ZNF346
Basic information
Region (hg38): 5:177022696-177081189
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 ZNF346 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 | 14 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 1 | 0 |
Variants in ZNF346
This is a list of pathogenic ClinVar variants found in the ZNF346 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-177022758-C-G | not specified | Likely benign (Dec 06, 2022) | ||
| 5-177022773-C-T | not specified | Uncertain significance (Apr 24, 2024) | ||
| 5-177022802-A-C | not specified | Uncertain significance (Oct 04, 2022) | ||
| 5-177022803-G-C | not specified | Uncertain significance (Oct 04, 2022) | ||
| 5-177022820-G-A | not specified | Uncertain significance (Nov 03, 2022) | ||
| 5-177022836-G-A | not specified | Uncertain significance (Oct 13, 2021) | ||
| 5-177022862-C-T | not specified | Uncertain significance (Nov 22, 2021) | ||
| 5-177022908-A-G | not specified | Uncertain significance (May 23, 2023) | ||
| 5-177041139-C-G | not specified | Uncertain significance (May 03, 2023) | ||
| 5-177041213-A-G | not specified | Uncertain significance (Jul 26, 2021) | ||
| 5-177044458-G-A | not specified | Uncertain significance (Feb 22, 2023) | ||
| 5-177044497-A-G | not specified | Uncertain significance (Feb 13, 2024) | ||
| 5-177050822-C-T | not specified | Uncertain significance (Jul 14, 2023) | ||
| 5-177050876-A-G | not specified | Uncertain significance (Aug 04, 2023) | ||
| 5-177050924-A-G | not specified | Uncertain significance (May 24, 2023) | ||
| 5-177064582-A-G | not specified | Uncertain significance (Jan 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZNF346 | protein_coding | protein_coding | ENST00000358149 | 7 | 58494 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.116 | 0.878 | 125736 | 0 | 5 | 125741 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 113 | 154 | 0.734 | 0.00000764 | 1924 |
| Missense in Polyphen | 26 | 49.874 | 0.52132 | 641 | ||
| Synonymous | 1.16 | 50 | 61.6 | 0.812 | 0.00000346 | 533 |
| Loss of Function | 2.44 | 4 | 13.8 | 0.290 | 5.83e-7 | 183 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds with low affinity to dsDNA and ssRNA, and with high affinity to dsRNA, with no detectable sequence specificity (PubMed:24521053). May bind to specific miRNA hairpins (PubMed:28431233). {ECO:0000269|PubMed:24521053, ECO:0000269|PubMed:28431233}.;
Recessive Scores
- pRec
- 0.0955
Intolerance Scores
- loftool
- 0.537
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.0985
- hipred
- Y
- hipred_score
- 0.743
- ghis
- 0.629
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.887
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zfp346
- Phenotype
- hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- positive regulation of apoptotic process
- Cellular component
- nucleus;nucleolus;cytoplasm
- Molecular function
- RNA binding;double-stranded RNA binding;protein binding;zinc ion binding;enzyme binding;miRNA binding