Is AGXT p.Arg360Pro (c.1079G>C) pathogenic?

AGXT p.Arg360Pro (c.1079G>C) is classified Likely pathogenic in AGXT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-09-08). AlphaMissense: likely pathogenic (0.9804); Absent from gnomAD v4.1; Associated with nephrolithiasis.

What condition is associated with AGXT p.Arg360Pro (c.1079G>C)?

AGXT p.Arg360Pro (c.1079G>C) is associated with nephrolithiasis, nephrocalcinosis (ClinVar).

How common is AGXT p.Arg360Pro (c.1079G>C) in the general population?

AGXT p.Arg360Pro (c.1079G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AGXT p.Arg360Pro (c.1079G>C)?

AlphaMissense predicts likely pathogenic (score 0.9804) — an in-silico prediction, not a clinical call.

AGXT p.Arg360Pro

c.1079G>C · rs180177161 · VCV548671

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9804 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

nephrolithiasis

Computational evidence

Protein change
AlphaMissense	0.9804	likely pathogenic ✓ concordant with ClinVar · top 1% in AGXT
REVEL	0.971	strongly pathogenic-leaning
SaProt	LLR -16.98	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.3, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 9,952 bp · p 0.92 · regional, not allelic
Overall
CADD	28.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: AGXT
Protein: p.Arg360Pro
Coding: c.1079G>C
MANE Select: NM_000030
dbSNP: rs180177161
Type: single nucleotide variant
Location: chr2:240878721 (GRCh38)
Gene constraint: LOEUF 1.251 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 98.30 · 17 PDB
Residue 360: a binding site; a β-strand

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

Disease context

nephrolithiasis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: nephrocalcinosis

Similar variants

AGXT p.Arg360Gln Pathogenic/Likely pathogenic ★★ same residue
AGXT p.Arg360Trp Pathogenic/Likely pathogenic ★★ same residue
AGXT p.Arg360= Likely benign ★ same residue
AGXT p.Gly161Ser Pathogenic ★★ same condition
AGXT p.Ile244Thr Pathogenic ★★ ⚠ same condition
AGXT c.358+1G>A Pathogenic ★★ same type
AGXT c.359-2A>G Likely pathogenic ★★ same type
AGXT c.423+1G>A Pathogenic/Likely pathogenic ★★ 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/agxt-p-arg360pro (accessed [today's date]).

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