AGT p.Pro393=
c.1179C>T · rs368537638 · VCV2972789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, nfe)
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 -0.028 | GERP -3.6 |
| Overall | ||
| CADD | 7.326 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
European (non-Finnish) · 195/1,180,040 alleles
Filtering AF
0.0146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0139%
Overall
0.0123%
199/1,614,084 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0165% | 6,051 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| Admixed American | 0.00167% | 60,014 |
| African / African-American | 0.00133% | 74,916 |
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
- AGT
- Protein
- p.Pro393=
- Coding
- c.1179C>T
- MANE Select
- NM_001384479
- dbSNP
- rs368537638
- Type
- single nucleotide variant
- Location
- chr1:230704256 (GRCh38)
- Gene constraint
- LOEUF 1.202 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.74 · 22 PDB
- Residue 393
- an α-helix
Similar variants
- AGT c.1060C>T Pathogenic/Likely pathogenic ★★ same type
- AGT c.829+1G>T Pathogenic/Likely pathogenic ★★ same type
- AGT c.1195G>A Uncertain significance ★★ ⚠ same type
- AGT c.856G>T Uncertain significance ★★ ⚠ same type
- AGT c.862C>T Uncertain significance ★★ ⚠ same type
- AGT c.-17G>C Uncertain significance ★★ ⚠ same type
- AGT p.Arg165Gln Uncertain significance ★★ same type
- AGT p.Arg366Leu Uncertain significance ★★ ⚠ same type
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/agt-p-pro393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown