UniProtKB/SwissProt variant VAR

Glutamate receptor ionotropic, NMDA 1
Gene: GRIN1
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Variant information Variant position:

662 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

LP/P [Disclaimer] 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 Glutamate (E) to Lysine (K) at position 662 (E662K, p.Glu662Lys). 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 medium size and acidic (E) to large size and basic (K) 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:

In NDHMSD; this mutation produces a significant increase in NMDA receptor-induced calcium currents; excessive calcium influx through NMDA receptor could lead to excitotoxic neuronal cell damage. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs387906635 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

IIVASYTANLAAFLVLDRPE E RITGINDPRLRNPSDKFIYA 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                         IIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA

                              IIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA

Mouse                         IIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA

Rat                           IIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA

Xenopus laevis                IIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA

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	19 – 938	Glutamate receptor ionotropic, NMDA 1
Topological domain	648 – 812	Extracellular
Glycosylation	674 – 674	N-linked (GlcNAc...) asparagine
Mutagenesis	642 – 642	I -> L. Slight decrease in glutamate and glycine agonist potency; mutant channels are activated at 2-fold higher glutamate and glycine concentrations.
Mutagenesis	644 – 644	V -> M. Increase in glutamate and glycine agonist potency; mutant channels are activated lower glutamate and glycine concentrations.
Mutagenesis	653 – 653	A -> G. Increase in glutamate and glycine agonist potency; mutant channels are activated lower glutamate and glycine concentrations.

Literature citations
Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability.
Hamdan F.F.; Gauthier J.; Araki Y.; Lin D.T.; Yoshizawa Y.; Higashi K.; Park A.R.; Spiegelman D.; Dobrzeniecka S.; Piton A.; Tomitori H.; Daoud H.; Massicotte C.; Henrion E.; Diallo O.; Shekarabi M.; Marineau C.; Shevell M.; Maranda B.; Mitchell G.; Nadeau A.; D'Anjou G.; Vanasse M.; Srour M.; Lafreniere R.G.; Drapeau P.; Lacaille J.C.; Kim E.; Lee J.R.; Igarashi K.; Huganir R.L.; Rouleau G.A.; Michaud J.L.;
Am. J. Hum. Genet. 88:306-316(2011)
Cited for: VARIANTS NDHMSD SER-560 INS AND LYS-662; CHARACTERIZATION OF VARIANTS NDHMSD SER-560 INS AND LYS-662;

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.

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q05586: Variant p.Glu662Lys