Is SNTA1 p.Pro273= (c.819G>A) pathogenic?

SNTA1 p.Pro273= (c.819G>A) is classified Likely benign in SNTA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-21). Ultra-rare (popmax 0.0111%, eas); Associated with Cardiovascular phenotype.

What condition is associated with SNTA1 p.Pro273= (c.819G>A)?

SNTA1 p.Pro273= (c.819G>A) is associated with Cardiovascular phenotype (ClinVar).

How common is SNTA1 p.Pro273= (c.819G>A) in the general population?

SNTA1 p.Pro273= (c.819G>A) is ultra-rare (popmax 0.0111%, eas) (gnomAD).

SNTA1 p.Pro273=

c.819G>A · rs761959794 · VCV1762383

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0111%, eas)

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 0.32	GERP -3.3, phastCons 0.93
Overall
CADD	2.638	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0111% East Asian · 5/44,888 alleles

Filtering AF 0.00434% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00276%

Overall 0.00143% 23/1,613,794 alleles · ultra-rare exomes 21/1,461,610 · genomes 2/152,184 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0111%	8,978
African / African-American	0.00267%	37,462
South Asian	0.0022%	45,532
Remaining individualsnot grpmax-eligible	0.0016%	62,484
European (non-Finnish)	0.0011%	90,771

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.Pro273=
Coding: c.819G>A
MANE Select: NM_003098
dbSNP: rs761959794
Type: single nucleotide variant
Location: chr20:33412665 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.00

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

Similar variants

SNTA1 p.Pro273Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
SNTA1 p.Pro273Ser Conflicting classifications of pathogenicity ★ ⚠ 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 p.Ala122Thr Uncertain significance ★★ ⚠ same condition
SNTA1 p.Ala255Pro Uncertain significance ★★ ⚠ same condition
SNTA1 p.Ala341Thr 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-pro273 (accessed [today's date]).

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