Is SCN10A p.Phe799= (c.2397T>C) pathogenic?

SCN10A p.Phe799= (c.2397T>C) is classified Likely benign in SCN10A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-27). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with SCN10A p.Phe799= (c.2397T>C)?

SCN10A p.Phe799= (c.2397T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is SCN10A p.Phe799= (c.2397T>C) in the general population?

SCN10A p.Phe799= (c.2397T>C) is absent from gnomAD v4.1 (gnomAD).

SCN10A p.Phe799=

c.2397T>C · VCV3438133

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

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 -0.086	GERP -4.1, phastCons 0.014
Overall
CADD	6.987	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SCN10A
Protein: p.Phe799=
Coding: c.2397T>C
MANE Select: NM_006514
Type: single nucleotide variant
Location: chr3:38728785 (GRCh38)
Gene constraint: LOEUF 1.058 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.06 · 8 PDB
Residue 799: an α-helix

Full SCN10A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SCN10A c.1093-3C>A Uncertain significance ★★ same condition
SCN10A c.270+2T>C Uncertain significance ★★ same condition
SCN10A c.271-2A>G Uncertain significance ★★ same condition
SCN10A c.470+5G>A Uncertain significance ★★ same condition
SCN10A p.Ala1170Asp Uncertain significance ★★ ⚠ same condition
SCN10A p.Ala1235Glu Uncertain significance ★★ ⚠ same condition
SCN10A p.Ala1235Val Uncertain significance ★★ ⚠ same condition
SCN10A p.Ala1304Thr Uncertain significance ★★ ⚠ 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/scn10a-p-phe799 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown