region Span ~59.3 kb

Loading mutation effect viewer...

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 ZDHHC13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019028.3. 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			85 clinvar	3 clinvar		88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	92	4	0	96

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019028.3	RefSeq	NP_061901.2	17	MANE Select
ENST00000446113.7	Ensembl	ENSP00000400113.2	17	MANE Select
NM_001001483.3	RefSeq	NP_001001483.1	13	Standard
ENST00000399351.7	Ensembl	ENSP00000382288.3	13	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
zdhhc13	Danio rerio	Structure: head Quality: increased size abnormal

Gene / Model

Organism

Observed Phenotype

zdhhc13

Danio rerio

Structure: head

Quality: increased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of I-kappaB kinase/NF-kappaB signaling
magnesium ion transmembrane transport

Molecular Function

magnesium ion transmembrane transporter activity
palmitoyltransferase activity
protein-cysteine S-palmitoyltransferase activity

Cellular Component

Golgi membrane
endoplasmic reticulum
membrane
integral component of membrane
cytoplasmic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000446113
Coding exons: 17
Length: 59324
Individuals with no LoFs: 124530
Homozygous LoFs: 0
Heterozygous LoFs: 108
Defined: 124638
p: 0.000433

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.752	256	292	0.876	0.0000133	4057
Missense (PolyPhen)		74	81.52	0.90776		1155
Synonymous	-0.228	103	100	1.03	0.00000449	1132
Loss of Function	0.512	31	34.2	0.906	0.00000175	438

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00065	0.00058	rare
Latino/Admixed American	0.00036	0.00035	rare
Ashkenazi Jewish	0.00070	0.00070	rare
East Asian	0.00042	0.00039	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00053	0.00051	rare
South Asian	0.00044	0.00042	rare
Other	0.00018	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Palmitoyltransferase for HTT and GAD2. May play a role in Mg(2+) transport. {ECO:0000250|UniProtKB:Q9CWU2}.;

Recessive Scores

pRec: 0.0740

Intolerance Scores

LoFtool: 0.938
RVIS EVS: 0.66
RVIS percentile EVS: 84.55

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.000672

Gene Damage Prediction

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