Is MAG p.Ser133Arg (c.399C>G) pathogenic?

MAG p.Ser133Arg (c.399C>G) is classified Pathogenic in MAG (ClinVar, No assertion criteria, 1 submitter; last evaluated 2015-09-01). AlphaMissense: likely pathogenic (0.9901); Absent from gnomAD v4.1; Associated with hereditary spastic paraplegia 75.

What condition is associated with MAG p.Ser133Arg (c.399C>G)?

MAG p.Ser133Arg (c.399C>G) is associated with hereditary spastic paraplegia 75 (ClinVar).

How common is MAG p.Ser133Arg (c.399C>G) in the general population?

MAG p.Ser133Arg (c.399C>G) 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.

What do computational predictors say about MAG p.Ser133Arg (c.399C>G)?

AlphaMissense predicts likely pathogenic (score 0.9901) — an in-silico prediction, not a clinical call.

MAG p.Ser133Arg

c.399C>G · rs2301600 · VCV218187

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9901 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary spastic paraplegia 75

Computational evidence

Protein change
AlphaMissense	0.9901	likely pathogenic ✓ concordant with ClinVar
REVEL	0.221	benign-leaning
SaProt	LLR -12.31	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.3	GERP -0.94, phastCons 0.11
Overall
CADD	21.9	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: MAG
Protein: p.Ser133Arg
Coding: c.399C>G
MANE Select: NM_000400 · reported on NM_002361
dbSNP: rs2301600
Type: single nucleotide variant
Location: chr19:35295965 (GRCh38)
Structure: AlphaFold pLDDT 87.74 · 55 PDB
Residue 133: the helicase atp-binding domain; an α-helix

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.Ser133= Benign ★★ same residue
ERCC2 p.Lys133Arg 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
MAG p.Arg425Gln Uncertain significance ★★ ⚠ same condition
MAG p.Arg465His 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-ser133arg (accessed [today's date]).

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