Is SNTA1 p.Pro353= (c.1059C>T) pathogenic?

SNTA1 p.Pro353= (c.1059C>T) is classified Likely benign in SNTA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-18). Absent from gnomAD v4.1; Associated with long QT syndrome.

What condition is associated with SNTA1 p.Pro353= (c.1059C>T)?

SNTA1 p.Pro353= (c.1059C>T) is associated with long QT syndrome (ClinVar).

How common is SNTA1 p.Pro353= (c.1059C>T) in the general population?

SNTA1 p.Pro353= (c.1059C>T) is absent from gnomAD v4.1 (gnomAD).

SNTA1 p.Pro353=

c.1059C>T · VCV4774405

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,607,294)

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 0.78	GERP -0.91, phastCons 1
Overall
CADD	8.299	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,607,294). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SNTA1
Protein: p.Pro353=
Coding: c.1059C>T
MANE Select: NM_003098
Type: single nucleotide variant
Location: chr20:33410313 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.00
Residue 353: 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 p.Pro353Ala Uncertain significance ★ ⚠ same residue
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

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-pro353 (accessed [today's date]).

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