SCN5A Variant F392Y

Summary of observed carriers, functional annotations, and structural context for SCN5A F392Y. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

16%

0/10 effective observations

Estimated BrS1 penetrance

29%

2/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

F392Y has not been reported in gnomAD. This residue resides in a Mild_Hotspot region for Brugada syndrome and a Mild_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 2 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 (%)
NA NA NA 0.919 37 18

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 – 0 0 0 0 –
Variant features alone – 15 13 0 2 – –

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 F392Y.
Neighbour residue Distance (Å) Observed variants
364 11
271 8 L271V,
1702 13
266 11 L266H,
276 13 L276P, L276Q,
363 15
387 13
362 14
270 12 Q270K,
1627 12
396 6 V396A, V396L,
385 11 A385T,
1624 11 V1624I,
355 9 F355C, F355I,
391 6
401 13 S401P,
388 10 I388S,
371 13 Q371E,
361 12
260 13
366 14
365 9
1706 14 Q1706H, Q1706H,
384 13 S384T,
354 13
386 11 G386R, G386E, G386R,
369 12 M369K,
378 10
402 14 F402L, F402L, F402L,
267 7
379 14
1625 15
262 13 S262G,
399 10
272 8
397 9 I397F, I397V, I397T,
274 15 G274C,
261 12
273 14
1628 14
392 0
389 7 Y389X, Y389H,
269 11
1620 12 T1620K, T1620M,
395 6
393 4
390 8
394 7
275 13 N275K, N275K,
264 7
382 10
265 9 A265V,
374 11 W374G,
1705 12
358 15
367 13 R367L, R367C, R367H,
263 11 V263I,
370 15 T370M,
381 9 c.1141-3C>A, c.1140+1G>A,
368 8
380 14
268 7 G268S,
377 10
398 12
400 11 G400A, G400R, G400E, G400R,
1621 13
353 15 T353I,
1623 13 R1623X, R1623Q, R1623L, c.4867delC,