Is MAT2A p.Phe353= (c.1059C>T) pathogenic?

MAT2A p.Phe353= (c.1059C>T) is classified Likely benign in MAT2A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-11-23). Ultra-rare (popmax 0.0386%, mid); Associated with familial thoracic aortic aneurysm and aortic dissection.

What condition is associated with MAT2A p.Phe353= (c.1059C>T)?

MAT2A p.Phe353= (c.1059C>T) is associated with familial thoracic aortic aneurysm and aortic dissection (ClinVar).

How common is MAT2A p.Phe353= (c.1059C>T) in the general population?

MAT2A p.Phe353= (c.1059C>T) is ultra-rare (popmax 0.0386%, mid) (gnomAD).

MAT2A p.Phe353=

Q: How is Familial thoracic aortic aneurysm and aortic dissection inherited?

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

c.1059C>T · rs199754006 · VCV511170

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0386%, mid)

Conditions

familial thoracic aortic aneurysm and aortic dissection

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 3.5	GERP 0.97, phastCons 1
Overall
CADD	13.85	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0386% Middle Eastern · 2/5,182 alleles

Filtering AF 0.00683% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00345%

Overall 0.00453% 73/1,612,892 alleles · ultra-rare exomes 62/1,460,706 · genomes 11/152,186 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0386%	2,591
Remaining individualsnot grpmax-eligible	0.016%	6,241
European (non-Finnish)	0.00483%	20,701
Admixed American	0.00333%	29,993
African / African-American	0.00133%	74,954
South Asian	0.0011%	91,014

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.Phe353=
Coding: c.1059C>T
MANE Select: NM_005911
dbSNP: rs199754006
Type: single nucleotide variant
Location: chr2:85543008 (GRCh38)
Gene constraint: LOEUF 0.158 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 96.08 · 59 PDB

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

Disease context

familial thoracic aortic aneurysm and aortic dissection — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial thoracic aortic aneurysm and aortic dissection (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood

Similar variants

MAT2A p.Phe353Ser Uncertain significance ★ ⚠ same residue
MAT2A c.292+4T>C Uncertain significance ★★ same condition
MAT2A c.549+3A>G Uncertain significance ★★ same condition
MAT2A c.952-3T>C Uncertain significance ★★ same condition
MAT2A p.Ala11Val Uncertain significance ★★ ⚠ same condition
MAT2A p.Arg177Cys Uncertain significance ★★ ⚠ same condition
MAT2A p.Arg312Gly Uncertain significance ★★ ⚠ same condition
MAT2A p.Arg343Gly 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/mat2a-p-phe353 (accessed [today's date]).

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