FBP1
Basic information
Region (hg38): 9:94603133-94640249
Previous symbols: [ "FBP" ]
Links
Phenotypes
GenCC
Source:
- fructose-1,6-bisphosphatase deficiency (Definitive), mode of inheritance: AR
- fructose-1,6-bisphosphatase deficiency (Strong), mode of inheritance: AR
- fructose-1,6-bisphosphatase deficiency (Strong), mode of inheritance: AR
- fructose-1,6-bisphosphatase deficiency (Strong), mode of inheritance: AR
- fructose-1,6-bisphosphatase deficiency (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Fructose-1,6-bisphosphatase deficiency | AR | Biochemical | The condition may be lethal in the perinatal period, but prompt recognition and treatment of lactic acidosis and hypoglycemia (eg, with IV/oral glucose, sodium bicarbonate) can be effective | Biochemical | 4193749; 4335192; 4341454; 4341015; 175754; 2347355; 1995492; 9382095; 12126934; 17705024; 19259699; 20096900; 22158280 |
ClinVar
This is a list of variants' phenotypes submitted to
- Fructose-biphosphatase deficiency (26 variants)
- not provided (3 variants)
- FBP1-related disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBP1 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 | 97 | 100 | ||||
missense | 10 | 42 | 60 | |||
nonsense | 8 | |||||
start loss | 1 | |||||
frameshift | 14 | 18 | ||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
splice region | 1 | 3 | 14 | 1 | 19 | |
non coding | 40 | 11 | 59 | |||
Total | 27 | 16 | 51 | 141 | 16 |
Highest pathogenic variant AF is 0.0000197
Variants in FBP1
This is a list of pathogenic ClinVar variants found in the FBP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-94603229-G-A | Fructose-biphosphatase deficiency | Uncertain significance (Jan 13, 2018) | ||
9-94603254-G-A | Fructose-biphosphatase deficiency | Uncertain significance (Jan 13, 2018) | ||
9-94603260-A-C | Fructose-biphosphatase deficiency | Conflicting classifications of pathogenicity (Oct 27, 2020) | ||
9-94603360-G-A | not specified • Fructose-biphosphatase deficiency | Benign (Aug 10, 2021) | ||
9-94603372-G-T | FBP1-related disorder | Likely benign (May 02, 2024) | ||
9-94603377-G-A | not specified | Likely benign (Apr 04, 2016) | ||
9-94603385-TG-T | Fructose-biphosphatase deficiency | Uncertain significance (Sep 07, 2022) | ||
9-94603389-C-A | Inborn genetic diseases | Uncertain significance (Jul 06, 2021) | ||
9-94603390-A-G | Fructose-biphosphatase deficiency | Likely benign (May 19, 2023) | ||
9-94603401-C-T | Fructose-biphosphatase deficiency | Uncertain significance (Jan 12, 2018) | ||
9-94603412-A-G | Fructose-biphosphatase deficiency | Pathogenic/Likely pathogenic (Dec 06, 2023) | ||
9-94603413-G-T | Fructose-biphosphatase deficiency | Uncertain significance (Feb 05, 2022) | ||
9-94603414-G-A | Fructose-biphosphatase deficiency | Likely benign (Jul 07, 2023) | ||
9-94603417-C-T | Fructose-biphosphatase deficiency | Likely benign (Dec 04, 2023) | ||
9-94603420-G-A | Fructose-biphosphatase deficiency | Likely benign (Oct 19, 2023) | ||
9-94603420-G-C | Fructose-biphosphatase deficiency | Likely benign (Dec 18, 2023) | ||
9-94603421-A-G | Fructose-biphosphatase deficiency | Uncertain significance (Oct 14, 2021) | ||
9-94603422-G-C | not specified | Likely benign (Mar 06, 2014) | ||
9-94603426-G-A | Fructose-biphosphatase deficiency | Likely benign (Jun 03, 2023) | ||
9-94603427-T-C | Fructose-biphosphatase deficiency | Uncertain significance (Dec 27, 2019) | ||
9-94603428-C-T | Fructose-biphosphatase deficiency • not specified | Uncertain significance (Jul 15, 2024) | ||
9-94603429-G-A | Fructose-biphosphatase deficiency | Likely benign (Sep 20, 2023) | ||
9-94603431-CG-C | Fructose-biphosphatase deficiency | Conflicting classifications of pathogenicity (Jan 16, 2024) | ||
9-94603432-G-A | Fructose-biphosphatase deficiency | Likely benign (Dec 26, 2023) | ||
