PIGP

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

Basic information

Region (hg38): 21:37062846-37073170

Previous symbols: [ "DSCR5" ]

Links

ENSG00000185808

∙ NCBI:51227 ∙ OMIM:605938 ∙ HGNC:3046 ∙ Uniprot:P57054 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

developmental and epileptic encephalopathy, 55 (Strong), mode of inheritance: AR
developmental and epileptic encephalopathy, 55 (Moderate), mode of inheritance: AR
genetic developmental and epileptic encephalopathy (Supportive), mode of inheritance: AD
developmental and epileptic encephalopathy, 55 (Strong), mode of inheritance: AR
multiple congenital anomalies-hypotonia-seizures syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 55	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	Neurologic	28334793

ClinVar

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

not_provided (129 variants)
Inborn_genetic_diseases (25 variants)
Developmental_and_epileptic_encephalopathy,_55 (5 variants)
PIGP-related_disorder (5 variants)
Developmental_and_epileptic_encephalopathy (2 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153682.3. 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				26 clinvar	1 clinvar	27
missense			48 clinvar		4 clinvar	52
nonsense			5 clinvar			5
start loss		1				1
frameshift		2 clinvar	2 clinvar			4
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	3	57	26	5

Highest pathogenic variant AF is 0.00007372813

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIGP	protein_coding	protein_coding	ENST00000464265	4	14001

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00189	0.743	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.558	92	78.1	1.18	0.00000349	1018
Missense in Polyphen		10	16.714	0.59829		241
Synonymous	-1.03	38	30.7	1.24	0.00000150	298
Loss of Function	0.882	5	7.63	0.655	3.22e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000233
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000598	0.000598
South Asian	0.000458	0.000457
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. {ECO:0000269|PubMed:10944123, ECO:0000269|PubMed:28334793}.;
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: 0.124

Intolerance Scores

loftool: 0.941
rvis_EVS: 0.55
rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

pHI: 0.125
hipred: N
hipred_score: 0.216
ghis: 0.447

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.671

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pigp
Phenotype

Zebrafish Information Network

Gene name: pigp
Affected structure: caudal fin
Phenotype tag: abnormal
Phenotype quality: folded

Gene ontology

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