Home  |  Contact

UniProtKB/Swiss-Prot Q3T906: Variant p.Cys523Arg

N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
Gene: GNPTAB
Chromosomal location: 12q23.3
Variant information

Variant position:  523
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Unclassified
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Cysteine (C) to Arginine (R) at position 523 (C523R, p.Cys523Arg).
Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:  Change from medium size and polar (C) to large size and basic (R)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Variant description:  Found in a patient with mucolipidosis type II or III; unknown pathological significance; decreased localization to the Golgi; decreased protein cleavage into alpha and beta subunits; decreased UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity.
Any additional useful information about the variant.



Sequence information

Variant position:  523
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1256
The length of the canonical sequence.

Location on the sequence:   SYCNQGCANSWLADKFCDQA  C NVLSCGFDAGDCGQDHFHEL
The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         SYCNQGCANSWLADKFCDQACNVLSCGFDAGDCGQDHFHEL

Mouse                         SYCNQGCANSWLADKFCDQACNVLSCGFDAGDCGQDHFHEL

Zebrafish                     SFCNQGCANSWLADKFCDQACNVLACGFDVGDCGQDNLNQL

Sequence annotation in neighborhood:  
The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.

TypePositionsDescription
Chain 1 – 928 N-acetylglucosamine-1-phosphotransferase subunit alpha
Repeat 505 – 545 LNR 2
Metal binding 516 – 516 Calcium
Metal binding 531 – 531 Calcium
Metal binding 534 – 534 Calcium
Disulfide bond 505 – 528
Disulfide bond 519 – 535
Alternative sequence 491 – 1256 Missing. In isoform 2.


Literature citations

Analysis of mucolipidosis II/III GNPTAB missense mutations identifies domains of UDP-GlcNAc:lysosomal enzyme GlcNAc-1-phosphotransferase involved in catalytic function and lysosomal enzyme recognition.
Qian Y.; van Meel E.; Flanagan-Steet H.; Yox A.; Steet R.; Kornfeld S.;
J. Biol. Chem. 290:3045-3056(2015)
Cited for: CHARACTERIZATION OF VARIANTS MLII LEU-81; ASP-182; PRO-205; LEU-334; LEU-348; LEU-374; ASN-732; ARG-928; VAL-955; CYS-986; PRO-1001; VAL-1054 AND MET-1236; CHARACTERIZATION OF VARIANTS MLIIIA GLN-4; TYR-15; VAL-190; GLN-334; PHE-399; THR-403; ALA-407; TYR-442; GLY-461; SER-468; TYR-505; PRO-587; PRO-926; TYR-956; GLY-1018 AND SER-1153; CHARACTERIZATION OF VARIANTS ARG-523; THR-592 AND TRP-785;

Dried blood spots allow targeted screening to diagnose mucopolysaccharidosis and mucolipidosis.
Cobos P.N.; Steglich C.; Santer R.; Lukacs Z.; Gal A.;
JIMD Rep. 15:123-132(2015)
Cited for: VARIANT MLII CYS-986; VARIANT ARG-523;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.