BAG4
Basic information
Region (hg38): 8:38176533-38213301
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (60 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAG4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004874.4. 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 | 2 | |||||
| missense | 60 | 62 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 62 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BAG4 | protein_coding | protein_coding | ENST00000287322 | 5 | 36769 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000187 | 0.995 | 125605 | 0 | 143 | 125748 | 0.000569 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.105 | 258 | 253 | 1.02 | 0.0000129 | 2880 |
| Missense in Polyphen | 60 | 71.285 | 0.84169 | 920 | ||
| Synonymous | 1.62 | 77 | 97.3 | 0.791 | 0.00000507 | 953 |
| Loss of Function | 2.47 | 10 | 22.7 | 0.440 | 0.00000107 | 263 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000393 | 0.000393 |
| Ashkenazi Jewish | 0.0102 | 0.0103 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000169 | 0.000167 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000984 | 0.000978 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release (By similarity). Prevents constitutive TNFRSF1A signaling. Negative regulator of PRKN translocation to damaged mitochondria. {ECO:0000250, ECO:0000269|PubMed:24270810}.;
- Pathway
- TNF signaling pathway - Homo sapiens (human);Oxidative Damage;Disease;Signal Transduction;tnfr1 signaling pathway;hiv-1 nef: negative effector of fas and tnf;tnf/stress related signaling;Regulation of HSF1-mediated heat shock response;Cellular responses to stress;ceramide signaling pathway;Cellular responses to external stimuli;TNF signaling;sodd/tnfr1 signaling pathway;Cellular response to heat stress;Death Receptor Signalling;Signaling by FGFR in disease;Signaling by plasma membrane FGFR1 fusions;TNFalpha;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;HIV-1 Nef: Negative effector of Fas and TNF-alpha;TNF receptor signaling pathway ;Diseases of signal transduction;Ceramide signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.153
Intolerance Scores
- loftool
- 0.396
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.01
Haploinsufficiency Scores
- pHI
- 0.259
- hipred
- Y
- hipred_score
- 0.664
- ghis
- 0.593
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bag4
- Phenotype
- normal phenotype; hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- protein folding;positive regulation of fibroblast migration;positive regulation of actin filament polymerization;positive regulation of peptidyl-serine phosphorylation;tumor necrosis factor-mediated signaling pathway;negative regulation of apoptotic process;positive regulation of cell adhesion;positive regulation of stress fiber assembly;positive regulation of protein kinase B signaling;cellular response to tumor necrosis factor;cellular response to epidermal growth factor stimulus;protein localization to plasma membrane;ruffle assembly;regulation of cellular response to heat;negative regulation of protein targeting to mitochondrion;negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity
- Cellular component
- nucleus;cytosol;plasma membrane
- Molecular function
- adenyl-nucleotide exchange factor activity;RNA binding;protein binding;ubiquitin protein ligase binding;chaperone binding