Paralogue Annotation for SCN5A residue 1260

Residue details

Gene: SCN5A
Reference Sequences: LRG: LRG_289, Ensembl variant: ENST00000333535 / ENSP00000328968
Amino Acid Position: 1260
Reference Amino Acid: A - Alanine
Protein Domain: TM Domain 3

Paralogue Variants mapped to SCN5A residue 1260

Paralogue	Variant	Associated Disease	Mapping Quality	Consensus	Pubmed
SCN9A	A1236E	Congenital indifference to pain	High	9	25995458, 25995458
SCN1A	A1273V	Dravet syndrome	High	9	26096185

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.

SCN5A	EERKTIKVLLEYADKMFTYVFVLEMLLKWV>A<YGF----KKYFTNAWCWLDFLIVDVSLVSL	1286
SCN1A	DQRKTIKTMLEYADKVFTYIFILEMLLKWV>A<YGY----QTYFTNAWCWLDFLIVDVSLVSL	1299
SCN2A	EQRKTIKTMLEYADKVFTYIFILEMLLKWV>A<YGF----QVYFTNAWCWLDFLIVDVSLVSL	1289
SCN3A	EQRKTIKTMLEYADKVFTYIFILEMLLKWV>A<YGF----QTYFTNAWCWLDFLIVDVSLVSL	1287
SCN4A	EQRRVIRTILEYADKVFTYIFIMEMLLKWV>A<YGF----KVYFTNAWCWLDFLIVDVSIISL	1112
SCN7A	DQRKTIKILLEYADMIFTYIFILEMLLKWM>A<YGF----KAYFSNGWYRLDFVVVIVFCLSL	1015
SCN8A	EQRKTIRTILEYADKVFTYIFILEMLLKWT>A<YGF----VKFFTNAWCWLDFLIVAVSLVSL	1279
SCN9A	ERKKTIKIILEYADKIFTYIFILEMLLKWI>A<YGY----KTYFTNAWCWLDFLIVDVSLVTL	1262
SCN10A	DQKPTVKALLEYTDRVFTFIFVFEMLLKWV>A<YGF----KKYFTNAWCWLDFLIVNISLISL	1233
SCN11A	ENQPKIQELLNCTDIIFTHIFILEMVLKWV>A<FGF----GKYFTSAWCCLDFIIVIVSVTTL	1137
CACNA1A	QPNAPRNNVLRYFDYVFTGVFTFEMVIKMI>D<LGLVLHQGAYFRDLWNILDFIVVSGALVAF	1328
CACNA1B	RTDSPRNNALKYLDYIFTGVFTFEMVIKMI>D<LGLLLHPGAYFRDLWNILDFIVVSGALVAF	1235
CACNA1C	QHTSFRNHILFYFDIVFTTIFTIEIALKMT>A<YGAFLHKGSFCRNYFNILDLLVVSVSLISF	984
CACNA1D	RSHSFRNTILGYFDYAFTAIFTVEILLKMT>T<FGAFLHKGAFCRNYFNLLDMLVVGVSLVSF	990
CACNA1E	LTNSERNKVLRYFDYVFTGVFTFEMVIKMI>D<QGLILQDGSYFRDLWNILDFVVVVGALVAF	1237
CACNA1F	RAHSFRNHILGYFDYAFTSIFTVEILLKMT>V<FGAFLHRGSFCRSWFNMLDLLVVSVSLISF	955
CACNA1G	DPHSAERIFLTLSNYIFTAVFLAEMTVKVV>A<LGWCFGEQAYLRSSWNVLDGLLVLISVIDI	1361
CACNA1H	DPGSTERVFLSVSNYIFTAIFVAEMMVKVV>A<LGLLSGEHAYLQSSWNLLDGLLVLVSLVDI	1379
CACNA1I	EAGSTERIFLTVSNYIFTAIFVGEMTLKVV>S<LGLYFGEQAYLRSSWNVLDGFLVFVSIIDI	1255
CACNA1S	RADSMRNQILKHFDIGFTSVFTVEIVLKMT>T<YGAFLHKGSFCRNYFNMLDLLVVAVSLISM	883
cons	> <

See full Alignment of Paralogues

Known Variants in SCN5A

Protein	CDS	Disease Classification	Disease	dbSNP links	Effect Prediction
p.A1260D	c.3779C>A	Putative Benign		rs199540275	SIFT: deleterious Polyphen: probably damaging