ZKSCAN3
Basic information
Region (hg38): 6:28349947-28369172
Previous symbols: [ "ZNF306", "ZNF309" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (47 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZKSCAN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024493.4. 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 | 0 | |||||
| missense | 45 | 48 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 3 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZKSCAN3 | protein_coding | protein_coding | ENST00000377255 | 5 | 19257 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.97e-11 | 0.225 | 125699 | 0 | 48 | 125747 | 0.000191 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.64 | 212 | 291 | 0.730 | 0.0000151 | 3539 |
| Missense in Polyphen | 70 | 94.945 | 0.73727 | 1174 | ||
| Synonymous | 1.11 | 100 | 115 | 0.869 | 0.00000621 | 1012 |
| Loss of Function | 0.844 | 19 | 23.4 | 0.812 | 0.00000136 | 267 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000756 | 0.000756 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000133 | 0.000132 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000425 | 0.000425 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional factor that binds to the consensus sequence 5'-[GT][AG][AGT]GGGG-3' and acts as a repressor of autophagy. Specifically represses expression of genes involved in autophagy and lysosome biogenesis/function such as MAP1LC3B, ULK1 or WIPI2. Associates with chromatin at the ITGB4 and VEGF promoters. Also acts as a transcription activator and promotes cancer cell progression and/or migration in various tumors and myelomas. {ECO:0000269|PubMed:18940803, ECO:0000269|PubMed:21057542, ECO:0000269|PubMed:22531714, ECO:0000269|PubMed:23434374}.;
- Pathway
- Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.667
- rvis_EVS
- 0.51
- rvis_percentile_EVS
- 80.1
Haploinsufficiency Scores
- pHI
- 0.160
- hipred
- N
- hipred_score
- 0.218
- ghis
- 0.471
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.629
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zkscan3
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;autophagy;lysosome organization;negative regulation of autophagy;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;negative regulation of cellular senescence
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;metal ion binding