SCN5A Variant V1980F
Summary of observed carriers, functional annotations, and structural context for SCN5A V1980F. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
5%
0/13 effective observations
Estimated BrS1 penetrance
8%
1/13 effective observations
Total carriers
3
0 BrS1 · 0 LQT3 · 3 unaffected
Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -4.56 | 0.995 | -2.98 | 0.623 | 0 | 6 |
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 | 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.
| Neighbour residue | Distance (Å) | Observed variants |
|---|---|---|
| 1965 | 15 | S1965G, S1965N, |
| 1966 | 14 | |
| 1967 | 14 | p.S1967LfsX12, |
| 1968 | 13 | I1968T, I1968S, I1968N, I1968V, I1968M, |
| 1969 | 13 | |
| 1970 | 12 | p.S1970_S1972del, |
| 1971 | 11 | |
| 1972 | 11 | |
| 1973 | 10 | F1973L, |
| 1974 | 9 | |
| 1975 | 8 | P1975T, |
| 1976 | 8 | S1976C, |
| 1977 | 7 | Y1977N, |
| 1978 | 5 | |
| 1979 | 4 | |
| 1980 | 0 | V1980F, |
| 1981 | 4 | |
| 1982 | 5 | R1982T, |
| 1983 | 7 | A1983V, A1983G, |
| 1984 | 8 | T1984I, |
| 1985 | 8 | S1985R, |
| 1986 | 9 | D1986N, D1986G, |
| 1987 | 10 | N1987K, |
| 1988 | 11 | L1988R, |
| 1989 | 11 | |
| 1990 | 12 | V1990L, |
| 1991 | 13 | R1991Q, R1991W, |
| 1992 | 13 | G1992A, |
| 1993 | 14 | |
| 1994 | 14 | |
| 1995 | 15 | Y1995X |