SCN5A p.Pro47=
c.141C>A · rs571894716 · VCV1585835
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, amr)
Conditions
1
cardiac rhythm disease
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.9 |
| Overall | ||
| CADD | 0.056 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
Admixed American · 4/59,906 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000682%
11/1,613,124 alleles · very rare
exomes 8/1,461,082 · genomes 3/152,042 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00668% | 14,976 |
| European (non-Finnish) | 0.000593% | 168,528 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SCN5A
- Protein
- p.Pro47=
- Coding
- c.141C>A
- MANE Select
- NM_000335
- dbSNP
- rs571894716
- Type
- single nucleotide variant
- Location
- chr3:38633167 (GRCh38)
- Gene constraint
- LOEUF 0.372 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.02 · 16 PDB
- Residue 47
- the 'disordered' region
Similar variants
- SCN5A p.Pro47Leu Uncertain significance ★ ⚠ same residue
- SCN5A c.1338+2T>A Pathogenic/Likely pathogenic ★★ same condition
- SCN5A c.2263-2A>G Likely pathogenic ★★ same condition
- SCN5A c.3508+1G>T Likely pathogenic ★★ same condition
- SCN5A c.3837+1G>A Pathogenic ★★ same condition
- SCN5A c.4242+1G>C Pathogenic/Likely pathogenic ★★ same condition
- SCN5A c.611+1G>A Pathogenic ★★ same condition
- SCN5A c.934+1G>A Pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/scn5a-p-pro47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown