Is MAG p.Glu229= (c.687G>A) pathogenic?

MAG p.Glu229= (c.687G>A) is classified Likely benign in MAG (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-15). Absent from gnomAD v4.1; Associated with hereditary spastic paraplegia 75.

What condition is associated with MAG p.Glu229= (c.687G>A)?

MAG p.Glu229= (c.687G>A) is associated with hereditary spastic paraplegia 75 (ClinVar).

How common is MAG p.Glu229= (c.687G>A) in the general population?

MAG p.Glu229= (c.687G>A) is absent from gnomAD v4.1 (gnomAD).

How is Autosomal recessive spastic paraplegia type 75 inherited?

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

MAG p.Glu229=

c.687G>A · rs2145611517 · VCV1656859

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,513,096)

Conditions

hereditary spastic paraplegia 75

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP -3.8, phastCons 1
Overall
CADD	8.848	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,513,096). 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: MAG
Protein: p.Glu229=
Coding: c.687G>A
MANE Select: NM_000400 · reported on NM_002361
dbSNP: rs2145611517
Type: single nucleotide variant
Location: chr19:35299825 (GRCh38)
Structure: AlphaFold pLDDT 87.74 · 55 PDB
Residue 229: the helicase atp-binding domain

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

Disease context

hereditary spastic paraplegia 75 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal recessive spastic paraplegia type 75 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

MAG p.Glu229Gln Uncertain significance ★★ ⚠ same residue
ERCC2 p.Ala229= Benign/Likely benign ★★ same residue
ERCC2 p.Ala229Thr Uncertain significance ★ ⚠ same residue
ERCC2 p.Ala229Val Uncertain significance ★ ⚠ same residue
MAG p.Arg508Ter Pathogenic/Likely pathogenic ★★ same condition
MAG p.Ala307Val Uncertain significance ★★ ⚠ same condition
MAG p.Ala490Thr Uncertain significance ★★ ⚠ same condition
MAG p.Arg316Leu 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/mag-p-glu229 (accessed [today's date]).

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