PIGY

Chr 4AR

phosphatidylinositol glycan anchor biosynthesis class Y

Also known as: HPMRS6, PIG-Y

The protein encoded by this gene is part of the GPI-N-acetylglucosaminyltransferase (GIP-GnT) complex which initiates the biosynthesis of glycosylphosphatidylinositol (GPI). GPI is synthesized in the endoplasmic reticulum and serves as an anchor for many surface proteins. Proteins containing GPI anchors can have an important role in cell-cell interactions. The transcript for this gene is bicistronic. The downstream open reading frame encodes this GPI-GnT complex protein, while the upstream open reading frame encodes a protein with unknown function, as represented by GeneID:100996939. [provided by RefSeq, Aug 2012]

OMIMResearchGenerating clinical summary…
MultiplemechanismARLOEUF 1.881 OMIM phenotype
Clinical SummaryPIGY
🧬
Gene-Disease Validity (ClinGen)
hyperphosphatasia with intellectual disability syndrome 6 · ARLimited

Limited evidence — not for standalone diagnostic reporting

Population Constraint (gnomAD)
Low constraint (pLI 0.10) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
3 unique Pathogenic / Likely Pathogenic· 12 VUS of 22 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
1.88LOEUF
pLI 0.097
Z-score 0.11
OE 0.89 (0.251.88)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
-0.32Z-score
OE missense 1.15 (0.901.49)
41 obs / 35.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.89 (0.251.88)
00.351.4
Missense OE?1.15 (0.901.49)
00.61.4
Synonymous OE?0.83
01.21.6
LoF obs/exp: 1 / 1.1Missense obs/exp: 41 / 35.6Syn Z: 0.52
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongPIGY-related glycosylphosphatidylinositol deficiencyOTHERAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6454th %ile
GOF
0.82top 10%
LOF
0.2969th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

22 submitted variants in ClinVar

Classification Summary

Pathogenic3
VUS12
Likely Benign4
Benign3
3
Pathogenic
12
VUS
4
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
1
1
0
3
Likely Pathogenic
0
0
0
0
0
VUS
0
12
0
0
12
Likely Benign
0
2
0
2
4
Benign
0
0
2
1
3
Total1153322

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

26 pathogenic / likely-pathogenic (of 26) ClinVar copy-number / structural variants overlap PIGY — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

PIGY · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →