FDPS
farnesyl diphosphate synthase
Basic information
Region (hg38): 1:155308747-155320666
Links
Phenotypes
GenCC
Source:
- disseminated superficial actinic porokeratosis (Supportive), mode of inheritance: AD
- porokeratosis 9, multiple types (Strong), mode of inheritance: AD
- porokeratosis 9, multiple types (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Porokeratosis 9, multiple types | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Dermatologic | 26202976 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (10 variants)
- not provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FDPS 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 | 1 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 1 | 10 | 1 | 0 |
Highest pathogenic variant AF is 0.0000395
Variants in FDPS
This is a list of pathogenic ClinVar variants found in the FDPS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FDPS | protein_coding | protein_coding | ENST00000356657 | 10 | 11919 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00562 | 0.993 | 125728 | 0 | 20 | 125748 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.09 | 193 | 241 | 0.802 | 0.0000138 | 2703 |
| Missense in Polyphen | 38 | 56.064 | 0.6778 | 764 | ||
| Synonymous | 1.92 | 73 | 97.0 | 0.752 | 0.00000540 | 824 |
| Loss of Function | 2.90 | 8 | 23.0 | 0.348 | 0.00000102 | 252 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000202 | 0.000202 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.;
- Disease
- DISEASE: Porokeratosis 9, multiple types (POROK9) [MIM:616631]: A form of porokeratosis, a disorder of faulty keratinization characterized by one or more atrophic patches surrounded by a distinctive hyperkeratotic ridgelike border called the cornoid lamella. The keratotic lesions can progress to overt cutaneous neoplasms, typically squamous cell carcinomas. Multiple clinical variants of porokeratosis are recognized, including porokeratosis of Mibelli, linear porokeratosis, disseminated superficial actinic porokeratosis, palmoplantar porokeratosis, and punctate porokeratosis. Different clinical presentations can be observed among members of the same family. Individuals expressing more than one variant have also been reported. {ECO:0000269|PubMed:26202976}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Mevalonate pathway;Influenza A - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Terpenoid backbone biosynthesis - Homo sapiens (human);Bisphosphonate Pathway, Pharmacodynamics;Simvastatin Action Pathway;Pravastatin Action Pathway;Atorvastatin Action Pathway;Hyper-IgD syndrome;Cholesteryl ester storage disease;Lysosomal Acid Lipase Deficiency (Wolman Disease);Alendronate Action Pathway;Rosuvastatin Action Pathway;Lovastatin Action Pathway;Mevalonic aciduria;Wolman disease;Risedronate Action Pathway;Cerivastatin Action Pathway;Pamidronate Action Pathway;Fluvastatin Action Pathway;Smith-Lemli-Opitz Syndrome (SLOS);Chondrodysplasia Punctata II, X Linked Dominant (CDPX2);CHILD Syndrome;Desmosterolosis;Hypercholesterolemia;Steroid Biosynthesis;Zoledronate Action Pathway;Ibandronate Action Pathway;Cholesterol Biosynthesis;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Activation of gene expression by SREBF (SREBP);Metabolism of lipids;Regulation of cholesterol biosynthesis by SREBP (SREBF);<i>trans, trans</i>-farnesyl diphosphate biosynthesis;Metabolism;superpathway of cholesterol biosynthesis;Metabolism of steroids;Steroids metabolism;Cholesterol biosynthesis;Activation of gene expression by SREBF (SREBP);superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)
(Consensus)
Recessive Scores
- pRec
- 0.351
Intolerance Scores
- loftool
- 0.943
- rvis_EVS
- 0.57
- rvis_percentile_EVS
- 81.99
Haploinsufficiency Scores
- pHI
- 0.176
- hipred
- N
- hipred_score
- 0.172
- ghis
- 0.450
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fdps
- Phenotype
Gene ontology
- Biological process
- cholesterol biosynthetic process;viral process;geranyl diphosphate biosynthetic process;farnesyl diphosphate biosynthetic process;regulation of cholesterol biosynthetic process
- Cellular component
- nucleoplasm;cytoplasm;cytosol
- Molecular function
- RNA binding;dimethylallyltranstransferase activity;geranyltranstransferase activity;metal ion binding