SCN5A Variant P1090Q

Summary of observed carriers, functional annotations, and structural context for SCN5A P1090Q. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

3%

0/11 effective observations

Estimated BrS1 penetrance

2%

0/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

P1090Q 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 0 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 (%)
-0.26 0 1 0.279 1 0

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 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.

Previously observed variants near P1090Q.
Neighbour residue Distance (Å) Observed variants
1075 15
1076 14
1077 14 c.3228+2delT,
1078 13
1079 13 S1079T, S1079F, S1079Y,
1080 12
1081 11
1082 11 V1082A,
1083 10 S1083C,
1084 9 G1084S, G1084R, G1084D,
1085 8
1086 8
1087 7
1088 5 A1088T, A1088V,
1089 4
1090 0 P1090Q, P1090L,
1091 4 D1091A, D1091Y,
1092 5
1093 7
1094 8
1095 8 W1095X, W1095C, W1095C,
1096 9 S1096C, S1096G,
1097 10 Q1097H, c.3288+2delT, Q1097H,
1098 11 V1098L, V1098L, V1098M,
1099 11
1100 12 A1100T, A1100V,
1101 13
1102 13 A1102T,
1103 14 S1103F, S1103Y,
1104 14
1105 15 E1105V, E1105X,