PIGW

phosphatidylinositol glycan anchor biosynthesis class W, the group of Phosphatidylinositol glycan anchor biosynthesis

Basic information

Region (hg38): 17:36534987-36539310

Links

ENSG00000277161NCBI:284098OMIM:610275HGNC:23213Uniprot:Q7Z7B1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Glycosylphosphatidylinositol biosynthesis defect 11ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Gastrointestinal; Neurologic24367057

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PIGW gene.

  • 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
clinvar
2
clinvar
83
missense
1
clinvar
155
clinvar
4
clinvar
3
clinvar
163
nonsense
8
clinvar
8
start loss
0
frameshift
1
clinvar
15
clinvar
16
inframe indel
6
clinvar
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)1293105
17-36537106-C-A Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (Nov 03, 2022)2782353
17-36537108-G-A Inborn genetic diseases Uncertain significance (Mar 20, 2023)2509915
17-36537113-G-A Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Oct 16, 2023)2731652
17-36537116-G-C Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (Jul 21, 2023)2042973
17-36537116-G-T Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (Aug 04, 2023)2012882
17-36537122-G-A Hyperphosphatasia with intellectual disability syndrome 5 Benign (Jul 31, 2023)2067972
17-36537135-A-G Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (May 22, 2022)576705
17-36537155-C-G Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Jun 13, 2022)793929
17-36537155-C-T Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Jun 23, 2023)1099021
17-36537156-G-A Hyperphosphatasia with intellectual disability syndrome 5 • Inborn genetic diseases Uncertain significance (Dec 18, 2023)2147486
17-36537159-C-T Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Sep 03, 2021)1661355
17-36537170-C-T Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Feb 24, 2022)1593996
17-36537175-G-A Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (Oct 07, 2021)1385052
17-36537178-T-C Hyperphosphatasia with intellectual disability syndrome 5 Pathogenic (Sep 08, 2022)1704328
17-36537201-C-T Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (May 31, 2022)739142
17-36537203-G-A Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Jun 11, 2022)2124336
17-36537206-C-CA Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (Apr 13, 2022)2126010
17-36537207-A-G Hyperphosphatasia with intellectual disability syndrome 5 • Inborn genetic diseases Conflicting classifications of pathogenicity (Apr 01, 2023)452328
17-36537217-T-C Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (Jul 05, 2022)2040846
17-36537226-T-G Inborn genetic diseases Uncertain significance (May 03, 2023)2542541
17-36537233-G-A Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Jun 25, 2023)2790912
17-36537234-TAC-T Hyperphosphatasia with intellectual disability syndrome 5 Uncertain significance (Oct 25, 2022)1360698
17-36537245-T-C Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Apr 09, 2023)2880761
17-36537248-T-C Hyperphosphatasia with intellectual disability syndrome 5 Likely benign (Feb 19, 2022)2099691

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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