Is ACE p.Met1Ile (c.3G>T) pathogenic?

ACE p.Met1Ile (c.3G>T) is classified Likely pathogenic in ACE (ClinVar, Single submitter, 1 submitter). Very rare (popmax 0.000482%, nfe); Associated with renal tubular dysgenesis of genetic origin.

What condition is associated with ACE p.Met1Ile (c.3G>T)?

ACE p.Met1Ile (c.3G>T) is associated with renal tubular dysgenesis of genetic origin (ClinVar).

How common is ACE p.Met1Ile (c.3G>T) in the general population?

ACE p.Met1Ile (c.3G>T) is very rare (popmax 0.000482%, nfe) (gnomAD).

ACE p.Met1Ile

c.3G>T · rs2510680823 · VCV2585611

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

start-loss

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000482%, nfe)

Conditions

renal tubular dysgenesis of genetic origin

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	start-loss	predicted loss-of-function
REVEL	0.235	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.9	GERP 2, phastCons 1
Overall
CADD	21.8	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000482% European (non-Finnish) · 5/1,036,490 alleles

Filtering AF 0.000141% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000103%

Overall 0.000382% 5/1,308,630 alleles · very rare exomes 5/1,157,466 · genomes 0/151,164 · joint denominator

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: ACE
Protein: p.Met1Ile
Coding: c.3G>T
MANE Select: NM_000789
dbSNP: rs2510680823
Type: single nucleotide variant
Location: chr17:63477097 (GRCh38)
Gene constraint: LOEUF 0.88 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.38 · 97 PDB

Full ACE gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

renal tubular dysgenesis of genetic origin — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACE p.Met1Thr Pathogenic/Likely pathogenic ★★ same residue
ACE p.Met1Lys Likely pathogenic ★ same residue
ACE p.Met1Arg Uncertain significance ★ same residue
ACE c.1342+1G>T Likely pathogenic ★★ same condition
ACE c.3503+1G>C Likely pathogenic ★★ same condition
ACE c.945+2T>G Likely pathogenic ★★ same condition
ACE p.Arg265Ter Pathogenic ★★ same condition
ACE p.Arg508Ter Pathogenic ★★ 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/ace-p-met1ile (accessed [today's date]).

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