ZDHHC17
zinc finger DHHC-type palmitoyltransferase 17, the group of Zinc fingers DHHC-type|Ankyrin repeat domain containing
Basic information
Region (hg38): 12:76764103-76853696
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC17 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 0 | 0 |
Variants in ZDHHC17
This is a list of pathogenic ClinVar variants found in the ZDHHC17 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-76764252-G-A | not specified | Uncertain significance (May 14, 2024) | ||
| 12-76764292-A-G | not specified | Uncertain significance (Jan 17, 2024) | ||
| 12-76764294-A-G | not specified | Uncertain significance (Dec 27, 2022) | ||
| 12-76805340-G-A | not specified | Uncertain significance (Apr 13, 2023) | ||
| 12-76809050-A-G | not specified | Uncertain significance (Jan 23, 2023) | ||
| 12-76809808-C-T | not specified | Uncertain significance (Apr 15, 2024) | ||
| 12-76809850-A-G | not specified | Uncertain significance (Jun 16, 2023) | ||
| 12-76809853-G-C | not specified | Uncertain significance (Jun 06, 2023) | ||
| 12-76815159-T-C | not specified | Uncertain significance (Jun 16, 2024) | ||
| 12-76822466-C-G | not specified | Uncertain significance (Apr 23, 2024) | ||
| 12-76822471-G-C | not specified | Uncertain significance (Mar 01, 2024) | ||
| 12-76822514-A-G | not specified | Uncertain significance (Aug 08, 2022) | ||
| 12-76827016-G-A | not specified | Uncertain significance (Nov 09, 2021) | ||
| 12-76828403-C-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 12-76828410-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
| 12-76842021-A-G | not specified | Uncertain significance (Jan 11, 2023) | ||
| 12-76846663-T-G | not specified | Uncertain significance (Sep 01, 2021) | ||
| 12-76848256-A-T | not specified | Uncertain significance (Nov 07, 2022) | ||
| 12-76848373-A-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 12-76848374-T-C | not specified | Uncertain significance (Dec 17, 2021) | ||
| 12-76849415-G-T | not specified | Uncertain significance (May 03, 2023) | ||
| 12-76849419-G-A | not specified | Uncertain significance (Jan 27, 2022) | ||
| 12-76849455-T-C | not specified | Uncertain significance (Jan 29, 2024) | ||
| 12-76850888-G-A | not specified | Uncertain significance (Nov 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZDHHC17 | protein_coding | protein_coding | ENST00000426126 | 17 | 90109 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000107 | 124630 | 0 | 9 | 124639 | 0.0000361 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.57 | 182 | 309 | 0.589 | 0.0000149 | 4157 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000158 | 0.000158 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000481 | 0.0000464 |
| European (Non-Finnish) | 0.0000359 | 0.0000265 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000351 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- TCR
(Consensus)
Recessive Scores
- pRec
- 0.203
Intolerance Scores
- loftool
- 0.382
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.91
Haploinsufficiency Scores
- pHI
- 0.580
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.651
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.814
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zdhhc17
- Phenotype
- cellular phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- zdhhc17
- Affected structure
- motor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- truncated
Gene ontology
- Biological process
- protein palmitoylation;lipoprotein transport;positive regulation of I-kappaB kinase/NF-kappaB signaling;magnesium ion transmembrane transport
- Cellular component
- Golgi membrane;Golgi apparatus;integral component of membrane;aggresome;cell junction;cytoplasmic vesicle membrane;Golgi-associated vesicle membrane;presynaptic membrane;intracellular membrane-bounded organelle
- Molecular function
- protein binding;magnesium ion transmembrane transporter activity;palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity;identical protein binding