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UniProtKB/Swiss-Prot Q12879: Variant p.Lys669Asn

Glutamate receptor ionotropic, NMDA 2A
Gene: GRIN2A
Variant information

Variant position:  669
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 Lysine (K) to Asparagine (N) at position 669 (K669N, p.Lys669Asn).
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 polar (N)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  0
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 FESD; no effect on localization to the cell membrane; changed glutamate-gated calcium ion channel activity characterized by increased glutamate and glycine potency.
Any additional useful information about the variant.



Sequence information

Variant position:  669
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1464
The length of the canonical sequence.

Location on the sequence:   LAAFMIQEEFVDQVTGLSDK  K FQRPHDYSPPFRFGTVPNGS
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                         LAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGS

Chimpanzee                    LAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGS

Mouse                         LAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGS

Rat                           LAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGS

Xenopus laevis                LAAFMIQEEFVDQVTGLSDNKFQRPHDYSPPFRFGTVPNGS

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 23 – 1464 Glutamate receptor ionotropic, NMDA 2A
Topological domain 646 – 816 Extracellular
Glycosylation 687 – 687 N-linked (GlcNAc...) asparagine
Helix 668 – 671


Literature citations

GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction.
Lesca G.; Rudolf G.; Bruneau N.; Lozovaya N.; Labalme A.; Boutry-Kryza N.; Salmi M.; Tsintsadze T.; Addis L.; Motte J.; Wright S.; Tsintsadze V.; Michel A.; Doummar D.; Lascelles K.; Strug L.; Waters P.; de Bellescize J.; Vrielynck P.; de Saint Martin A.; Ville D.; Ryvlin P.; Arzimanoglou A.; Hirsch E.; Vincent A.; Pal D.; Burnashev N.; Sanlaville D.; Szepetowski P.;
Nat. Genet. 45:1061-1066(2013)
Cited for: VARIANTS FESD SER-184; SER-295; ARG-483; TRP-504; HIS-518; THR-548; VAL-652; ASN-669; THR-694; THR-716; ASN-731; ASN-933 AND ASN-1251; VARIANT GLY-1276; CHARACTERIZATION OF VARIANTS FESD HIS-518 AND VAL-652;

Mechanistic insight into NMDA receptor dysregulation by rare variants in the GluN2A and GluN2B agonist binding domains.
Swanger S.A.; Chen W.; Wells G.; Burger P.B.; Tankovic A.; Bhattacharya S.; Strong K.L.; Hu C.; Kusumoto H.; Zhang J.; Adams D.R.; Millichap J.J.; Petrovski S.; Traynelis S.F.; Yuan H.;
Am. J. Hum. Genet. 99:1261-1280(2016)
Cited for: VARIANTS FESD ALA-506 AND GLY-685; CHARACTERIZATION OF VARIANT FESD ARG-436; ARG-483; TRP-504; ALA-506; HIS-518; MET-531; ASN-669; GLY-685; THR-694; SER-699; VAL-705; LYS-714; THR-716; THR-727; ASN-731; LEU-734; GLU-772; CHARACTERIZATION OF VARIANT MET-452;

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.