Is MAG p.Asn492= (c.1476C>T) pathogenic?

MAG p.Asn492= (c.1476C>T) is classified Likely benign in MAG (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-19). Absent from gnomAD v4.1; Associated with hereditary spastic paraplegia 75.

What condition is associated with MAG p.Asn492= (c.1476C>T)?

MAG p.Asn492= (c.1476C>T) is associated with hereditary spastic paraplegia 75 (ClinVar).

How common is MAG p.Asn492= (c.1476C>T) in the general population?

MAG p.Asn492= (c.1476C>T) 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.Asn492=

c.1476C>T · VCV4769823

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 2.1	GERP 1.2, phastCons 1
Overall
CADD	11.32	PHRED · no single calibrated threshold — expert panels disagree

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.Asn492=
Coding: c.1476C>T
MANE Select: NM_000400 · reported on NM_002361
Type: single nucleotide variant
Location: chr19:35310118 (GRCh38)
Structure: AlphaFold pLDDT 87.74 · 55 PDB
Residue 492: the 'mediates interaction with mms19' region; a UniProt-annotated variant site (in ttd1; mild)

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

ERCC2 p.Pro492= Likely benign ★★ same residue
ERCC2 p.Pro492Arg Uncertain significance ★ ⚠ same residue
KLC3 p.Arg492Gln Uncertain significance ★ ⚠ same residue
KLC3 p.Arg492Leu 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-asn492 (accessed [today's date]).

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