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
• developmental and epileptic encephalopathy (Supportive), mode of inheritance: AD
• developmental and epileptic encephalopathy, 55 (Strong), 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.

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.

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				29	2	31
missense			52		5	57
nonsense			4			4
start loss		1	3			4
frameshift		1	5			6
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				6	1	7
non coding			2	19	2	23
Total	0	2	67	48	9

Variants in PIGP

This is a list of pathogenic ClinVar variants found in the PIGP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
21-37065602-CT-C		Early infantile epileptic encephalopathy with suppression bursts • Developmental and epileptic encephalopathy, 55	Pathogenic/Likely pathogenic (Nov 27, 2023)
21-37065606-G-A			Likely benign (Dec 13, 2023)
21-37065607-G-A			Uncertain significance (Nov 27, 2023)
21-37065611-C-A		Inborn genetic diseases	Uncertain significance (Mar 30, 2024)
21-37065611-C-G			Uncertain significance (Feb 08, 2022)
21-37065618-G-A			Benign (Jan 25, 2024)
21-37065626-G-A			Uncertain significance (Aug 15, 2022)
21-37065635-C-G			Uncertain significance (Oct 03, 2023)
21-37065642-A-G			Likely benign (Oct 13, 2022)
21-37065644-A-C			Uncertain significance (May 31, 2022)
21-37065646-A-G			Uncertain significance (Dec 11, 2023)
21-37065651-T-G		PIGP-related disorder	Benign (Feb 01, 2024)
21-37065653-T-C		Inborn genetic diseases	Uncertain significance (Nov 08, 2024)
21-37065654-T-A		Inborn genetic diseases	Uncertain significance (Mar 30, 2024)
21-37065655-A-C			Uncertain significance (Apr 28, 2021)
21-37065660-T-G			Benign (Jan 30, 2024)
21-37065665-T-A		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
21-37065665-T-C			Uncertain significance (May 30, 2022)
21-37065669-C-T			Likely benign (May 16, 2023)
21-37065673-T-C		Inborn genetic diseases	Uncertain significance (Nov 25, 2024)
21-37065678-G-A			Likely benign (Mar 22, 2023)
21-37065678-G-GT			Uncertain significance (Apr 18, 2021)
21-37065680-A-G			Uncertain significance (Jun 04, 2022)
21-37065695-G-A			Uncertain significance (Apr 29, 2024)
21-37065696-A-G			Likely benign (Oct 07, 2023)

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

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