Human Gene GALNS (uc010cid.3) Description and Page Index
  Description: Homo sapiens galactosamine (N-acetyl)-6-sulfate sulfatase (GALNS), mRNA.
RefSeq Summary (NM_000512): This gene encodes N-acetylgalactosamine-6-sulfatase which is a lysosomal exohydrolase required for the degradation of the glycosaminoglycans, keratan sulfate, and chondroitin 6-sulfate. Sequence alterations including point, missense and nonsense mutations, as well as those that affect splicing, result in a deficiency of this enzyme. Deficiencies of this enzyme lead to Morquio A syndrome, a lysosomal storage disorder. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC056151.1, BC050684.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000268695.10/ ENSP00000268695.5 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:88,880,142-88,923,374 Size: 43,233 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr16:88,880,847-88,909,575 Size: 28,729 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:88,880,142-88,923,374)mRNA (may differ from genome)Protein (528 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIneXtProtPubMedReactome
Stanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: GALNS_HUMAN
DESCRIPTION: RecName: Full=N-acetylgalactosamine-6-sulfatase; EC=3.1.6.4; AltName: Full=Chondroitinsulfatase; Short=Chondroitinase; AltName: Full=Galactose-6-sulfate sulfatase; AltName: Full=N-acetylgalactosamine-6-sulfate sulfatase; Short=GalNAc6S sulfatase; Flags: Precursor;
CATALYTIC ACTIVITY: Hydrolysis of the 6-sulfate groups of the N- acetyl-D-galactosamine 6-sulfate units of chondroitin sulfate and of the D-galactose 6-sulfate units of keratan sulfate.
COFACTOR: Binds 1 calcium ion per subunit (By similarity).
SUBUNIT: Oligomer of disulfide linked 40- and 15 kDa polypeptides.
SUBCELLULAR LOCATION: Lysosome.
PTM: The conversion to 3-oxoalanine (also known as C- formylglycine, FGly), of a serine or cysteine residue in prokaryotes and of a cysteine residue in eukaryotes, is critical for catalytic activity (By similarity).
DISEASE: Defects in GALNS are the cause of mucopolysaccharidosis type 4A (MPS4A) [MIM:253000]; also known as Morquio A syndrome. MPS4A is a form of mucopolysaccharidosis type 4, an autosomal recessive lysosomal storage disease characterized by intracellular accumulation of keratan sulfate and chondroitin-6-sulfate. Key clinical features include short stature, skeletal dysplasia, dental anomalies, and corneal clouding. Intelligence is normal and there is no direct central nervous system involvement, although the skeletal changes may result in neurologic complications. There is variable severity, but patients with the severe phenotype usually do not survive past the second or third decade of life.
SIMILARITY: Belongs to the sulfatase family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/GALNS";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GALNS
CDC HuGE Published Literature: GALNS
Positive Disease Associations: Hematocrit , Hemoglobins
Related Studies:
  1. Hematocrit
    , , . [PubMed 0]
  2. Hemoglobins
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: GALNS
Diseases sorted by gene-association score: mucopolysaccharidosis iva* (1670), mucopolysaccharidosis iv* (450), mucopolysaccharidosis-plus syndrome (22), mucopolysaccharidosis is (16), kniest dysplasia (11), mucopolysaccharidosis ii (10), sed congenita (9), ketothiolase deficiency (9), mucopolysaccharidosis type vi (9), gangliosidosis gm1 (8), larsen syndrome (7), mucopolysaccharidosis vii (7), spondyloepiphyseal dysplasia with congenital joint dislocations (7), tracheomalacia (6), mucolipidosis iii alpha/beta (5), brachyolmia (5), lysosomal storage disease (5), multiple sulfatase deficiency (5), inherited metabolic disorder (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.10 RPKM in Testis
Total median expression: 308.19 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 -122.40241-0.508 Picture PostScript Text
3' UTR -249.49705-0.354 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
IPR017849 - Alkaline_Pase-like_a/b/a
IPR017850 - Alkaline_phosphatase_core
IPR000917 - Sulfatase
IPR024607 - Sulfatase_CS

Pfam Domains:
PF00884 - Sulfatase
PF01663 - Type I phosphodiesterase / nucleotide pyrophosphatase
PF14707 - C-terminal region of aryl-sulfatase

SCOP Domains:
53649 - Alkaline phosphatase-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

4FDI
- X-ray MuPIT

4FDJ
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P34059
FrontTopSide
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
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0003943 N-acetylgalactosamine-4-sulfatase activity
GO:0008484 sulfuric ester hydrolase activity
GO:0016787 hydrolase activity
GO:0043890 N-acetylgalactosamine-6-sulfatase activity
GO:0046872 metal ion binding

Biological Process:
GO:0008152 metabolic process
GO:0042340 keratan sulfate catabolic process
GO:0043312 neutrophil degranulation

Cellular Component:
GO:0005576 extracellular region
GO:0005764 lysosome
GO:0035578 azurophil granule lumen
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC007825 - Homo sapiens galactosamine (N-acetyl)-6-sulfate sulfatase, mRNA (cDNA clone IMAGE:2989923), partial cds.
AY129021 - Homo sapiens clone FP18463 unknown mRNA.
BC056151 - Homo sapiens galactosamine (N-acetyl)-6-sulfate sulfatase, mRNA (cDNA clone MGC:64985 IMAGE:6026248), complete cds.
AK131096 - Homo sapiens mRNA for FLJ00319 protein.
BX649181 - Homo sapiens mRNA; cDNA DKFZp686M2125 (from clone DKFZp686M2125).
AK124834 - Homo sapiens cDNA FLJ42844 fis, clone BRCOC2014033.
BC050684 - Homo sapiens galactosamine (N-acetyl)-6-sulfate sulfatase, mRNA (cDNA clone MGC:60259 IMAGE:6091623), complete cds.
AK021488 - Homo sapiens cDNA FLJ11426 fis, clone HEMBA1001059, highly similar to Human N-acetylgalactosamine 6-sulphatase (GALNS) gene, exon 14.
JD357262 - Sequence 338286 from Patent EP1572962.
JD396686 - Sequence 377710 from Patent EP1572962.
JD492555 - Sequence 473579 from Patent EP1572962.
JD489396 - Sequence 470420 from Patent EP1572962.
JD563721 - Sequence 544745 from Patent EP1572962.
JD099977 - Sequence 81001 from Patent EP1572962.
JD266063 - Sequence 247087 from Patent EP1572962.
JD296221 - Sequence 277245 from Patent EP1572962.
JD406554 - Sequence 387578 from Patent EP1572962.
AK294390 - Homo sapiens cDNA FLJ53977 complete cds, highly similar to N-acetylgalactosamine-6-sulfatase precursor (EC 3.1.6.4).
AK308269 - Homo sapiens cDNA, FLJ98217.
JD075477 - Sequence 56501 from Patent EP1572962.
AK312655 - Homo sapiens cDNA, FLJ93045, highly similar to Homo sapiens galactosamine (N-acetyl)-6-sulfate sulfatase (Morquiosyndrome, mucopolysaccharidosis type IVA) (GALNS), mRNA.
KJ891218 - Synthetic construct Homo sapiens clone ccsbBroadEn_00612 GALNS gene, encodes complete protein.
KR711073 - Synthetic construct Homo sapiens clone CCSBHm_00019862 GALNS (GALNS) mRNA, encodes complete protein.
KR711074 - Synthetic construct Homo sapiens clone CCSBHm_00019890 GALNS (GALNS) mRNA, encodes complete protein.
KR711075 - Synthetic construct Homo sapiens clone CCSBHm_00019906 GALNS (GALNS) mRNA, encodes complete protein.
AK310392 - Homo sapiens cDNA, FLJ17434.
BC018027 - Homo sapiens galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio syndrome, mucopolysaccharidosis type IVA), mRNA (cDNA clone IMAGE:4796652).

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00531 - Glycosaminoglycan degradation
hsa01100 - Metabolic pathways
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein P34059 (Reactome details) participates in the following event(s):

R-HSA-6798751 Exocytosis of azurophil granule lumen proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: AK308269, GALNS_HUMAN, P34059, Q86VK3
UCSC ID: uc010cid.3
RefSeq Accession: NM_000512
Protein: P34059 (aka GALNS_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene GALNS:
mps4a (Mucopolysaccharidosis Type IVA )

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK308269.1
exon count: 15CDS single in 3' UTR: no RNA size: 1804
ORF size: 1587CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 2482.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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