PIGH

phosphatidylinositol glycan anchor biosynthesis class H, the group of Phosphatidylinositol glycan anchor biosynthesis|Glycosylphosphatidylinositol-N-acetylglucosaminyltransferase complex

Basic information

Region (hg38): 14:67581955-67600286

Links

ENSG00000100564

∙ NCBI:5283 ∙ OMIM:600154 ∙ HGNC:8964 ∙ Uniprot:Q14442 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

glycosylphosphatidylinositol biosynthesis defect 17 (Strong), mode of inheritance: AR
glycosylphosphatidylinositol biosynthesis defect 17 (Strong), mode of inheritance: AR
glycosylphosphatidylinositol biosynthesis defect 17 (Limited), mode of inheritance: AR
glycosylphosphatidylinositol biosynthesis defect 17 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Glycosylphosphatidylinositol biosynthesis defect 17	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	Biochemical; Musculoskeletal; Neurologic	29573052; 29603516; 33156547; 35445667

ClinVar

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

Inborn_genetic_diseases (26 variants)
PIGH-related_disorder (6 variants)
not_provided (3 variants)
Glycosylphosphatidylinositol_biosynthesis_defect_17 (3 variants)
Prostate_cancer (1 variants)
not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGH gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004569.5. 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				2 clinvar	2 clinvar	4
missense	1 clinvar	1 clinvar	26 clinvar			28
nonsense						0
start loss	1					1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	1	26	2	2

Highest pathogenic variant AF is 0.000034087938

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIGH	protein_coding	protein_coding	ENST00000216452	4	18333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.231	0.739	125719	0	12	125731	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.948	69	95.0	0.726	0.00000441	1200
Missense in Polyphen		20	25.009	0.79972		317
Synonymous	1.73	25	38.7	0.646	0.00000179	376
Loss of Function	1.81	2	7.26	0.276	3.07e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000118	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000812	0.0000791
Middle Eastern	0.000118	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Part of the complex catalyzing the transfer of N- acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.;
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;Phosphatidylinositol phosphate metabolism (Consensus)

Recessive Scores

pRec: 0.125

Intolerance Scores

loftool: 0.392
rvis_EVS: -0.23
rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

pHI: 0.252
hipred: N
hipred_score: 0.336
ghis: 0.608

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.571

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Pigh
Phenotype: homeostasis/metabolism 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: cellular protein modification process;GPI anchor biosynthetic process;preassembly of GPI anchor in ER membrane
Cellular component: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex;endoplasmic reticulum;endoplasmic reticulum membrane
Molecular function: catalytic activity;phosphatidylinositol N-acetylglucosaminyltransferase activity