Expasy logo

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q99250: Variant p.Thr1420Met

Sodium channel protein type 2 subunit alpha
Gene: SCN2A
Feedback?
Variant information Variant position: help 1420 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Threonine (T) to Methionine (M) at position 1420 (T1420M, p.Thr1420Met). 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: help Change from medium size and polar (T) to medium size and hydrophobic (M) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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: help Found in a patient with autism spectrum disorder; likely pathogenic; decreased voltage-gated sodium channel activity; faster channel inactivation; fewer channels contribution to macroscopic currents and fewer channels expressed on membrane. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1420 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 2005 The length of the canonical sequence.
Location on the sequence: help NVKVNFDNVGLGYLSLLQVA T FKGWMDIMYAAVDSRNVELQ 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences.
Human                         NVKVNFDNVGLGYLSLLQVATFKGWMDIMYAAVDSRNVELQ

Mouse                         NVKVNFDNVGLGYLSLLQVATFKGWMDIMYAAVDSRNVELQ

Rat                           NVKVNFDNVGLGYLSLLQVATFKGWMDIMYAAVDSRNVELQ

Sequence annotation in neighborhood: help 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 1 – 2005 Sodium channel protein type 2 subunit alpha
Intramembrane 1409 – 1430 Pore-forming
Repeat 1190 – 1504 III
Site 1429 – 1429 Binds Mu-conotoxin KIIIA
Helix 1409 – 1420



Literature citations
Opposing Effects on NaV1.2 Function Underlie Differences Between SCN2A Variants Observed in Individuals With Autism Spectrum Disorder or Infantile Seizures.
Ben-Shalom R.; Keeshen C.M.; Berrios K.N.; An J.Y.; Sanders S.J.; Bender K.J.;
Biol. Psychiatry 82:224-232(2017)
Cited for: VARIANTS ASN-12; GLY-82; HIS-379; CYS-937; HIS-937; 959-CYS--LYS-2005 DEL; 1013-GLY--LYS-2005 DEL; ARG-1386 AND MET-1420; CHARACTERIZATION OF VARIANTS ASN-12; GLY-82; HIS-379; CYS-937; HIS-937; 959-CYS--LYS-2005 DEL; 1013-GLY--LYS-2005 DEL; ARG-1386 AND MET-1420; INVOLVEMENT IN AUTISM SPECTRUM DISORDER; FUNCTION; TRANSPORTER ACTIVITY;
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.