Human Gene GALNS (uc002flz.4) 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: 12 Strand: -
Coding Region
   Position: hg19 chr16:88,880,847-88,898,456 Size: 17,610 Coding Exon Count: 6 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
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 (205 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
HGNCLynxMGIPubMedStanford SOURCETreefam

-  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
  Press "+" in the title bar above to open this section.

-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -317.43772-0.411 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

Pfam Domains:
PF00884 - Sulfatase
PF14707 - C-terminal region of aryl-sulfatase

SCOP Domains:
53649 - Alkaline phosphatase-like

ModBase Predicted Comparative 3D Structure on Q96I49
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    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0008484 sulfuric ester hydrolase activity

Biological Process:
GO:0008152 metabolic process

-  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
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

-  Other Names for This Gene
  Alternate Gene Symbols: BX649181, Q96I49, Q96I49_HUMAN
UCSC ID: uc002flz.4
RefSeq Accession: NM_000512
Protein: Q96I49

-  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: BX649181.1
exon count: 12CDS single in 3' UTR: no RNA size: 2104
ORF size: 618CDS single in intron: no Alignment % ID: 99.69
txCdsPredict score: 648.00frame shift in genome: no % Coverage: 92.82
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.