Is MAGED2 p.Pro113fs (c.338del) pathogenic?

MAGED2 p.Pro113fs (c.338del) is classified Likely pathogenic in MAGED2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-25). Associated with Bartter disease type 5.

What condition is associated with MAGED2 p.Pro113fs (c.338del)?

MAGED2 p.Pro113fs (c.338del) is associated with Bartter disease type 5 (ClinVar).

How is Bartter syndrome inherited?

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

MAGED2 p.Pro113fs

c.338del · VCV4888402

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Bartter disease type 5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7	GERP 2, phastCons 1

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

Variant & gene context

Gene: MAGED2
Protein: p.Pro113fs
Coding: c.338del
MANE Select: NM_177433
Type: Deletion
Location: chrX:54810012 (GRCh38)
Structure: AlphaFold pLDDT 59.89
Residue 113: the 'disordered' region

Full MAGED2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bartter disease type 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Bartter syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

MAGED2 p.Pro113Leu Likely benign ★ same residue
MAGED2 p.Pro153Ser Uncertain significance ★★ ⚠ same condition
MAGED2 p.Ala208= Benign ★★ same condition
MAGED2 p.Pro272= Benign/Likely benign ★★ same condition
MAGED2 p.Ser327= Benign ★★ same condition
MAGED2 p.Ser84= Benign ★★ same condition
MAGED2 p.Thr132= Benign ★★ same condition
MAGED2 c.1386+1G>A 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/maged2-p-pro113fs (accessed [today's date]).

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