PIGB

phosphatidylinositol glycan anchor biosynthesis class B, the group of Dolichyl D-mannosyl phosphate dependent mannosyltransferases|Phosphatidylinositol glycan anchor biosynthesis

Basic information

Region (hg38): 15:55318959-55355648

Links

ENSG00000069943 ∙ NCBI:9488 ∙ OMIM:604122 ∙ HGNC:8959 ∙ Uniprot:Q92521 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy, 80 (Strong), mode of inheritance: AR
• developmental and epileptic encephalopathy, 80 (Moderate), mode of inheritance: AR
• developmental and epileptic encephalopathy, 80 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 80	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	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	31256876

ClinVar

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

• not provided (226 variants)
• Inborn genetic diseases (21 variants)
• Developmental and epileptic encephalopathy, 80 (17 variants)
• not specified (2 variants)
• Hyperphosphatasia with intellectual disability syndrome 1 (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGB 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			2	42	3	47
missense		1	109	1	9	120
nonsense	6		2			8
start loss						0
frameshift	4		3			7
inframe indel			1			1
splice donor/acceptor (+/-2bp)		4	2			6
splice region			10	10	2	22
non coding	1		4	28	3	36
Total	11	5	123	71	15

Highest pathogenic variant AF is 0.0000396

Variants in PIGB

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

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

Position	Type	Phenotype	Significance	ClinVar
15-55319235-A-G		Developmental and epileptic encephalopathy, 80	Benign (Sep 05, 2021)
15-55319249-G-T		not specified	Uncertain significance (Dec 15, 2023)
15-55319258-G-A			Uncertain significance (Jun 26, 2022)
15-55319259-G-A			Likely benign (Jan 24, 2024)
15-55319260-C-G			Uncertain significance (Nov 27, 2023)
15-55319260-C-T		Inborn genetic diseases	Uncertain significance (May 27, 2022)
15-55319263-C-T			Likely benign (Oct 08, 2023)
15-55319267-G-T			Uncertain significance (Apr 09, 2023)
15-55319267-G-GC			Pathogenic (Jun 06, 2023)
15-55319274-C-T			Likely benign (Apr 10, 2023)
15-55319275-G-A		See cases	Uncertain significance (Mar 01, 2023)
15-55319287-G-A			Uncertain significance (Apr 09, 2023)
15-55319288-G-A			Uncertain significance (Jun 14, 2022)
15-55319288-G-C			Uncertain significance (Aug 14, 2021)
15-55319290-G-A		Inborn genetic diseases	Uncertain significance (Mar 24, 2022)
15-55319303-G-A			Uncertain significance (Jan 26, 2022)
15-55319308-A-G		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
15-55319321-T-A			Uncertain significance (Apr 17, 2022)
15-55319323-C-T			Pathogenic (Sep 19, 2022)
15-55319337-C-A			Uncertain significance (Sep 16, 2022)
15-55319338-G-A			Uncertain significance (Feb 20, 2022)
15-55319338-G-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
15-55319339-G-C			Uncertain significance (May 01, 2022)
15-55319341-A-T			Pathogenic (Jan 23, 2023)
15-55319347-A-G			Uncertain significance (Jul 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIGB	protein_coding	protein_coding	ENST00000164305	12	36689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.85e-11	0.526	124611	0	42	124653	0.000168

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.595	239	266	0.897	0.0000126	3617
Missense in Polyphen		71	91.54	0.77562		1246
Synonymous	0.295	88	91.6	0.961	0.00000420	1015
Loss of Function	1.30	20	27.3	0.732	0.00000135	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000640	0.000637
Ashkenazi Jewish	0.00	0.00
East Asian	0.000398	0.000389
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000155	0.000150
Middle Eastern	0.000398	0.000389
South Asian	0.0000988	0.0000980
Other	0.000176	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mannosyltransferase involved in glycosylphosphatidylinositol-anchor biosynthesis. Transfers the third alpha-1,2-mannose to Man2-GlcN-acyl-PI during GPI precursor assembly. {ECO:0000269|PubMed:8861954}.
• 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: 0.0985

Haploinsufficiency Scores

• pHI: 0.0483
• hipred: N
• hipred_score: 0.250
• ghis: 0.395

Essentials

• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pigb

Gene ontology

• Biological process: GPI anchor biosynthetic process;preassembly of GPI anchor in ER membrane;mannosylation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: mannosyltransferase activity;glycolipid mannosyltransferase activity