Is SNTA1 p.Pro70= (c.210G>T) pathogenic?

SNTA1 p.Pro70= (c.210G>T) is classified Likely benign in SNTA1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-06-16). Very rare (popmax 0.0038%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with SNTA1 p.Pro70= (c.210G>T)?

SNTA1 p.Pro70= (c.210G>T) is associated with Cardiovascular phenotype, long QT syndrome (ClinVar).

How common is SNTA1 p.Pro70= (c.210G>T) in the general population?

SNTA1 p.Pro70= (c.210G>T) is very rare (popmax 0.0038%, nfe) (gnomAD).

SNTA1 p.Pro70=

c.210G>T · rs751651742 · VCV1195792

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0038%, nfe)

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 -2.4	GERP -2.7
Overall
CADD	5.879	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0038% European (non-Finnish) · 40/1,053,932 alleles

Filtering AF 0.00286% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00252%

Overall 0.00313% 42/1,340,886 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00398%	25,117
European (non-Finnish)grpmax	0.0038%	26,348

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: SNTA1
Protein: p.Pro70=
Coding: c.210G>T
MANE Select: NM_003098
dbSNP: rs751651742
Type: single nucleotide variant
Location: chr20:33443411 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.00
Residue 70: the ph 1 domain; the 'disordered' region

Full SNTA1 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

Also linked: long QT syndrome

Similar variants

SNTA1 p.Pro70Gln 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.Ala122Thr Uncertain significance ★★ ⚠ same condition
SNTA1 p.Ala255Pro 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-pro70 (accessed [today's date]).

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