SCN5A Variant L959P
Summary of observed carriers, functional annotations, and structural context for SCN5A L959P. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
11%
0/13 effective observations
Estimated BrS1 penetrance
7%
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 (%) |
|---|---|---|---|---|---|
| -6.78 | 1 | -2.06 | 0.86 | 2 | 17 |
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 |
|---|---|---|
| 944 | 15 | |
| 945 | 14 | D945G, |
| 946 | 14 | |
| 947 | 13 | |
| 948 | 13 | |
| 949 | 12 | |
| 950 | 11 | P950X, |
| 951 | 11 | D951X, c.2850delT, |
| 952 | 10 | E952K, |
| 953 | 9 | D953E, D953Y, D953E, |
| 954 | 8 | R954G, |
| 955 | 8 | p.E955DfsX74, |
| 956 | 7 | M956I, M956I, M956I, M956T, |
| 957 | 5 | |
| 958 | 4 | |
| 959 | 0 | L959P, |
| 960 | 4 | Q960K, |
| 961 | 5 | |
| 962 | 7 | |
| 963 | 8 | |
| 964 | 8 | A964G |
| 965 | 9 | R965C, R965H, R965L, |
| 966 | 10 | |
| 967 | 11 | Q967R, |
| 968 | 11 | |
| 969 | 12 | G969C, G969S, |
| 970 | 13 | |
| 971 | 13 | R971C, R971H, |
| 972 | 14 | c.2914_2923delTTTGTCAAGC, |
| 973 | 14 | |
| 974 | 15 | K974D, |