Is SNTA1 p.Val397= (c.1191G>C) pathogenic?

SNTA1 p.Val397= (c.1191G>C) is classified Likely benign in SNTA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-09-23). Absent from gnomAD v4.1; Associated with long QT syndrome.

What condition is associated with SNTA1 p.Val397= (c.1191G>C)?

SNTA1 p.Val397= (c.1191G>C) is associated with long QT syndrome (ClinVar).

How common is SNTA1 p.Val397= (c.1191G>C) in the general population?

SNTA1 p.Val397= (c.1191G>C) is absent from gnomAD v4.1 (gnomAD).

SNTA1 p.Val397=

c.1191G>C · rs1555816721 · VCV527043

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

long QT syndrome

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 4.9	GERP 1.7, phastCons 1
Overall
CADD	12.49	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: SNTA1
Protein: p.Val397=
Coding: c.1191G>C
MANE Select: NM_003098
dbSNP: rs1555816721
Type: single nucleotide variant
Location: chr20:33410181 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.00
Residue 397: the ph 2 domain

Full SNTA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

long QT syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SNTA1 c.1425+1G>A Uncertain significance ★★ same condition
SNTA1 c.497-3C>T Uncertain significance ★★ same condition
SNTA1 c.497-5A>G Uncertain significance ★★ same condition
SNTA1 c.702-3C>T Uncertain significance ★★ same condition
SNTA1 c.910-3C>T Uncertain significance ★★ same condition
SNTA1 p.Ala255Pro Uncertain significance ★★ ⚠ same condition
SNTA1 p.Ala261Val Uncertain significance ★★ ⚠ same condition
SNTA1 p.Ala289Thr 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/snta1-p-val397 (accessed [today's date]).

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