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UniProtKB/Swiss-Prot Q9Y6Y9: Variant p.Arg56Gly

Lymphocyte antigen 96
Gene: LY96
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 Arginine (R) to Glycine (G) at position 56 (R56G, p.Arg56Gly).
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 (R) to glycine (G)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
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

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:  160
The length of the canonical sequence.

Location on the sequence:   YCDKMQYPISINVNPCIELK  R SKGLLHIFYIPRRDLKQLYF
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                         YCDKMQYPISINVNPCIELKRSKGLLHIFYIPRRDLKQLYF

Mouse                         YCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYF

Bovine                        YCDDMKFPISVKVEPCVTIKGTKGKLHLYYIARRDIQKLYL

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 19 – 160 Lymphocyte antigen 96
Disulfide bond 37 – 148
Alternative sequence 38 – 68 DKMQYPISINVNPCIELKRSKGLLHIFYIPR -> G. In isoform 2.


Literature citations

MD-2, a molecule that confers lipopolysaccharide responsiveness on Toll-like receptor 4.
Shimazu R.; Akashi S.; Ogata H.; Nagai Y.; Fukudome K.; Miyake K.; Kimoto M.;
J. Exp. Med. 189:1777-1782(1999)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT GLY-56; FUNCTION; INTERACTION WITH TLR4; SUBCELLULAR LOCATION;

ESOP-1, a secreted protein expressed in the hematopoietic, nervous, and reproductive systems of embryonic and adult mice.
Kato K.; Morrison A.M.; Nakano T.; Tashiro K.; Honjo T.;
Blood 96:362-364(2000)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT GLY-56;

Molecular genetic analysis of an endotoxin nonresponder mutant cell line. A point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.
Schromm A.B.; Lien E.; Henneke P.; Chow J.C.; Yoshimura A.; Heine H.; Latz E.; Monks B.G.; Schwartz D.A.; Miyake K.; Golenbock D.T.;
J. Exp. Med. 194:79-88(2001)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); MUTAGENESIS OF CYS-95; VARIANT GLY-56;

Natural selection in the TLR-related genes in the course of primate evolution.
Nakajima T.; Ohtani H.; Satta Y.; Uno Y.; Akari H.; Ishida T.; Kimura A.;
Immunogenetics 60:727-735(2008)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT GLY-56;

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 1); VARIANT GLY-56;

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.