UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1882

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 Arginine (R) to Glutamine (Q) at position 1882 (R1882Q, p.Arg1882Gln).

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 medium size and polar (Q)

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 DEE11; increased neuronal excitability; increased peak sodium current densities; gain of function.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs794727444 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1882

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

Protein sequence length:

2005

The length of the canonical sequence.

Location on the sequence:

TKRVLGESGEMDALRIQMEE R FMASNPSKVSYEPITTTLKR

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                         TKRVLGESGEMDALRIQMEERFMASNPSKVSYEPITTTLKR

Mouse                         TKRVLGESGEMDALRIQMEERFMASNPSKVSYEPITTTLKR

Rat                           TKRVLGESGEMDALRIQMEERFMASNPSKVSYEPITTTLKR

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	1 – 2005	Sodium channel protein type 2 subunit alpha
Topological domain	1776 – 2005	Cytoplasmic
Helix	1870 – 1886

Literature citations

Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1.
Carvill G.L.; Heavin S.B.; Yendle S.C.; McMahon J.M.; O'Roak B.J.; Cook J.; Khan A.; Dorschner M.O.; Weaver M.; Calvert S.; Malone S.; Wallace G.; Stanley T.; Bye A.M.; Bleasel A.; Howell K.B.; Kivity S.; Mackay M.T.; Rodriguez-Casero V.; Webster R.; Korczyn A.; Afawi Z.; Zelnick N.; Lerman-Sagie T.; Lev D.; Moeller R.S.; Gill D.; Andrade D.M.; Freeman J.L.; Sadleir L.G.; Shendure J.; Berkovic S.F.; Scheffer I.E.; Mefford H.C.;
Nat. Genet. 45:825-830(2013)
Cited for: VARIANTS DEE11 ILE-136; ASN-905; CYS-928 AND GLN-1882;

SCN2A encephalopathy: A major cause of epilepsy of infancy with migrating focal seizures.
Howell K.B.; McMahon J.M.; Carvill G.L.; Tambunan D.; Mackay M.T.; Rodriguez-Casero V.; Webster R.; Clark D.; Freeman J.L.; Calvert S.; Olson H.E.; Mandelstam S.; Poduri A.; Mefford H.C.; Harvey A.S.; Scheffer I.E.;
Neurology 85:958-966(2015)
Cited for: VARIANTS DEE11 ILE-136; LYS-218; LEU-856; ASN-905; CYS-928; ARG-1593; VAL-1634 AND GLN-1882; VARIANT BFIS3 SER-240; VARIANT LYS-976;

Improving diagnosis and broadening the phenotypes in early-onset seizure and severe developmental delay disorders through gene panel analysis.
Trump N.; McTague A.; Brittain H.; Papandreou A.; Meyer E.; Ngoh A.; Palmer R.; Morrogh D.; Boustred C.; Hurst J.A.; Jenkins L.; Kurian M.A.; Scott R.H.;
J. Med. Genet. 53:310-317(2016)
Cited for: VARIANTS DEE11 MET-873; ILE-987; LYS-999; VAL-999; GLN-1260; GLU-1260; 1435-ARG--LYS-2005 DEL; PRO-1479; PRO-1650; PHE-1829 AND GLN-1882;

Diagnostic targeted resequencing in 349 patients with drug-resistant pediatric epilepsies identifies causative mutations in 30 different genes.
Parrini E.; Marini C.; Mei D.; Galuppi A.; Cellini E.; Pucatti D.; Chiti L.; Rutigliano D.; Bianchini C.; Virdo S.; De Vita D.; Bigoni S.; Barba C.; Mari F.; Montomoli M.; Pisano T.; Rosati A.; Guerrini R.;
Hum. Mutat. 38:216-225(2017)
Cited for: VARIANT GLY-191; VARIANTS DEE11 ILE-251; VAL-263; VAL-896; VAL-1316; VAL-1323; TYR-1344; THR-1548 AND GLN-1882;

Dynamic action potential clamp predicts functional separation in mild familial and severe de novo forms of SCN2A epilepsy.
Berecki G.; Howell K.B.; Deerasooriya Y.H.; Cilio M.R.; Oliva M.K.; Kaplan D.; Scheffer I.E.; Berkovic S.F.; Petrou S.;
Proc. Natl. Acad. Sci. U.S.A. 115:E5516-E5525(2018)
Cited for: VARIANTS DEE11 GLN-853 AND GLN-1882; CHARACTERIZATION OF VARIANTS DEE11 GLN-853 AND GLN-1882; VARIANT BFIS3 VAL-1563; CHARACTERIZATION OF VARIANT BFIS3 VAL-1563; FUNCTION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q99250: Variant p.Arg1882Gln