ZDHHC21
Basic information
Region (hg38): 9:14586766-14693432
Links
Phenotypes
GenCC
Source:
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 ZDHHC21 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in ZDHHC21
This is a list of pathogenic ClinVar variants found in the ZDHHC21 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-14618986-G-A | not specified | Uncertain significance (Feb 13, 2024) | ||
| 9-14619013-G-T | not specified | Uncertain significance (Oct 02, 2023) | ||
| 9-14619035-G-C | not specified | Uncertain significance (Mar 07, 2024) | ||
| 9-14619045-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
| 9-14619091-G-A | not specified | Uncertain significance (Aug 17, 2022) | ||
| 9-14639982-T-C | not specified | Uncertain significance (Mar 21, 2023) | ||
| 9-14658756-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 9-14658808-C-T | not specified | Uncertain significance (Sep 22, 2022) | ||
| 9-14658843-T-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| 9-14662218-G-T | not specified | Uncertain significance (Apr 27, 2024) | ||
| 9-14662288-T-C | not specified | Uncertain significance (Aug 15, 2023) | ||
| 9-14672884-C-T | not specified | Uncertain significance (Apr 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZDHHC21 | protein_coding | protein_coding | ENST00000380916 | 7 | 82401 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0284 | 0.962 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.322 | 131 | 142 | 0.924 | 0.00000714 | 1748 |
| Missense in Polyphen | 18 | 36.944 | 0.48723 | 461 | ||
| Synonymous | -3.68 | 76 | 44.7 | 1.70 | 0.00000216 | 467 |
| Loss of Function | 2.26 | 5 | 14.2 | 0.353 | 6.76e-7 | 180 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000298 | 0.0000298 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000718 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Palmitoylates sex steroid hormone receptors, including ESR1, PGR and AR, thereby regulating their targeting to the plasma membrane. This affects rapid intracellular signaling by sex hormones via ERK and AKT kinases and the generation of cAMP, but does not affect that mediated by their nuclear receptor (By similarity). {ECO:0000250, ECO:0000269|PubMed:22031296}.;
- Pathway
- Metabolism of nitric oxide;eNOS activation;eNOS activation and regulation;Metabolism
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.484
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 37.11
Haploinsufficiency Scores
- pHI
- 0.137
- hipred
- N
- hipred_score
- 0.380
- ghis
- 0.596
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.797
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zdhhc21
- Phenotype
- pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- hair follicle development;protein targeting to membrane;peptidyl-L-cysteine S-palmitoylation;protein palmitoylation;sebaceous gland development;regulation of nitric-oxide synthase activity
- Cellular component
- Golgi membrane;endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of membrane
- Molecular function
- palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity