Is AGXT p.Ser287Thr (c.860_861delinsCG) pathogenic?

AGXT p.Ser287Thr (c.860861delinsCG) is classified Pathogenic in AGXT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2014-11-27). Absent from gnomAD; Associated with primary hyperoxaluria type 1.

What condition is associated with AGXT p.Ser287Thr (c.860_861delinsCG)?

AGXT p.Ser287Thr (c.860_861delinsCG) is associated with primary hyperoxaluria type 1 (ClinVar).

How common is AGXT p.Ser287Thr (c.860_861delinsCG) in the general population?

AGXT p.Ser287Thr (c.860_861delinsCG) is absent from gnomAD (gnomAD).

How is Primary hyperoxaluria inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

AGXT p.Ser287Thr

c.860_861delinsCG · rs180177289 · VCV204205

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

primary hyperoxaluria type 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP -0.16, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 9,952 bp · p 0.92 · regional, not allelic

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: AGXT
Protein: p.Ser287Thr
Coding: c.860_861delinsCG
MANE Select: NM_000030
dbSNP: rs180177289
Type: Indel
Location: chr2:240877550 (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 287: a UniProt-annotated variant site (in hp1); an α-helix

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

Disease context

primary hyperoxaluria type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary hyperoxaluria (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Germany)

Similar variants

AGXT p.Cys173_His174delinsTrpAsn Pathogenic/Likely pathogenic ★★ same condition
AGXT p.Met1Asn Pathogenic ★★ same condition
AGXT c.166-11_166-8delinsTGCATGCAAGAT Likely pathogenic ★ same condition
AGXT c.680+480_776+69delinsTGAGA Pathogenic ★ same condition
AGXT p.Ala277fs Pathogenic ★ same condition
AGXT p.Gly82fs Pathogenic ★ same condition
AGXT p.Leu179fs Likely pathogenic ★ same condition
AGXT p.Leu276Glu Likely 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/agxt-p-ser287thr (accessed [today's date]).

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