Is SNTA1 p.Arg5= (c.13A>C) pathogenic?

SNTA1 p.Arg5= (c.13A>C) is classified Likely benign in SNTA1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-13). Very rare (popmax 0.00792%, amr); Associated with Cardiovascular phenotype.

What condition is associated with SNTA1 p.Arg5= (c.13A>C)?

SNTA1 p.Arg5= (c.13A>C) is associated with Cardiovascular phenotype, long QT syndrome (ClinVar).

How common is SNTA1 p.Arg5= (c.13A>C) in the general population?

SNTA1 p.Arg5= (c.13A>C) is very rare (popmax 0.00792%, amr) (gnomAD).

SNTA1 p.Arg5=

c.13A>C · rs980437334 · VCV699388

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00792%, amr)

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 2.5	GERP -2.8, phastCons 1
Overall
CADD	13.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00792% Admixed American · 2/25,258 alleles

Filtering AF 0.00453% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00413%

Overall 0.00489% 60/1,227,682 alleles · very rare exomes 51/1,076,714 · genomes 9/150,968 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00792%	12,629
European (non-Finnish)	0.00579%	17,265
Remaining individualsnot grpmax-eligible	0.0023%	43,442

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.Arg5=
Coding: c.13A>C
MANE Select: NM_003098
dbSNP: rs980437334
Type: single nucleotide variant
Location: chr20:33443608 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.00
Residue 5: 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 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
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-arg5 (accessed [today's date]).

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