Paralogue Annotation for SCN5A residue 1488

Residue details

Gene: SCN5A
Reference Sequences: LRG: LRG_289, Ensembl variant: ENST00000333535 / ENSP00000328968
Amino Acid Position: 1488
Reference Amino Acid: T - Threonine
Protein Domain: Interdomain Linker III-IV

Paralogue Variants mapped to SCN5A residue 1488

Paralogue	Variant	Associated Disease	Mapping Quality	Consensus	Pubmed
SCN4A	T1313A	Paramyotonia congenita	High	5	14617673
SCN9A	T1464I	Paroxysmal extreme pain disorder	High	5	17145499
SCN4A	T1313M	Hyperkalaemic periodic paralysis	High	5

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	SFFTLNLFIGVIIDNFNQQKKKLGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1503
SCN1A	SFFTLNLFIGVIIDNFNQQKKKFGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1516
SCN2A	SFFTLNLFIGVIIDNFNQQKKKFGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1506
SCN3A	SFFTLNLFIGVIIDNFNQQKKKFGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1501
SCN4A	SFFTLNLFIGVIIDNFNQQKKKLGGKDIFM>T<EEQKKYY------NAM---KK-L----G-S	1328
SCN7A	VFLPLSMLITVIIDNFNKHKIKLGGSNIFI>T<VKQRKQY------RRL---KK-L----M-Y	1226
SCN8A	SFFTLNLFIGVIIDNFNQQKKKFGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1497
SCN9A	SFFTLNLFIGVIIDNFNQQKKKLGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1479
SCN10A	GFFTLNLFVGVIIDNFNQQKKKLGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1451
SCN11A	SFFTLNLFIGVIIDNFNQQQKKLGGQDIFM>T<EEQKKYY------NAM---KK-L----G-S	1341
CACNA1A	PFFFVNIFVALIIITFQEQGDKM----MEE>Y<SLEKNER------ACI---DFAI------S	1540
CACNA1B	PFFFVNIFVALIIITFQEQGDKV----MSE>C<SLEKNER------ACI---DFAI------S	1446
CACNA1C	AFFMMNIFVGFVIVTFQEQGEQE----YKN>C<ELDKNQR------QCV---EYAL------K	1195
CACNA1D	AFFMMNIFVGFVIVTFQEQGEKE----YKN>C<ELDKNQR------QCV---EYAL------K	1201
CACNA1E	PFFFVNIFVALIIITFQEQGDKM----MEE>C<SLEKNER------ACI---DFAI------S	1452
CACNA1F	AFFMMNIFVGFVIITFRAQGEQE----YQN>C<ELDKNQR------QCV---EYAL------K	1166
CACNA1G	AFFVLNMFVGVVVENFHKCRQHQEEEEARR>R<EEKRLRRLEKKRRNLML--DDVI-----AS	1578
CACNA1H	SFFVLNMFVGVVVENFHKCRQHQEAEEARR>R<EEK----------RLRRLERRRRSTFPSPE	1593
CACNA1I	SFFVLNMFVGVVVENFHKCRQHQEAEEARR>R<EEK----------RLRRLEKKRR------K	1463
CACNA1S	AFFMMNIFVGFVIVTFQEQGETE----YKN>C<ELDKNQR------QCV---QYAL------K	1094
cons	> <

See full Alignment of Paralogues

Known Variants in SCN5A

Protein	CDS	Disease Classification	Disease	dbSNP links	Effect Prediction
p.T1488R	c.4463C>G	Inherited Arrhythmia	LQTS	rs199473259	SIFT: deleterious Polyphen: possibly damaging
Reports		Inherited Arrhythmia	LQTS	Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Heart Rhythm. 2009 6(9):1297-303. 19716085