MTX2 — 39 ClinVar variants
All ClinVar germline MTX2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 27 flagged for review →
7 Pathogenic · 2 Likely pathogenic · 1 Benign · 29 Uncertain significance
Full MTX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 27
Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.
Predictors lean, ClinVar uncertain 22
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- MTX2 p.Arg257His Uncertain significance Multiple submitters
- MTX2 p.Ala158Gly Uncertain significance Single submitter
- MTX2 p.Ala40Gly Uncertain significance Single submitter
- MTX2 p.Ala5Ser Uncertain significance Single submitter
- MTX2 p.Asn241Asp Uncertain significance Single submitter
- MTX2 p.Asn38Ser Uncertain significance Single submitter
- MTX2 p.Asp256His Uncertain significance Single submitter
- MTX2 p.Gln45Pro Uncertain significance Single submitter
- MTX2 p.Glu116Ala Uncertain significance Single submitter
- MTX2 p.Ile172Val Uncertain significance Single submitter
- MTX2 p.Ile75Met Uncertain significance Single submitter
- MTX2 p.Ile75Phe Uncertain significance Single submitter
- MTX2 p.Leu227Met Uncertain significance Single submitter
- MTX2 p.Lys237Asn Uncertain significance Single submitter
- MTX2 p.Pro201Ser Uncertain significance Single submitter
- MTX2 p.Pro68Ser Uncertain significance Single submitter
- MTX2 p.Ser194Pro Uncertain significance Single submitter
- MTX2 p.Ser67Pro Uncertain significance Single submitter
- MTX2 p.Thr221Ile Uncertain significance Single submitter
- MTX2 p.Tyr128Cys Uncertain significance Single submitter
- MTX2 p.Val137Ile Uncertain significance Single submitter
- MTX2 p.Val44Ala Uncertain significance Single submitter
Predictors split 5
The independent predictors disagree with each other — read with care.
All MTX2 variants
Pathogenic 7
- c.136-1G>C Single submitter mandibuloacral dysplasia progeroid syndrome
- c.378+1G>A Single submitter mandibuloacral dysplasia progeroid syndrome
- c.208+3_208+6del No assertion criteria Progeroid mandibuloacral dysplasia
- c.544-1G>C No assertion criteria Progeroid mandibuloacral dysplasia
- p.Met1Lys No assertion criteria Progeroid mandibuloacral dysplasia
- p.Ser98_Leu99insTer No assertion criteria mandibuloacral dysplasia progeroid syndrome
- p.Tyr202fs No assertion criteria Progeroid mandibuloacral dysplasia
Likely pathogenic 2
- c.135+2T>C Single submitter mandibuloacral dysplasia progeroid syndrome
- c.208+1G>A Single submitter mandibuloacral dysplasia progeroid syndrome
Benign 1
- p.Gln191= Single submitter
Uncertain significance 29
- p.Arg257His Multiple submitters ⚠
- p.Ala158Gly Single submitter ⚠
- p.Ala40Gly Single submitter ⚠
- p.Ala5Ser Single submitter ⚠
- p.Asn241Asp Single submitter ⚠
- p.Asn38Ser Single submitter ⚠
- p.Asn62Asp Single submitter ⚠
- p.Asp256His Single submitter ⚠
- p.Asp37Asn Single submitter ⚠
- p.Gln45Pro Single submitter ⚠
- p.Glu116Ala Single submitter ⚠
- p.Ile172Val Single submitter ⚠
- p.Ile249Thr Single submitter
- p.Ile75Met Single submitter ⚠
- p.Ile75Phe Single submitter ⚠
- p.Leu227Met Single submitter ⚠
- p.Lys237Asn Single submitter ⚠
- p.Met115Ile Single submitter ⚠
- p.Met169Ile Single submitter ⚠
- p.Phe8Ser Single submitter ⚠
- p.Pro201Ser Single submitter ⚠
- p.Pro68Ser Single submitter ⚠
- p.Ser194Pro Single submitter ⚠
- p.Ser67Pro Single submitter ⚠
- p.Thr221Ile Single submitter ⚠
- p.Thr224Ala Single submitter
- p.Tyr128Cys Single submitter ⚠
- p.Val137Ile Single submitter ⚠
- p.Val44Ala Single submitter ⚠