Human Gene PIGL (ENST00000225609.10) from GENCODE V44
  Description: Homo sapiens phosphatidylinositol glycan anchor biosynthesis class L (PIGL), mRNA. (from RefSeq NM_004278)
RefSeq Summary (NM_004278): 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 localizes to the endoplasmic reticulum. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000225609.10
Gencode Gene: ENSG00000108474.17
Transcript (Including UTRs)
   Position: hg38 chr17:16,217,210-16,326,411 Size: 109,202 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg38 chr17:16,217,227-16,325,898 Size: 108,672 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr17:16,217,210-16,326,411)mRNA (may differ from genome)Protein (252 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase; EC=; AltName: Full=Phosphatidylinositol-glycan biosynthesis class L protein; Short=PIG-L;
FUNCTION: Involved in the second step of GPI biosynthesis. De-N- acetylation of N-acetylglucosaminyl-phosphatidylinositol.
CATALYTIC ACTIVITY: 6-(N-acetyl-alpha-D-glucosaminyl)-1- phosphatidyl-1D-myo-inositol + H(2)O = 6-(alpha-D-glucosaminyl)-1- phosphatidyl-1D-myo-inositol + acetate.
PATHWAY: Glycolipid biosynthesis; glycosylphosphatidylinositol- anchor biosynthesis.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass membrane protein (By similarity).
DISEASE: Defects in PIGL are the cause of coloboma, congenital heart disease, ichthyosiform dermatosis, mental retardation and ear anomalies syndrome (CHIME) [MIM:280000]. An extremely rare autosomal recessive multisystem disorder clinically characterized by colobomas, congenital heart defects, migratory ichthyosiform dermatosis, mental retardation, and ear anomalies including conductive hearing loss. Other clinical features include distinctive facial features, abnormal growth, genitourinary abnormalities, seizures, and feeding difficulties.
SIMILARITY: Belongs to the PIGL family.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: PIGL
Diseases sorted by gene-association score: chime syndrome* (1668), hyperphosphatasia-intellectual disability syndrome* (143), coloboma (9), heart disease (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.25 RPKM in Cervix - Endocervix
Total median expression: 163.77 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00170.000 Picture PostScript Text
3' UTR -144.60513-0.282 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003737 - GlcNAc_PIno_de-acetylase
IPR024078 - LmbE-like_dom

Pfam Domains:
PF02585 - GlcNAc-PI de-N-acetylase

ModBase Predicted Comparative 3D Structure on Q9Y2B2
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
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Gene Details    Gene Details
Gene Sorter    Gene Sorter
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000225 N-acetylglucosaminylphosphatidylinositol deacetylase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0006506 GPI anchor biosynthetic process
GO:0016254 preassembly of GPI anchor in ER membrane

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  HQ447574 - Synthetic construct Homo sapiens clone IMAGE:100070916; CCSB014853_01 phosphatidylinositol glycan anchor biosynthesis, class L (PIGL) gene, encodes complete protein.
LF384749 - JP 2014500723-A/192252: Polycomb-Associated Non-Coding RNAs.
MA620326 - JP 2018138019-A/192252: Polycomb-Associated Non-Coding RNAs.
AK302523 - Homo sapiens cDNA FLJ59164 complete cds, highly similar to N-acetylglucosaminyl-phosphatidylinositolde-N-acetylase (EC
AK292932 - Homo sapiens cDNA FLJ76635 complete cds, highly similar to Homo sapiens phosphatidylinositol glycan, class L (PIGL), mRNA.
AK296120 - Homo sapiens cDNA FLJ50779 complete cds, moderately similar to N-acetylglucosaminyl-phosphatidylinositolde-N-acetylase (EC
BC068197 - Homo sapiens phosphatidylinositol glycan anchor biosynthesis, class L, mRNA (cDNA clone MGC:71885 IMAGE:6711166), complete cds.
AB017165 - Homo sapiens PIG-L mRNA, complete cds.
CU686621 - Synthetic construct Homo sapiens gateway clone IMAGE:100023164 5' read PIGL mRNA.
JD247518 - Sequence 228542 from Patent EP1572962.
JD038945 - Sequence 19969 from Patent EP1572962.
JD168676 - Sequence 149700 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00563 - Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q9Y2B2 (Reactome details) participates in the following event(s):

R-HSA-162857 N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate
R-HSA-162710 Synthesis of glycosylphosphatidylinositol (GPI)
R-HSA-163125 Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8KA67, ENST00000225609.1, ENST00000225609.2, ENST00000225609.3, ENST00000225609.4, ENST00000225609.5, ENST00000225609.6, ENST00000225609.7, ENST00000225609.8, ENST00000225609.9, NM_004278, PIGL_HUMAN, Q9Y2B2, uc002gpv.1, uc002gpv.2, uc002gpv.3, uc002gpv.4, uc002gpv.5
UCSC ID: ENST00000225609.10
RefSeq Accession: NM_004278
Protein: Q9Y2B2 (aka PIGL_HUMAN)
CCDS: CCDS11176.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.