UniProtKB/Swiss-Prot P21549: Variant p.Thr9Asn

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 9 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: LB/B 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: From Threonine (T) to Asparagine (N) at position 9 (T9N, p.Thr9Asn). 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: Similar physico-chemical property. Both residues are medium size and polar. The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: 0 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
Polymorphism: Variant p.Pro11Leu acts synergistically with other variants in AGXT producing specific enzymatic phenotypes in HP1 patients. The combined presence of variants p.Pro11Leu and p.Ile340Met defines the minor AGXT allele, whereas their absence defines the major allele. The minor allele has frequencies of 20% in normal European and North American populations, and 50% in HP1 patients. Additional information on the polymorphism described.
Variant description: No loss of alanine--glyoxylate aminotransferase activity. Any additional useful information about the variant.
Other resources: Links to websites of interest for the variant.

• Variant rs115014558 [ dbSNP | Ensembl ]

Sequence information

Variant position: 9 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 392 The length of the canonical sequence.
Location on the sequence: MASHKLLV T PPKALLKPLSIPNQLLLGPG 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.
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.

Type	Positions	Description
Chain	1 – 392	Alanine--glyoxylate aminotransferase
Modified residue	9 – 9	Phosphothreonine

Literature citations

Implications of genotype and enzyme phenotype in pyridoxine response of patients with type I primary hyperoxaluria.
Monico C.G.; Olson J.B.; Milliner D.S.;
Am. J. Nephrol. 25:183-188(2005)
Cited for: VARIANTS HP1 VAL-139 DEL; ARG-156; LEU-158; ARG-190; GLU-201; LEU-233; THR-244 AND ARG-253; VARIANT ASN-9; Intra-familial clinical heterogeneity: absence of genotype-phenotype correlation in primary hyperoxaluria type 1 in Israel.
Frishberg Y.; Rinat C.; Shalata A.; Khatib I.; Feinstein S.; Becker-Cohen R.; Weismann I.; Wanders R.J.A.; Rumsby G.; Roels F.; Mandel H.;
Am. J. Nephrol. 25:269-275(2005)
Cited for: VARIANTS HP1 ARG-41; ARG-108; ARG-156; ARG-190; ARG-195; HIS-243; THR-244; MET-279; THR-287; CYS-289 AND PRO-298; VARIANT ASN-9; Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1.
Williams E.; Rumsby G.;
Clin. Chem. 53:1216-1221(2007)
Cited for: VARIANTS HP1 CYS-36; ARG-41; GLU-41; PRO-150; ILE-152; ARG-156; LEU-158; CYS-161; SER-161; PRO-166; ARG-170; TYR-173; CYS-233; HIS-233; THR-244 AND ARG-253; VARIANT ASN-9; CHARACTERIZATION OF VARIANTS HP1 CYS-36; GLU-41; PRO-150; ARG-156; LEU-158; CYS-161; SER-161; PRO-166; TYR-173; CYS-233; HIS-233 AND ARG-253; CHARACTERIZATION OF VARIANT ASN-9;