UniProtKB/Swiss-Prot P05362: Variant p.Lys56Met

Intercellular adhesion molecule 1
Gene: ICAM1
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Variant information Variant position:

56 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 Lysine (K) to Methionine (M) at position 56 (K56M, p.Lys56Met). 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 large size and basic (K) to medium size and hydrophobic (M) 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 p.Lys56Met, known as ICAM1-Kilifi, may influence susceptibility to cerebral malaria [MIM:611162]. Additional information on the polymorphism described.
Variant description:

Probable risk factor for cerebral malaria at homozygosity. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs5491 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

VILPRGGSVLVTCSTSCDQP K LLGIETPLPKKELLLPGNNR 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                         VILPRGGSVLVTCSTSCDQPKL-LGIETPLPKKELLLPGNNR

Gorilla                       VILPRGGSVLVTCSTSCDQPTL-LGIETPLPKKELLLLGNN

Rhesus macaque                VILPRGGSVKVNCSASCDQPIS-LGMETPLPKKEILPGGNN

Chimpanzee                    VILPRGGSVQVTCSTSCDQPDL-LGIETPLPKKELLLGGNN

Mouse                         AFLPQGGSVQVNCSSSCKEDLS-LGLETQWLKDE-LESGPN

Rat                           AFLPRGGSVQVNCSSSCEDENLGLGLETNWMKDE-LSSGHN

Bovine                        AIIPRGDSLTVNCSNSCDQKST-FGLETVLIKEE-VGRGDN

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	28 – 532	Intercellular adhesion molecule 1
Topological domain	28 – 480	Extracellular
Domain	41 – 103	Ig-like C2-type 1
Disulfide bond	48 – 92
Disulfide bond	52 – 96
Beta strand	56 – 61

Literature citations
Submission
SeattleSNPs variation discovery resource;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT MET-56; VARIANTS ARG-241; LEU-352; GLN-397 AND TRP-478; A high frequency African coding polymorphism in the N-terminal domain of ICAM-1 predisposing to cerebral malaria in Kenya.
Fernandez-Reyes D.; Craig A.G.; Kyes S.A.; Peshu N.; Snow R.W.; Berendt A.R.; Marsh K.; Newbold C.I.;
Hum. Mol. Genet. 6:1357-1360(1997)
Cited for: VARIANT MET-56; ASSOCIATION WITH SUSCEPTIBILITY TO MALARIA; Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis.
Halushka M.K.; Fan J.-B.; Bentley K.; Hsie L.; Shen N.; Weder A.; Cooper R.; Lipshutz R.; Chakravarti A.;
Nat. Genet. 22:239-247(1999)
Cited for: VARIANT MET-56; VARIANT GLU-469;

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.