FAF2
Basic information
Region (hg38): 5:176447627-176510074
Previous symbols: [ "UBXD8" ]
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 FAF2 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in FAF2
This is a list of pathogenic ClinVar variants found in the FAF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-176486427-C-G | not specified | Uncertain significance (Apr 12, 2023) | ||
| 5-176489006-A-C | not specified | Uncertain significance (Mar 20, 2024) | ||
| 5-176492201-C-G | not specified | Uncertain significance (Jun 27, 2023) | ||
| 5-176492204-C-T | not specified | Uncertain significance (Mar 14, 2023) | ||
| 5-176492261-T-C | not specified | Uncertain significance (Nov 17, 2022) | ||
| 5-176492281-A-T | not specified | Uncertain significance (Oct 22, 2021) | ||
| 5-176492321-A-G | not specified | Uncertain significance (Nov 01, 2021) | ||
| 5-176494006-A-G | not specified | Uncertain significance (Dec 28, 2022) | ||
| 5-176494230-A-G | not specified | Uncertain significance (Oct 05, 2021) | ||
| 5-176496513-A-G | not specified | Uncertain significance (Feb 17, 2024) | ||
| 5-176496546-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 5-176496635-A-G | not specified | Uncertain significance (Nov 03, 2023) | ||
| 5-176496648-C-T | not specified | Uncertain significance (Dec 06, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FAF2 | protein_coding | protein_coding | ENST00000261942 | 11 | 62447 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000886 | 125734 | 0 | 2 | 125736 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.52 | 144 | 258 | 0.558 | 0.0000150 | 2910 |
| Missense in Polyphen | 30 | 67.732 | 0.44292 | 699 | ||
| Synonymous | 0.390 | 86 | 90.7 | 0.948 | 0.00000468 | 837 |
| Loss of Function | 4.66 | 2 | 29.2 | 0.0686 | 0.00000173 | 303 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays an important role in endoplasmic reticulum- associated degradation (ERAD) that mediates ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:18711132, PubMed:24215460). By controlling the steady- state expression of the IGF1R receptor, indirectly regulates the insulin-like growth factor receptor signaling pathway (PubMed:26692333). Involved in inhibition of lipid droplet degradation by binding to phospholipase PNPL2 and inhibiting its activity by promoting dissociation of PNPL2 from its endogenous activator, ABHD5 which inhibits the rate of triacylglycerol hydrolysis (PubMed:23297223). {ECO:0000269|PubMed:18711132, ECO:0000269|PubMed:23297223, ECO:0000269|PubMed:24215460, ECO:0000269|PubMed:26692333}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- loftool
- 0.210
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.567
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.666
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.911
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Faf2
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; liver/biliary system phenotype;
Gene ontology
- Biological process
- response to unfolded protein;ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;lipid droplet organization;negative regulation of catalytic activity;neutrophil degranulation
- Cellular component
- extracellular region;endoplasmic reticulum;lipid droplet;VCP-NPL4-UFD1 AAA ATPase complex;azurophil granule lumen
- Molecular function
- protein binding;ubiquitin protein ligase binding;lipase binding;ubiquitin binding;lipase inhibitor activity