ZDHHC6
protein-codingzinc finger DHHC-type palmitoyltransferase 6, the group of Zinc fingers DHHC-type
Gene summary
Enables palmitoyltransferase activity and protein-cysteine S-stearoyltransferase activity. Involved in intracellular signal transduction. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.1 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 ZDHHC6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022494.3. 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 | 3 | 4 | |||
| missense | 47 | 47 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 51 | 0 | 3 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071939.1 | 10 | MANE Select | |
| Ensembl | ENSP00000358413.3 | 10 | MANE Select | |
| RefSeq | NP_001290063.1 | 10 | Standard | |
| RefSeq | NP_001338011.1 | 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
- protein binding
- palmitoyltransferase activity
- protein-cysteine S-palmitoyltransferase activity
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- Golgi apparatus
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369405
- Coding exons
- 10
- Length
- 16615
- Individuals with no LoFs
- 125708
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125741
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.707 | 191 | 221 | 0.866 | 0.0000109 | 2730 |
| Missense (PolyPhen) | 44 | 53.637 | 0.82034 | 659 | ||
| Synonymous | 1.29 | 57 | 70.8 | 0.805 | 0.00000354 | 726 |
| Loss of Function | 2.40 | 12 | 25.0 | 0.481 | 0.00000128 | 301 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000088 | 0.000087 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00019 | 0.00018 | rare |
| South Asian | 0.00011 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Endoplasmic reticulum palmitoyl acyltransferase that mediates palmitoylation of proteins such as AMFR, CALX, ITPR1 and TFRC (PubMed:22314232, PubMed:22728137, PubMed:25368151, PubMed:28826475). Palmitoylates calnexin (CALX), which is required for its association with the ribosome-translocon complex and efficient folding of glycosylated proteins (PubMed:22314232). Mediates palmitoylation of AMFR, promoting AMFR distribution to the peripheral endoplasmic reticulum (PubMed:22728137). Together with SELENOK, palmitoylates ITPR1 in immune cells, leading to regulate ITPR1 stability and function (PubMed:25368151). {ECO:0000269|PubMed:22314232, ECO:0000269|PubMed:22728137, ECO:0000269|PubMed:25368151, ECO:0000269|PubMed:28826475}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.829
- RVIS EVS
- 0.08
- RVIS percentile EVS
- 60.09
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.343
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |