FAF1
Basic information
Region (hg38): 1:50437028-50960267
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 FAF1 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 | 26 | 26 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 26 | 0 | 0 |
Variants in FAF1
This is a list of pathogenic ClinVar variants found in the FAF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-50475675-A-G | not specified | Uncertain significance (Feb 16, 2023) | ||
1-50490593-G-A | not specified | Uncertain significance (May 23, 2024) | ||
1-50491713-A-C | Benign (Mar 29, 2018) | |||
1-50535413-T-C | not specified | Uncertain significance (Jun 17, 2024) | ||
1-50535437-A-T | not specified | Uncertain significance (Jun 17, 2024) | ||
1-50535451-G-A | not specified | Uncertain significance (Mar 25, 2024) | ||
1-50539663-G-A | not specified | Uncertain significance (Jun 27, 2022) | ||
1-50539676-G-A | not specified | Uncertain significance (Feb 26, 2024) | ||
1-50567089-G-T | not specified | Uncertain significance (Jul 14, 2022) | ||
1-50567114-A-C | not specified | Uncertain significance (Nov 08, 2024) | ||
1-50567147-T-C | not specified | Uncertain significance (Dec 04, 2024) | ||
1-50567196-T-G | not specified | Uncertain significance (Aug 11, 2022) | ||
1-50567216-T-C | not specified | Uncertain significance (Dec 21, 2022) | ||
1-50582622-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
1-50582648-A-T | not specified | Uncertain significance (Jul 15, 2021) | ||
1-50583701-C-T | not specified | Uncertain significance (Sep 24, 2024) | ||
1-50584688-T-A | not specified | Uncertain significance (Dec 20, 2023) | ||
1-50584706-C-A | not specified | Uncertain significance (Sep 20, 2023) | ||
1-50584711-G-A | not specified | Uncertain significance (Jun 12, 2023) | ||
1-50584742-C-G | not specified | Uncertain significance (Dec 13, 2023) | ||
1-50584800-A-T | not specified | Uncertain significance (Jan 02, 2024) | ||
1-50596142-C-G | not specified | Uncertain significance (Aug 11, 2022) | ||
1-50596156-A-G | not specified | Uncertain significance (Dec 02, 2021) | ||
1-50596206-G-C | not specified | Uncertain significance (Apr 14, 2022) | ||
1-50596215-A-G | not specified | Uncertain significance (Jun 17, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FAF1 | protein_coding | protein_coding | ENST00000396153 | 19 | 520786 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.999 | 0.00105 | 125740 | 0 | 7 | 125747 | 0.0000278 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.13 | 246 | 359 | 0.684 | 0.0000195 | 4273 |
Missense in Polyphen | 45 | 95.515 | 0.47113 | 1074 | ||
Synonymous | 1.27 | 107 | 125 | 0.855 | 0.00000669 | 1202 |
Loss of Function | 5.29 | 5 | 41.9 | 0.119 | 0.00000227 | 480 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.000199 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000931 | 0.0000924 |
European (Non-Finnish) | 0.0000267 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-binding protein (PubMed:19722279). Required for the progression of DNA replication forks by targeting DNA replication licensing factor CDT1 for degradation (PubMed:26842564). Potentiates but cannot initiate FAS-induced apoptosis (By similarity). {ECO:0000250|UniProtKB:P54731, ECO:0000269|PubMed:19722279, ECO:0000269|PubMed:26842564}.;
- Pathway
- Necroptosis - Homo sapiens (human);Retinoblastoma (RB) in Cancer;Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;VEGFA-VEGFR2 Signaling Pathway;fas signaling pathway (cd95);TNFalpha
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.189
- rvis_EVS
- -0.42
- rvis_percentile_EVS
- 25.56
Haploinsufficiency Scores
- pHI
- 0.400
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.621
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Faf1
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- faf1
- Affected structure
- ceratobranchial cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- apoptotic process;cytoplasmic sequestering of NF-kappaB;cell death;positive regulation of cell death;regulation of cell adhesion;positive regulation of protein complex assembly;regulation of protein catabolic process;positive regulation of apoptotic process;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of DNA replication;regulation of protein kinase activity;positive regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of cellular protein catabolic process
- Cellular component
- nucleus;nuclear envelope;cytosol;CD95 death-inducing signaling complex;VCP-NPL4-UFD1 AAA ATPase complex;perinuclear region of cytoplasm
- Molecular function
- protein binding;protein kinase regulator activity;protein kinase binding;protein domain specific binding;heat shock protein binding;ubiquitin protein ligase binding;ubiquitin binding;NF-kappaB binding