SCN5A Variant D2000Y
Summary of observed carriers, functional annotations, and structural context for SCN5A D2000Y. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
5%
0/13 effective observations
Estimated BrS1 penetrance
6%
0/13 effective observations
Total carriers
3
0 BrS1 · 0 LQT3 · 3 unaffected
Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -3.34 | 0.938 | -0.68 | 0.461 | 3 | 2 |
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
| Source | Year | Carriers | Unaffected | LQT3 | BrS1 | Other | Other Disease |
|---|---|---|---|---|---|---|---|
| Literature, cohort, and gnomAD | – | 3 | 3 | 0 | 0 | – | |
| Variant features alone | – | 15 | 15 | 0 | 0 | – | – |
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.
| Neighbour residue | Distance (Å) | Observed variants |
|---|---|---|
| 1985 | 15 | S1985R, |
| 1986 | 14 | D1986N, D1986G, |
| 1987 | 14 | N1987K, |
| 1988 | 13 | L1988R, |
| 1989 | 13 | |
| 1990 | 12 | V1990L, |
| 1991 | 11 | R1991Q, R1991W, |
| 1992 | 11 | G1992A, |
| 1993 | 10 | |
| 1994 | 9 | |
| 1995 | 8 | Y1995X, |
| 1996 | 8 | S1996N, S1996R, |
| 1997 | 7 | H1997R, |
| 1998 | 5 | |
| 1999 | 4 | |
| 2000 | 0 | D2000Y, |
| 2001 | 4 | |
| 2002 | 5 | A2002T, |
| 2003 | 7 | D2003N, |
| 2004 | 8 | F2004V, F2004L, p.F2004dup, F2004I, |
| 2005 | 8 | P2005L, P2005S, P2005A, |
| 2006 | 9 | P2006T, p.Pro2006del, P2006A, p.P2006LfsX32, |
| 2007 | 10 | p.S2007FfsX7, |
| 2008 | 11 | P2008L, |
| 2009 | 11 | D2009E, |
| 2010 | 12 | R2010G, |
| 2011 | 13 | |
| 2012 | 13 | R2012H, R2012C |
| 2013 | 14 | |
| 2014 | 14 | |
| 2015 | 15 |