ZDHHC17
protein-codingzinc finger DHHC-type palmitoyltransferase 17, the group of Zinc fingers DHHC-type|Ankyrin repeat domain containing
Gene summary
Enables identical protein binding activity and protein-cysteine S-palmitoyltransferase activity. Involved in lipoprotein transport; protein palmitoylation; and regulation of programmed cell death. Located in Golgi membrane and Golgi-associated vesicle membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~89.6 kbGenCC 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 ZDHHC17 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015336.4. 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 | 2 | ||||
| missense | 72 | 72 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 78 | 0 | 0 | 78 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056151.2 | 17 | MANE Select | |
| Ensembl | ENSP00000403397.2 | 17 | MANE Select | |
| RefSeq | NP_001346555.1 | 17 | Standard | |
| Ensembl | ENSP00000447871.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| zdhhc17 | Danio rerio | Structure: motor neuron Quality: truncated abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- TCR
Biological Process
- protein palmitoylation
- lipoprotein transport
- positive regulation of I-kappaB kinase/NF-kappaB signaling
- magnesium ion transmembrane transport
Molecular Function
- protein binding
- magnesium ion transmembrane transporter activity
- palmitoyltransferase activity
- protein-cysteine S-palmitoyltransferase activity
- identical protein binding
Cellular Component
- Golgi membrane
- Golgi apparatus
- integral component of membrane
- aggresome
- cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000426126
- Coding exons
- 17
- Length
- 90109
- Individuals with no LoFs
- 124630
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 124639
- p
- 0.0000361
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.57 | 182 | 309 | 0.589 | 0.0000149 | 4157 |
| Missense (PolyPhen) | 52 | 111.7 | 0.46552 | 1657 | ||
| Synonymous | 0.829 | 92 | 103 | 0.896 | 0.00000520 | 1105 |
| Loss of Function | 5.15 | 2 | 34.8 | 0.0575 | 0.00000170 | 449 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.000093 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000048 | 0.000046 | rare |
| European (Non-Finnish) | 0.000036 | 0.000027 | rare |
| South Asian | 0.000035 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Palmitoyltransferase specific for a subset of neuronal proteins, including SNAP25, DLG4/PSD95, GAD2, SYT1 and HTT (PubMed:15603740, PubMed:15489887, PubMed:19139280, PubMed:28757145). Palmitoylates MPP1 in erythrocytes (PubMed:22496366). May be involved in the sorting or targeting of critical proteins involved in the initiating events of endocytosis at the plasma membrane (PubMed:12393793). May play a role in Mg(2+) transport (PubMed:18794299). {ECO:0000269|PubMed:12393793, ECO:0000269|PubMed:15489887, ECO:0000269|PubMed:15603740, ECO:0000269|PubMed:18794299, ECO:0000269|PubMed:19139280, ECO:0000269|PubMed:22496366, ECO:0000269|PubMed:28757145}.;
Recessive Scores
- pRec
- 0.203
Intolerance Scores
- LoFtool
- 0.382
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.814
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |