Is MTM1 p.Pro149= (c.447A>G) pathogenic?

MTM1 p.Pro149= (c.447A>G) is classified Likely benign in MTM1 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-03-31). Very rare (popmax 0.00219%, amr); Associated with X-linked myotubular myopathy.

What condition is associated with MTM1 p.Pro149= (c.447A>G)?

MTM1 p.Pro149= (c.447A>G) is associated with X-linked myotubular myopathy (ClinVar).

How common is MTM1 p.Pro149= (c.447A>G) in the general population?

MTM1 p.Pro149= (c.447A>G) is very rare (popmax 0.00219%, amr) (gnomAD).

How is X-linked centronuclear myopathy inherited?

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

MTM1 p.Pro149=

c.447A>G · rs782149231 · VCV736964

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00219%, amr)

Conditions

X-linked myotubular myopathy

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 1.5	GERP -2, phastCons 1
Overall
CADD	8.347	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00219% Admixed American · 1/45,737 alleles

Filtering AF 0.00127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00105%

Overall 0.00167% 20/1,196,686 alleles · very rare exomes 19/1,084,642 · genomes 1/112,044 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00219%	45,737
Remaining individualsnot grpmax-eligible	0.00212%	47,171
European (non-Finnish)	0.00204%	49,061

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: MTM1
Protein: p.Pro149=
Coding: c.447A>G
MANE Select: NM_000252
dbSNP: rs782149231
Type: single nucleotide variant
Location: chrX:150638945 (GRCh38)
Structure: AlphaFold pLDDT 90.10

Full MTM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

X-linked myotubular myopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked centronuclear myopathy (Orphanet):

Inheritance: X-linked recessive
Onset: Antenatal, Neonatal
Prevalence: 1-9 / 100 000 (France)

Similar variants

MTM1 p.Pro149Arg Benign ★ ⚠ same residue
MTM1 c.1644+1G>A Pathogenic ★★★ same condition
MTM1 p.Arg224Ter Pathogenic ★★★ same condition
MTM1 p.Arg69Cys Pathogenic ★★★ same condition
MTM1 p.Gln451= Likely pathogenic ★★★ same condition
MTM1 p.Glu404Lys Pathogenic ★★★ same condition
MTM1 p.Pro205Leu Pathogenic ★★★ same condition
MTM1 p.Trp230Arg Likely pathogenic ★★★ 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/mtm1-p-pro149 (accessed [today's date]).

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