UniProtKB/Swiss-Prot Q30201: Variant p.Val53Met

Hereditary hemochromatosis protein
Gene: HFE
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Variant information Variant position:

53 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 Valine (V) to Methionine (M) at position 53 (V53M, p.Val53Met). 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 hydrophobic. 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:

Genetic variations in HFE may influence the transferrin serum levels. Iron is essential for biochemical functions such as oxygen transport and oxidative phosphorylation. Excessive iron can cause iron-overload-related liver diseases, whereas iron deficiency can lead to anemia. Iron status can be assessed by measuring the levels of serum iron, serum transferrin, transferrin saturation with iron, and serum ferritin. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs28934889 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

LFMGASEQDLGLSLFEALGY V DDQLFVFYDHESRRVEPRTP 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                         LFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTP

Chimpanzee                    LFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTP

Mouse                         LFMGASEPDLGLPLFEARGYVDDQLFVSYNHESRRAEPRAP

Rat                           LFMGASKPDLGLPFFEALGYVDDQLFVSYNHESRRAEPRAP

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	23 – 348	Hereditary hemochromatosis protein
Topological domain	23 – 306	Extracellular
Region	23 – 114	Alpha-1
Alternative sequence	26 – 114	RSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKE -> Q. In isoform 2 and isoform 4.
Alternative sequence	27 – 298	Missing. In isoform 11.
Alternative sequence	27 – 206	Missing. In isoform 6.
Beta strand	48 – 53

Literature citations
Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS MET-53; ASP-63; GLN-224 AND TYR-282; Spectrum of mutations in the HFE gene implicated in haemochromatosis and porphyria.
de Villiers J.N.P.; Hillermann R.; Loubser L.; Kotze M.J.;
Hum. Mol. Genet. 8:1517-1522(1999)
Cited for: VARIANTS HFE1 ASP-63; HIS-127 AND MET-330; VARIANTS MET-53 AND MET-59;

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.