Is AGTR1 p.Phe293fs (c.879del) pathogenic?

AGTR1 p.Phe293fs (c.879del) is classified Likely pathogenic in AGTR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-15). No gnomAD frequency available for this variant; Associated with renal tubular dysgenesis.

What condition is associated with AGTR1 p.Phe293fs (c.879del)?

AGTR1 p.Phe293fs (c.879del) is associated with renal tubular dysgenesis (ClinVar).

How common is AGTR1 p.Phe293fs (c.879del) in the general population?

AGTR1 p.Phe293fs (c.879del) is no gnomAD frequency available for this variant (gnomAD).

AGTR1 p.Phe293fs

c.879del · rs2107975850 · VCV1328400

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

renal tubular dysgenesis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.3	GERP 1.8, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: AGTR1
Protein: p.Phe293fs
Coding: c.879del
MANE Select: NM_000685
dbSNP: rs2107975850
Type: Deletion
Location: chr3:148741911 (GRCh38)
Gene constraint: LOEUF 1.113 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.55 · 14 PDB
Residue 293: an α-helix

Full AGTR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

AGTR1 p.Phe293Cys Uncertain significance ★ ⚠ same residue
AGTR1 p.Asn200fs Likely pathogenic ★★ same condition
AGTR1 p.Ala114Thr Uncertain significance ★★ ⚠ same condition
AGTR1 p.Asn298Ser Uncertain significance ★★ ⚠ same condition
AGTR1 p.Gly203= Uncertain significance ★★ same condition
AGTR1 p.Ile103Thr Uncertain significance ★★ ⚠ same condition
AGTR1 p.Ile38Thr Uncertain significance ★★ ⚠ same condition
AGTR1 p.Pro233Thr 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/agtr1-p-phe293fs (accessed [today's date]).

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