UniProtKB/Swiss-Prot Q9HBG7: Variant p.Met602Val

T-lymphocyte surface antigen Ly-9
Gene: LY9
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Variant information Variant position:

602 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 Methionine (M) to Valine (V) at position 602 (M602V, p.Met602Val). 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
Variant description:

Decreases interaction with SH2D1A and INPP5D 2-fold, reduced T-cell response. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs509749 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

DYDPVTPYVTEVESVVGENT M YAQVFNLQGKTPVSQKEESS 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                         DYDPVTPYVTEVESVVGENTMYAQV-FNLQGKTPVSQKEESS

Mouse                         EYEAITPYDKVDGSMDEEDMAYIQVSLNVQGETPLPQKKED

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	48 – 655	T-lymphocyte surface antigen Ly-9
Topological domain	477 – 655	Cytoplasmic
Motif	601 – 606	ITSM 1
Modified residue	603 – 603	Phosphotyrosine

Literature citations
Gene structure of the mouse leukocyte cell surface molecule Ly9.
Tovar V.; de la Fuente M.A.; Pizcueta P.; Bosch J.; Engel P.;
Immunogenetics 51:788-793(2000)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT VAL-602; Isolation and characterization of cDNA clones for Humly9: the human homologue of mouse Ly9.
Sandrin M.S.; Henning M.M.; Lo M.F.; Baker E.; Sutherland G.R.; McKenzie I.F.;
Immunogenetics 43:13-19(1996)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 32-654 (ISOFORM 2); VARIANT VAL-602; A polymorphism in a phosphotyrosine signalling motif of CD229 (Ly9, SLAMF3) alters SH2 domain binding and T-cell activation.
Margraf S.; Garner L.I.; Wilson T.J.; Brown M.H.;
Immunology 146:392-400(2015)
Cited for: INTERACTION WITH SH2D1A AND INPP5D; CHARACTERIZATION OF VARIANT VAL-602; DOMAIN; PHOSPHORYLATION AT TYR-603;

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.