Paralogue Annotation for SCN5A residue 1250

Residue details

Gene: SCN5A
Reference Sequences: LRG: LRG_289, Ensembl variant: ENST00000333535 / ENSP00000328968
Amino Acid Position: 1250
Reference Amino Acid: F - Phenylalanine
Protein Domain: TM Domain 3


Paralogue Variants mapped to SCN5A residue 1250

ParalogueVariantAssociated DiseaseMapping QualityConsensusPubmed
SCN1AF1263LMyoclonic epilepsy of infancyHigh9 12566275

To assess whether the paralogue annotation here confidently predicts that variation at this residue is pathogenic, it is important to check the reports in the Pubmed links above to ascertain that the mutations in these paralogues have been proved likely to be disease-causing. It is also important to check that the direction of effect of the variant in the paralogue is compatible with your observed phenotype in SCN5A.



SCN5AGALAFEDIYLEERKTIKVLLEYADKMFTYV>F<VLEMLLKWVAYGF----KKYFTNAWCWLDF1276
SCN1AGALAFEDIYIDQRKTIKTMLEYADKVFTYI>F<ILEMLLKWVAYGY----QTYFTNAWCWLDF1289
SCN2AGALAFEDIYIEQRKTIKTMLEYADKVFTYI>F<ILEMLLKWVAYGF----QVYFTNAWCWLDF1279
SCN3AGALAFEDIYIEQRKTIKTMLEYADKVFTYI>F<ILEMLLKWVAYGF----QTYFTNAWCWLDF1277
SCN4AGALAFEDIYIEQRRVIRTILEYADKVFTYI>F<IMEMLLKWVAYGF----KVYFTNAWCWLDF1102
SCN7AGTLAFEDIYMDQRKTIKILLEYADMIFTYI>F<ILEMLLKWMAYGF----KAYFSNGWYRLDF1005
SCN8AGALAFEDIYIEQRKTIRTILEYADKVFTYI>F<ILEMLLKWTAYGF----VKFFTNAWCWLDF1269
SCN9AGALAFEDIYIERKKTIKIILEYADKIFTYI>F<ILEMLLKWIAYGY----KTYFTNAWCWLDF1252
SCN10AGSLAFEDYYLDQKPTVKALLEYTDRVFTFI>F<VFEMLLKWVAYGF----KKYFTNAWCWLDF1223
SCN11AGALIFEDVHLENQPKIQELLNCTDIIFTHI>F<ILEMVLKWVAFGF----GKYFTSAWCCLDF1127
CACNA1AIALAAEDPV-QPNAPRNNVLRYFDYVFTGV>F<TFEMVIKMIDLGLVLHQGAYFRDLWNILDF1318
CACNA1BIALAAEDPV-RTDSPRNNALKYLDYIFTGV>F<TFEMVIKMIDLGLLLHPGAYFRDLWNILDF1225
CACNA1CISLAAEDPV-QHTSFRNHILFYFDIVFTTI>F<TIEIALKMTAYGAFLHKGSFCRNYFNILDL974
CACNA1DAALAAEDPI-RSHSFRNTILGYFDYAFTAI>F<TVEILLKMTTFGAFLHKGAFCRNYFNLLDM980
CACNA1EIALAAEDPV-LTNSERNKVLRYFDYVFTGV>F<TFEMVIKMIDQGLILQDGSYFRDLWNILDF1227
CACNA1FVSLAAEDPI-RAHSFRNHILGYFDYAFTSI>F<TVEILLKMTVFGAFLHRGSFCRSWFNMLDL945
CACNA1GITIAMERPKIDPHSAERIFLTLSNYIFTAV>F<LAEMTVKVVALGWCFGEQAYLRSSWNVLDG1351
CACNA1HVTIALERPDIDPGSTERVFLSVSNYIFTAI>F<VAEMMVKVVALGLLSGEHAYLQSSWNLLDG1369
CACNA1IITIALERPQIEAGSTERIFLTVSNYIFTAI>F<VGEMTLKVVSLGLYFGEQAYLRSSWNVLDG1245
CACNA1SAALAAEDPI-RADSMRNQILKHFDIGFTSV>F<TVEIVLKMTTYGAFLHKGSFCRNYFNMLDL873
cons                              > <                              

See full Alignment of Paralogues


Known Variants in SCN5A

ProteinCDSDisease ClassificationDiseasedbSNP linksEffect Prediction
p.F1250Lc.3748T>C Inherited ArrhythmiaLQTSrs45589741SIFT: deleterious
Polyphen: probably damaging
ReportsOther Cardiac Phenotype Allelic variants in long-QT disease genes in patients with drug-associated torsades de pointes. Circulation. 2002 105(16):1943-8. 11997281
Inherited ArrhythmiaLQTS Genetic variations of KCNQ1, KCNH2, SCN5A, KCNE1, and KCNE2 in drug-induced long QT syndrome patients. J Mol Med (Berl). 2004 82(3):182-8. 14760488