PIGW

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

Basic information

Region (hg38): 17:36534987-36539310

Links

ENSG00000277161

∙ NCBI:284098 ∙ OMIM:610275 ∙ HGNC:23213 ∙ Uniprot:Q7Z7B1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 ClinVar and linked to the PIGW gene.

Hyperphosphatasia_with_intellectual_disability_syndrome_5 (276 variants)
Inborn_genetic_diseases (62 variants)
not_provided (28 variants)
not_specified (7 variants)
PIGW-related_disorder (2 variants)
Hypercoagulability_syndrome_due_to_glycosylphosphatidylinositol_deficiency (1 variants)
Abnormal_skeletal_morphology (1 variants)
Cleft_palate (1 variants)
Global_developmental_delay (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. These statistics are base on transcript: NM_001346754.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				93 clinvar	2 clinvar	95
missense	5 clinvar		170 clinvar	8 clinvar	1 clinvar	184
nonsense		2 clinvar	9 clinvar			11
start loss						0
frameshift		2 clinvar	19 clinvar			21
splice donor/acceptor (+/-2bp)						0
Total	5	4	198	101	3

Highest pathogenic variant AF is 0.000194528

Loading clinvar variants...

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

	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