PIGF
Basic information
Region (hg38): 2:46580936-46617055
Links
Phenotypes
GenCC
Source:
- onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome | AR | 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 | Craniofacial; Musculoskeletal; Neurologic | 33386993 |
ClinVar
This is a list of variants' phenotypes submitted to
- Short stature with microcephaly and distinctive facies (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGF 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 | 15 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 4 | |||||
| Total | 0 | 0 | 18 | 1 | 2 |
Variants in PIGF
This is a list of pathogenic ClinVar variants found in the PIGF 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 |
|---|---|---|---|---|---|
| PIGF | protein_coding | protein_coding | ENST00000281382 | 5 | 36183 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000720 | 0.772 | 125696 | 0 | 27 | 125723 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.555 | 115 | 99.4 | 1.16 | 0.00000455 | 1382 |
| Missense in Polyphen | 33 | 29.39 | 1.1228 | 414 | ||
| Synonymous | -0.0485 | 39 | 38.6 | 1.01 | 0.00000200 | 424 |
| Loss of Function | 1.02 | 6 | 9.35 | 0.642 | 3.93e-7 | 139 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000447 | 0.000447 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000970 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in GPI-anchor biosynthesis through the transfer of ethanolamine phosphate to the third mannose of GPI. {ECO:0000250}.;
- Pathway
- Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Homo sapiens (human);VEGF Signaling Pathway;Exercise-induced Circadian Regulation;Synthesis of glycosylphosphatidylinositol (GPI);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Phosphatidylinositol phosphate metabolism
(Consensus)
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.250
- rvis_EVS
- 0.33
- rvis_percentile_EVS
- 73.27
Haploinsufficiency Scores
- pHI
- 0.647
- hipred
- N
- hipred_score
- 0.216
- ghis
- 0.511
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0482
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pigf
- Phenotype
- 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); skeleton phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- GPI anchor biosynthetic process;preassembly of GPI anchor in ER membrane
- Cellular component
- endoplasmic reticulum membrane;integral component of membrane
- Molecular function
- ethanolaminephosphotransferase activity