UniProtKB/Swiss-Prot P00387: Variant p.Thr117Ser

NADH-cytochrome b5 reductase 3
Gene: CYB5R3
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Variant information Variant position:

117 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 Serine (S) at position 117 (T117S, p.Thr117Ser). 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 (T) to small size and polar (S) 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:

Ser-117 seems to only be found in persons of African origin. The allele frequency is 0.23 in African Americans. It was not found in Caucasians, Asians, Indo-Aryans, or Arabs. There seems to be no effect on the enzyme activity. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs1800457 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

ISSDDDKGFVDLVIKVYFKD T HPKFPAGGKMSQYLESMQIG 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                         ISSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMQIG

                              VSSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIG

Mouse                         VSSDDDKGFVDLVVKVYFKDTHPKFPAGGKMSQYLENMKIG

Rat                           VSSDDDKGFVDLVVKVYFKDTHPKFPAGGKMSQYLENMNIG

Bovine                        VSSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIG

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	2 – 301	NADH-cytochrome b5 reductase 3
Domain	40 – 152	FAD-binding FR-type
Binding site	109 – 109
Binding site	111 – 111
Binding site	114 – 114
Binding site	126 – 126
Binding site	127 – 127
Binding site	128 – 128
Modified residue	120 – 120	N6-acetyllysine
Mutagenesis	128 – 128	S -> A. Decreased NADH-cytochrome b5 reductase activity, highly increases Km for NADH and decreases Kcat.
Beta strand	115 – 118

Literature citations
Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT SER-117; A high-frequency polymorphism of NADH-cytochrome b5 reductase in African-Americans.
Jenkins M.M.; Prchal J.T.;
Hum. Genet. 99:248-250(1997)
Cited for: VARIANT SER-117;

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.