UniProtKB/Swiss-Prot P51854: Variant p.Ile152Thr

Transketolase-like protein 1
Gene: TKTL1
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Variant information Variant position:

152 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 Isoleucine (I) to Threonine (T) at position 152 (I152T, p.Ile152Thr). 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 hydrophobic (I) to medium size and polar (T) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

-1 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 Lys-317 is typically present in extinct archaic humans, Neanderthals and Denisovans, as well as in other primates. It is rare in modern human population with a frequency of 0.03%. No homozygote is reported in the Genome Aggregation Database (gnomAD v2.1.1). The modern human variant Arg-317 is thought to lead to a greater neocortical neurogenesis compared to archaic human Lys-317, in particular in the frontal lobe. It is currently unknown if the presence of variant Lys-317 in modern humans is associated with a disease or has any effect on cognitive skills. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs17852259 [ dbSNP | Ensembl ]

Sequence information Variant position:

152 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

596 The length of the canonical sequence.
Location on the sequence:

GSVWEAMAFASYYSLDNLVA I FDVNRLGHSGALPAEHCINI 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                         GSVWEAMAFASYYSLDNLVAIFDVNRLGHSGALPAEHCINI

Mouse                         GSVWEAFAFASYYNLDNLMAIFDVNRIGHSSSMSVEHCIAI

Bovine                        GSVWEALAFASHYSLDNLVAIFDVNRLTHSTTLPLEHSIDV

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 – 596	Transketolase-like protein 1
Binding site	156 – 156
Binding site	156 – 156
Binding site	158 – 158

Literature citations
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3); VARIANTS PHE-24 AND THR-152;

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.