SCN5A Variant D1551Y

Summary of observed carriers, functional annotations, and structural context for SCN5A D1551Y. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

4%

0/11 effective observations

Estimated BrS1 penetrance

16%

1/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

D1551Y is present in 1 alleles in gnomAD. This residue resides in a Non_Hotspot region for Brugada syndrome and a Non_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 0 individuals for LQT3.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
-6.8 0.972 -3.67 0.885 9 1

PROVEAN scores below -2 suggest deleterious impact. REVEL scores above 0.5–0.75 are often interpreted as likely pathogenic. PolyPhen-2 scores above 0.85 are typically pathogenic. Penetrance density summarises neighbouring residue risk (Kroncke et al. 2019).

Reported carrier data

Observed carriers by publication or cohort.
Source Year Carriers Unaffected LQT3 BrS1 Other Other Disease
Literature, cohort, and gnomAD – 1 1 0 0 –
Variant features alone – 15 14 0 1 – –

Totals may differ from individual publications due to duplicate patients removed during curation.

Nearby variants

Neighbouring residues within 15 Ångström provide structural context. Variants listed in the right-most column have been observed clinically or in gnomAD.

Previously observed variants near D1551Y.
Neighbour residue Distance (Å) Observed variants
277 10
276 14 L276Q, L276P,
270 12 Q270K,
1552 6 Q1552R, Q1552L,
355 15 F355I, F355C,
1549 7
278 13 H278D, H278R,
1556 11
356 9 D356N,
1558 13
1557 9 I1557V,
343 8
354 14
1550 4
1560 13 L1560F, L1560F
357 12
272 15
274 9 G274C,
273 8
1553 7 S1553R, S1553R, S1553R,
269 12
345 12
275 12 N275K, N275K,
347 15
1548 9 E1548K, G1548K,
1555 12 E1555K,
342 14
1551 0 D1551N, D1551Y,
346 14 E346K, E346G, E346X, E346D, E346D,
1547 12 V1547L, V1547L,
1554 9
344 11 A344S,