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UniProtKB/Swiss-Prot P35498: Variant p.His939Gln

Sodium channel protein type 1 subunit alpha
Gene: SCN1A
Variant information

Variant position:  939
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 Histidine (H) to Glutamine (Q) at position 939 (H939Q, p.His939Gln).
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 polar.
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 DRVT; results in a non-functional channel.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  939
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  2009
The length of the canonical sequence.

Location on the sequence:   CVCKIASDCQLPRWHMNDFF  H SFLIVFRVLCGEWIETMWDC
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                         CVCKIASDCQLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC

Mouse                         CVCKIATDCKLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC

Rat                           CVCKIATDCKLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC

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 1 – 2009 Sodium channel protein type 1 subunit alpha
Intramembrane 937 – 957 Pore-forming
Repeat 750 – 1022 II
Disulfide bond 919 – 919 Interchain; with SCN2B or SCN4B
Disulfide bond 919 – 919 Interchain; with the conotoxin GVIIJ (when the channel is not linked to SCN2B or SCN4B; the bond to SCN2B or SCN4B protects the channel from the inhibition by toxin)


Literature citations

De novo SCN1A mutations are a major cause of severe myoclonic epilepsy of infancy.
Claes L.; Ceulemans B.; Audenaert D.; Smets K.; Loefgren A.; Del-Favero J.; Ala-Mello S.; Basel-Vanagaite L.; Plecko B.; Raskin S.; Thiry P.; Wolf N.I.; Van Broeckhoven C.; De Jonghe P.;
Hum. Mutat. 21:615-621(2003)
Cited for: VARIANTS DRVT HIS-393; GLN-939; ARG-959; ARG-1434; SER-1661 AND GLU-1749;

Nonfunctional SCN1A is common in severe myoclonic epilepsy of infancy.
Ohmori I.; Kahlig K.M.; Rhodes T.H.; Wang D.W.; George A.L. Jr.;
Epilepsia 47:1636-1642(2006)
Cited for: CHARACTERIZATION OF VARIANTS DRVT GLU-177; SER-227; HIS-393; ASN-426; GLN-939; ARG-959; PHE-1289 DEL AND ILE-1909;

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.