9-94603436-G-A | not specified | Uncertain significance (Jul 17, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FBP1 | protein_coding | protein_coding | ENST00000415431 | 7 | 37117 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0791 | 0.911 | 125738 | 0 | 10 | 125748 | 0.0000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.740 | 170 | 199 | 0.853 | 0.0000110 | 2189 |
Missense in Polyphen | 50 | 73.921 | 0.67639 | 787 | ||
Synonymous | -1.45 | 100 | 83.2 | 1.20 | 0.00000532 | 673 |
Loss of Function | 2.25 | 4 | 12.7 | 0.316 | 5.40e-7 | 174 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000114 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000443 | 0.0000439 |
Middle Eastern | 0.000114 | 0.000109 |
South Asian | 0.000131 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate in the presence of divalent cations, acting as a rate-limiting enzyme in gluconeogenesis. Plays a role in regulating glucose sensing and insulin secretion of pancreatic beta-cells. Appears to modulate glycerol gluconeogenesis in liver. Important regulator of appetite and adiposity; increased expression of the protein in liver after nutrient excess increases circulating satiety hormones and reduces appetite-stimulating neuropeptides and thus seems to provide a feedback mechanism to limit weight gain. {ECO:0000269|PubMed:16497803, ECO:0000269|PubMed:18375435, ECO:0000269|PubMed:22517657}.;
- Disease
- DISEASE: Fructose-1,6-bisphosphatase deficiency (FBP1D) [MIM:229700]: An autosomal recessive metabolic disorder characterized by impaired gluconeogenesis, and episodes of hypoglycemia and metabolic acidosis that can be lethal in newborn infants or young children. {ECO:0000269|PubMed:12126934, ECO:0000269|PubMed:25601412, ECO:0000269|PubMed:9382095}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Glycolysis / Gluconeogenesis - Homo sapiens (human);Fructose and mannose metabolism - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Pentose phosphate pathway - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Pentose Phosphate Pathway;Fructose intolerance, hereditary;Gluconeogenesis;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Glucose-6-phosphate dehydrogenase deficiency;Ribose-5-phosphate isomerase deficiency;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Transaldolase deficiency;Fructose and Mannose Degradation;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Fructosuria;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Glycogenosis, Type IB;Angiopoietin Like Protein 8 Regulatory Pathway;Glycolysis and Gluconeogenesis;Metabolism of carbohydrates;Fructose Mannose metabolism;Glycolysis Gluconeogenesis;Metabolism;Pentose phosphate cycle;gluconeogenesis;Gluconeogenesis;Glucose metabolism
(Consensus)
Recessive Scores
- pRec
- 0.507
Intolerance Scores
- loftool
- 0.460
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.374
- hipred
- Y
- hipred_score
- 0.754
- ghis
- 0.425
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.990
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fbp1
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;sucrose biosynthetic process;fructose metabolic process;fructose 6-phosphate metabolic process;gluconeogenesis;regulation of gluconeogenesis;dephosphorylation;negative regulation of cell growth;fructose 1,6-bisphosphate metabolic process;cellular response to drug;negative regulation of glycolytic process;negative regulation of Ras protein signal transduction;protein homotetramerization;cellular response to magnesium ion
- Cellular component
- nucleus;cytoplasm;cytosol;extracellular exosome
- Molecular function
- protein binding;AMP binding;fructose 1,6-bisphosphate 1-phosphatase activity;identical protein binding;metal ion binding;monosaccharide binding