ZDHHC3
Basic information
Region (hg38): 3:44915257-44976185
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001135179.2. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 23 | 23 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 24 | 0 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ZDHHC3 | protein_coding | protein_coding | ENST00000296127 | 7 | 60929 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0277 | 0.970 | 125733 | 0 | 15 | 125748 | 0.0000596 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.08 | 112 | 193 | 0.580 | 0.0000109 | 2170 |
Missense in Polyphen | 26 | 64.005 | 0.40622 | 757 | ||
Synonymous | 0.494 | 68 | 73.4 | 0.927 | 0.00000465 | 609 |
Loss of Function | 2.69 | 6 | 18.5 | 0.324 | 0.00000112 | 186 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000214 | 0.000213 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000704 | 0.0000703 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Palmitoyltransferase with broad specificity (PubMed:21926431, PubMed:23034182). Palmitoylates GABA receptors on their gamma subunit (GABRG1, GABRG2 and GABRG3), which regulates synaptic clustering and/or cell surface stability (By similarity). Palmitoylates glutamate receptors GRIA1 and GRIA2, which leads to their retention in Golgi. May also palmitoylate DLG4, DNAJC5 and SNAP25 (By similarity). {ECO:0000250|UniProtKB:Q8R173, ECO:0000269|PubMed:21926431, ECO:0000269|PubMed:23034182}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.708
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.280
- hipred
- Y
- hipred_score
- 0.627
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.692
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zdhhc3
- Phenotype
Gene ontology
- Biological process
- protein targeting to membrane;peptidyl-L-cysteine S-palmitoylation;protein palmitoylation;localization within membrane;protein localization to photoreceptor outer segment
- Cellular component
- Golgi membrane;endoplasmic reticulum;Golgi apparatus;membrane;integral component of membrane
- Molecular function
- palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity