ZFAND6
Basic information
Region (hg38): 15:80059568-80140292
Previous symbols: [ "ZA20D3" ]
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 ZFAND6 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 | 11 | ||||
| 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 | 1 | 0 |
Variants in ZFAND6
This is a list of pathogenic ClinVar variants found in the ZFAND6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-80121729-C-G | not specified | Uncertain significance (Dec 19, 2023) | ||
| 15-80121796-C-G | not specified | Uncertain significance (May 15, 2024) | ||
| 15-80121810-A-G | not specified | Uncertain significance (Dec 21, 2023) | ||
| 15-80122704-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
| 15-80122732-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 15-80122740-T-C | not specified | Uncertain significance (Aug 09, 2021) | ||
| 15-80122740-T-G | Likely benign (Jun 13, 2018) | |||
| 15-80122784-A-C | not specified | Uncertain significance (May 09, 2023) | ||
| 15-80131236-A-C | not specified | Uncertain significance (Mar 30, 2024) | ||
| 15-80131239-C-A | not specified | Uncertain significance (Dec 27, 2023) | ||
| 15-80131240-C-T | not specified | Uncertain significance (May 20, 2024) | ||
| 15-80131266-A-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 15-80137540-A-G | not specified | Uncertain significance (Apr 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZFAND6 | protein_coding | protein_coding | ENST00000261749 | 5 | 78826 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.462 | 0.533 | 125693 | 0 | 12 | 125705 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.988 | 80 | 109 | 0.734 | 0.00000545 | 1353 |
| Missense in Polyphen | 19 | 39.052 | 0.48653 | 500 | ||
| Synonymous | -0.415 | 39 | 35.8 | 1.09 | 0.00000169 | 380 |
| Loss of Function | 2.34 | 2 | 9.99 | 0.200 | 4.19e-7 | 140 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000102 | 0.000102 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000939 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in regulation of TNF-alpha induced NF-kappa-B activation and apoptosis. Involved in modulation of 'Lys-48'- linked polyubiquitination status of TRAF2 and decreases association of TRAF2 with RIPK1. Required for PTS1 target sequence-dependent protein import into peroxisomes and PEX5 stability; may cooperate with PEX6. In vitro involved in PEX5 export from the cytosol to peroxisomes (By similarity). {ECO:0000250, ECO:0000269|PubMed:19285159, ECO:0000269|PubMed:21810480}.;
- Pathway
- Metabolism of proteins;Peroxisomal protein import
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.306
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.26
Haploinsufficiency Scores
- pHI
- 0.597
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.761
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zfand6
- Phenotype
Gene ontology
- Biological process
- protein targeting to peroxisome;apoptotic process;negative regulation of apoptotic process;regulation of I-kappaB kinase/NF-kappaB signaling;cellular response to tumor necrosis factor
- Cellular component
- cellular_component;cytosol
- Molecular function
- molecular_function;DNA binding;protein binding;zinc ion binding;polyubiquitin modification-dependent protein binding