Is MAT2A p.Glu70= (c.210A>G) pathogenic?

MAT2A p.Glu70= (c.210A>G) is classified Likely benign in MAT2A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-10). Very rare (popmax 0.000124%).

How common is MAT2A p.Glu70= (c.210A>G) in the general population?

MAT2A p.Glu70= (c.210A>G) is very rare (popmax 0.000124%) (gnomAD).

MAT2A p.Glu70=

c.210A>G · VCV4955788

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000124%)

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 2.2	GERP -0.077, phastCons 1
Overall
CADD	10.91	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000124%

Overall 0.000124% 2/1,614,132 alleles · very rare exomes 2/1,461,818 · genomes 0/152,314 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MAT2A
Protein: p.Glu70=
Coding: c.210A>G
MANE Select: NM_005911
Type: single nucleotide variant
Location: chr2:85541295 (GRCh38)
Gene constraint: LOEUF 0.158 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 96.08 · 59 PDB
Residue 70: a β-strand; a binding site

Full MAT2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAT2A c.292+4T>C Uncertain significance ★★ same type
MAT2A c.549+3A>G Uncertain significance ★★ same type
MAT2A c.952-3T>C Uncertain significance ★★ same type
MAT2A p.Ala11Val Uncertain significance ★★ ⚠ same type
MAT2A p.Arg177Cys Uncertain significance ★★ ⚠ same type
MAT2A p.Arg312Gly Uncertain significance ★★ ⚠ same type
MAT2A p.Arg343Gly Uncertain significance ★★ ⚠ same type
MAT2A p.Arg356Cys Uncertain significance ★★ ⚠ same type

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/mat2a-p-glu70 (accessed [today's date]).

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