FGGY
Basic information
Region (hg38): 1:59296638-59810647
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 FGGY 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 | 36 | 38 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 37 | 2 | 0 |
Variants in FGGY
This is a list of pathogenic ClinVar variants found in the FGGY region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-59321589-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
1-59321617-G-A | not specified | Uncertain significance (Oct 28, 2023) | ||
1-59321662-A-G | not specified | Uncertain significance (Jan 23, 2024) | ||
1-59321712-T-C | not specified | Uncertain significance (Feb 27, 2023) | ||
1-59340039-C-G | not specified | Uncertain significance (Aug 02, 2021) | ||
1-59340041-G-C | not specified | Uncertain significance (Oct 20, 2023) | ||
1-59340048-C-A | not specified | Uncertain significance (Feb 03, 2022) | ||
1-59346247-G-A | not specified | Likely benign (Dec 08, 2023) | ||
1-59346256-A-G | not specified | Uncertain significance (Dec 19, 2022) | ||
1-59346346-G-T | not specified | Uncertain significance (Apr 01, 2024) | ||
1-59346396-G-A | not specified | Uncertain significance (Jan 10, 2022) | ||
1-59346397-A-G | not specified | Uncertain significance (Jun 23, 2023) | ||
1-59378777-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
1-59378809-T-C | not specified | Uncertain significance (Jul 06, 2022) | ||
1-59378831-C-G | not specified | Uncertain significance (May 18, 2022) | ||
1-59457019-A-T | not specified | Uncertain significance (Oct 06, 2021) | ||
1-59457020-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
1-59457044-A-G | not specified | Uncertain significance (Jan 23, 2024) | ||
1-59512350-G-A | not specified | Uncertain significance (Apr 06, 2023) | ||
1-59512377-T-C | not specified | Uncertain significance (Jan 29, 2024) | ||
1-59512392-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
1-59512398-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
1-59554153-G-A | not specified | Uncertain significance (Jul 20, 2022) | ||
1-59554187-G-A | not specified | Uncertain significance (Jun 10, 2022) | ||
1-59554222-A-T | not specified | Uncertain significance (Feb 16, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FGGY | protein_coding | protein_coding | ENST00000371218 | 16 | 471038 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.19e-18 | 0.0174 | 124906 | 3 | 839 | 125748 | 0.00335 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.116 | 331 | 325 | 1.02 | 0.0000173 | 3738 |
Missense in Polyphen | 136 | 134.43 | 1.0117 | 1510 | ||
Synonymous | -0.670 | 137 | 127 | 1.08 | 0.00000773 | 1131 |
Loss of Function | 0.574 | 29 | 32.5 | 0.891 | 0.00000158 | 374 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00455 | 0.00454 |
Ashkenazi Jewish | 0.000397 | 0.000397 |
East Asian | 0.000382 | 0.000326 |
Finnish | 0.00462 | 0.00463 |
European (Non-Finnish) | 0.00485 | 0.00484 |
Middle Eastern | 0.000382 | 0.000326 |
South Asian | 0.000981 | 0.000948 |
Other | 0.00376 | 0.00375 |
dbNSFP
Source:
- Disease
- DISEASE: Amyotrophic lateral sclerosis (ALS) [MIM:105400]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5- 10% of the cases. {ECO:0000269|PubMed:17671248}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.141
Intolerance Scores
- loftool
- 0.301
- rvis_EVS
- 0.34
- rvis_percentile_EVS
- 73.7
Haploinsufficiency Scores
- pHI
- 0.105
- hipred
- N
- hipred_score
- 0.216
- ghis
- 0.454
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.158
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fggy
- Phenotype
Gene ontology
- Biological process
- pentose metabolic process;carbohydrate phosphorylation;neuron cellular homeostasis
- Cellular component
- cellular_component;cell
- Molecular function
- D-ribulokinase activity