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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q3T906: Variant p.Asp407Ala

N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
Gene: GNPTAB
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Variant information Variant position: help 407 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance
Residue change: help From Aspartate (D) to Alanine (A) at position 407 (D407A, p.Asp407Ala). 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: help Change from medium size and acidic (D) to small size and hydrophobic (A) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -2 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: help In MLIIIA; no effect on protein abundance; no effect on localization to the Golgi; no effect on protein cleavage into alpha and beta subunits; decreased UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 407 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1256 The length of the canonical sequence.
Location on the sequence: help AIESHIHRIEGLSQKFIYLN D DVMFGKDVWPDDFYSHSKGQ 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         AIESHIHRIEGLSQKFIYLNDDVMFGKDVWPDDFYSHSKGQ

Mouse                         AIESHIHRIEGLSQKFIYLNDDVMFGKDVWPDDFYSHSKGQ

Zebrafish                     AIETHIHRIPGLSQKFIYLNDDVMFGKDVWPDDFYSHSKGQ
Sequence annotation in neighborhood: help 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
Beta strand 407 – 411



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; Missense mutations in N-acetylglucosamine-1-phosphotransferase alpha/beta subunit gene in a patient with mucolipidosis III and a mild clinical phenotype.
Tiede S.; Muschol N.; Reutter G.; Cantz M.; Ullrich K.; Braulke T.;
Am. J. Med. Genet. A 137:235-240(2005)
Cited for: VARIANT MLIIIA ALA-407; VARIANT GLY-662;
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.