PIGL (phosphatidylinositol glycan anchor biosynthesis class L)

Gene

• Entrez ID: 9487
• Gene name: Phosphatidylinositol glycan anchor biosynthesis class L
• Gene symbol: PIGL
• Synonyms (NCBI Gene): CHIME
• Chromosome: 17
• Chromosome location: 17p11.2
• Summary: This gene encodes an enzyme that catalyzes the second step of glycosylphosphatidylinositol (GPI) biosynthesis, which is the de-N-acetylation of N-acetylglucosaminylphosphatidylinositol (GlcNAc-PI). Study of a similar rat enzyme suggests that this protein

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs139004722	C>A,G,T	Pathogenic, uncertain-significance	3 prime UTR variant, stop gained, coding sequence variant, downstream transcript variant, genic downstream transcript variant, missense variant
rs145303331	T>C	Pathogenic, pathogenic-likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, intron variant, genic downstream transcript variant
rs758633805	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs768198327	G>A,T	Likely-pathogenic	Genic downstream transcript variant, splice donor variant, downstream transcript variant
rs770084126	G>A	Pathogenic	Splice acceptor variant
rs1064794861	C>-	Likely-pathogenic	3 prime UTR variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs1064795400	C>T	Likely-pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2295753	hsa-miR-2467-3p	CLIP-seq
MIRT2295754	hsa-miR-3678-3p	CLIP-seq
MIRT2295755	hsa-miR-450b-5p	CLIP-seq
MIRT2295756	hsa-miR-4738-5p	CLIP-seq
MIRT2295757	hsa-miR-4781-5p	CLIP-seq
MIRT2295758	hsa-miR-485-5p	CLIP-seq
MIRT2295759	hsa-miR-507	CLIP-seq
MIRT2295760	hsa-miR-557	CLIP-seq
MIRT2295761	hsa-miR-766	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000225	Function	N-acetylglucosaminylphosphatidylinositol deacetylase activity	IBA
GO:0000225	Function	N-acetylglucosaminylphosphatidylinositol deacetylase activity	IEA
GO:0000225	Function	N-acetylglucosaminylphosphatidylinositol deacetylase activity	ISS
GO:0000225	Function	N-acetylglucosaminylphosphatidylinositol deacetylase activity	NAS	10085243
GO:0000225	Function	N-acetylglucosaminylphosphatidylinositol deacetylase activity	TAS
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	14742432
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006506	Process	GPI anchor biosynthetic process	IEA
GO:0006506	Process	GPI anchor biosynthetic process	IMP	10085243
GO:0006506	Process	GPI anchor biosynthetic process	NAS	10085243
GO:0006506	Process	GPI anchor biosynthetic process	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA

Other IDs

• MIM: 605947
• HGNC: 8966
• e!Ensembl: ENSG00000108474

Protein

• UniProt ID: Q9Y2B2
• Protein name: N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase (EC 3.5.1.89) (Phosphatidylinositol-glycan biosynthesis class L protein) (PIG-L)
• Protein function: Catalyzes the second step of glycosylphosphatidylinositol (GPI) biosynthesis, which is the de-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02585	PIG-L	44 → 168	GlcNAc-PI de-N-acetylase	Family

• Sequence:

  MEAMWLLCVALAVLAWGFLWVWDSSERMKSREQGGRLGAESRTLLVIAHPDDEAMFFAPT
  VLGLARLRHWVYLLCFSAGNYYNQGETRKKELLQSCDVLGIPLSSVMIIDNRDFPDDPGM
  QWDTEHVARVLLQHIEVNGINLVVTFDAGGVSGHSNHIALYAAVRALHSEGKLPKGCSVL
  TLQSVNVLRKYISLLDLPLSLLHTQDVLFVLNSKEVAQAKKAMSCHRSQLLWFRRLYIIF
  SRYMRINSLSFL

• Sequence length: 252

Pathways

KEGG:

Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
Metabolic pathways

Reactome:

Synthesis of glycosylphosphatidylinositol (GPI)

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
CHIME syndrome	Likely pathogenic; Pathogenic	rs2142864883, rs768198327, rs773591135, rs2142610073, rs145303331, rs758633805, rs139004722, rs770084126	RCV001782627 RCV001823085 RCV002274225 RCV002052272 RCV000023501 RCV000023502 RCV000023503 RCV000023504
Hyperphosphatasia with intellectual disability syndrome 1	Likely pathogenic	rs773591135	RCV002274225
Intellectual disability	Pathogenic	rs145303331	RCV005624705
PIGL-related disorder	Likely pathogenic; Pathogenic	rs773591135, rs145303331	RCV002508967 RCV002508918
Syndromic intellectual disability	Pathogenic	rs770084126	RCV005627336

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Familial cancer of breast	Uncertain significance	rs184077858	RCV005888207
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity	rs114670807	RCV005888206

Associations from Text Mining
Disease Name	Relationship Type	References
Burkitt Lymphoma	Associate	19302917
Carcinoma Hepatocellular	Associate	37280393
Coloboma	Associate	35258128
Developmental Disabilities	Associate	28327575
Glycosylphosphatidylinositol deficiency	Associate	19302917
Hyperostosis corticalis deformans juvenilis	Associate	30813920
Hyperphosphatasia with Mental Retardation	Associate	30813920
Intellectual Disability	Associate	22444671, 23561847, 30813920, 35258128
Muscle Hypotonia	Associate	23561847
Neoplasms	Associate	37280393
Seizures	Associate	23561847
Skin Diseases	Associate	35258128
Zunich neuroectodermal syndrome	Associate	22444671, 35258128