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UniProtKB/Swiss-Prot P05362: Variant p.Lys56Met

Intercellular adhesion molecule 1
Gene: ICAM1
Variant information

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

Type of variant:  Polymorphism
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

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:  Homozygotes with ICAM1-Kalifi Met-56 seem to have an increased risk for cerebral malaria [MIM:611162].
Additional information on the polymorphism described.

Variant description:  In Kilifi; at homozygosity it is associated with increased susceptibility to cerebral malaria.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



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                         VILPRGGSVLVTCSTSC-DQPKLLGIETPLPKKELLLPGNNR

Gorilla                       VILPRGGSVLVTCSTSC-DQPTLLGIETPLPKKELLLLGNN

Rhesus macaque                VILPRGGSVKVNCSASC-DQPISLGMETPLPKKEILPGGNN

Chimpanzee                    VILPRGGSVQVTCSTSC-DQPDLLGIETPLPKKELLLGGNN

Mouse                         AFLPQGGSVQVNCSSSC-KEDLSLGLETQWLKDELES-GPN

Rat                           AFLPRGGSVQVNCSSSCEDENLGLGLETNWMKDELSS-GHN

Bovine                        AIIPRGDSLTVNCSNSC-DQKSTFGLETVLIKEEVGR-GDN

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.

TypePositionsDescription
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 KILIFI 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 KILIFI 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 KILIFI 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.