PIGW
Basic information
Region (hg38): 17:36534987-36539310
Links
Phenotypes
GenCC
Source:
- hyperphosphatasia with intellectual disability syndrome 5 (Limited), mode of inheritance: AR
- hyperphosphatasia with intellectual disability syndrome 5 (Strong), mode of inheritance: AR
- hyperphosphatasia with intellectual disability syndrome 5 (Moderate), mode of inheritance: AR
- hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency (Supportive), mode of inheritance: AR
- hyperphosphatasia-intellectual disability syndrome (Supportive), mode of inheritance: AR
- hyperphosphatasia with intellectual disability syndrome 5 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Glycosylphosphatidylinositol biosynthesis defect 11 | 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; Gastrointestinal; Neurologic | 24367057 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
- Hyperphosphatasia with intellectual disability syndrome 5 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGW 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 | 81 | 83 | ||||
missense | 155 | 163 | ||||
nonsense | 8 | |||||
start loss | 0 | |||||
frameshift | 15 | 16 | ||||
inframe indel | 6 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 1 | 1 | 184 | 85 | 5 |
Highest pathogenic variant AF is 0.0000197
Variants in PIGW
This is a list of pathogenic ClinVar variants found in the PIGW region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-36536882-A-A | Benign (Jul 27, 2018) | |||
17-36537106-C-A | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (Nov 03, 2022) | ||
17-36537108-G-A | Inborn genetic diseases | Uncertain significance (Mar 20, 2023) | ||
17-36537113-G-A | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Oct 16, 2023) | ||
17-36537116-G-C | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (Jul 21, 2023) | ||
17-36537116-G-T | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (Aug 04, 2023) | ||
17-36537122-G-A | Hyperphosphatasia with intellectual disability syndrome 5 | Benign (Jul 31, 2023) | ||
17-36537135-A-G | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (May 22, 2022) | ||
17-36537155-C-G | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Jun 13, 2022) | ||
17-36537155-C-T | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Jun 23, 2023) | ||
17-36537156-G-A | Hyperphosphatasia with intellectual disability syndrome 5 • Inborn genetic diseases | Uncertain significance (Dec 18, 2023) | ||
17-36537159-C-T | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Sep 03, 2021) | ||
17-36537170-C-T | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Feb 24, 2022) | ||
17-36537175-G-A | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (Oct 07, 2021) | ||
17-36537178-T-C | Hyperphosphatasia with intellectual disability syndrome 5 | Pathogenic (Sep 08, 2022) | ||
17-36537201-C-T | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (May 31, 2022) | ||
17-36537203-G-A | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Jun 11, 2022) | ||
17-36537206-C-CA | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (Apr 13, 2022) | ||
17-36537207-A-G | Hyperphosphatasia with intellectual disability syndrome 5 • Inborn genetic diseases | Conflicting classifications of pathogenicity (Apr 01, 2023) | ||
17-36537217-T-C | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (Jul 05, 2022) | ||
17-36537226-T-G | Inborn genetic diseases | Uncertain significance (May 03, 2023) | ||
17-36537233-G-A | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Jun 25, 2023) | ||
17-36537234-TAC-T | Hyperphosphatasia with intellectual disability syndrome 5 | Uncertain significance (Oct 25, 2022) | ||
17-36537245-T-C | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Apr 09, 2023) | ||
17-36537248-T-C | Hyperphosphatasia with intellectual disability syndrome 5 | Likely benign (Feb 19, 2022) |
GnomAD
Source:
dbNSFP
Source:
- Function
- FUNCTION: Required for the transport of GPI-anchored proteins to the plasma membrane (PubMed:24367057). Probable acetyltransferase, which acetylates the inositol ring of phosphatidylinositol during biosynthesis of GPI-anchor. Acetylation during GPI-anchor biosynthesis is not essential for the subsequent mannosylation and is usually removed soon after the attachment of GPIs to proteins (By similarity). {ECO:0000250|UniProtKB:Q7TSN4, ECO:0000269|PubMed:24367057}.;
- Disease
- DISEASE: Glycosylphosphatidylinositol biosynthesis defect 11 (GPIBD11) [MIM:616025]: An autosomal recessive neurologic disorder characterized by developmental delay, mental retardation, tonic seizures associated with hypsarrhythmia, dysmorphic facial features, and elevated serum alkaline phosphatase. {ECO:0000269|PubMed:24367057}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Homo sapiens (human);Synthesis of glycosylphosphatidylinositol (GPI);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins
(Consensus)
Recessive Scores
- pRec
- 0.0819
Intolerance Scores
- loftool
- 0.297
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.92
Haploinsufficiency Scores
- pHI
- 0.344
- hipred
- N
- hipred_score
- 0.144
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.442
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pigw
- Phenotype
Gene ontology
- Biological process
- GPI anchor metabolic process;GPI anchor biosynthetic process;preassembly of GPI anchor in ER membrane;protein localization to plasma membrane
- Cellular component
- endoplasmic reticulum membrane;integral component of membrane
- Molecular function
- O-acyltransferase activity;glucosaminyl-phosphotidylinositol O-acyltransferase activity