MTAP — 178 ClinVar variants
All ClinVar germline MTAP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 43 flagged for review →
1 Conflicting · 67 Benign · 5 Benign/Likely benign · 4 Likely benign · 101 Uncertain significance
Full MTAP gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 43
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 agree, ClinVar conflicts 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
MTAP p.Trp263Leu
Conflicting
Single submitter
diaphyseal medullary stenosis-bone malignancy syndrome
Predictors lean, ClinVar uncertain 29
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
MTAP p.Gln75Arg
Uncertain significance
Multiple submitters
diaphyseal medullary stenosis-bone malignancy syndrome
- MTAP p.Ala244Thr Uncertain significance Single submitter
- MTAP p.Ala76Val Uncertain significance Single submitter
- MTAP p.Arg176Cys Uncertain significance Single submitter
- MTAP p.Arg176His Uncertain significance Single submitter
- MTAP p.Arg235Gln Uncertain significance Single submitter
- MTAP p.Arg235Trp Uncertain significance Single submitter
- MTAP p.Arg29Lys Uncertain significance Single submitter
-
MTAP p.Arg63Gly
Uncertain significance
Single submitter
diaphyseal medullary stenosis-bone malignancy syndrome
- MTAP p.Asn52Asp Uncertain significance Single submitter
- MTAP p.Asp126Asn Uncertain significance Single submitter
- MTAP p.Cys145Phe Uncertain significance Single submitter
- MTAP p.Cys223Arg Uncertain significance Single submitter
- MTAP p.Gln257Arg Uncertain significance Single submitter
- MTAP p.Glu83Ala Uncertain significance Single submitter
- MTAP p.Gly39Val Uncertain significance Single submitter
- MTAP p.His61Arg Uncertain significance Single submitter
- MTAP p.Leu159Val Uncertain significance Single submitter
-
MTAP p.Lys40Arg
Uncertain significance
Single submitter
diaphyseal medullary stenosis-bone malignancy syndrome
- MTAP p.Lys40Gln Uncertain significance Single submitter
- MTAP p.Pro143Leu Uncertain significance Single submitter
- MTAP p.Thr118Ala Uncertain significance Single submitter
- MTAP p.Thr253Ser Uncertain significance Single submitter
- MTAP p.Thr36Ser Uncertain significance Single submitter
- MTAP p.Thr5Ile Uncertain significance Single submitter
- MTAP p.Thr6Ser Uncertain significance Single submitter
-
MTAP p.Thr93Ile
Uncertain significance
Single submitter
diaphyseal medullary stenosis-bone malignancy syndrome
- MTAP p.Trp224Arg Uncertain significance Single submitter
- MTAP p.Val203Ile Uncertain significance Single submitter
Predictors split 13
The independent predictors disagree with each other — read with care.
-
MTAP p.Trp189Leu
Benign
Multiple submitters
diaphyseal medullary stenosis-bone malignancy syndrome
-
MTAP p.Ala191Val
Uncertain significance
Single submitter
diaphyseal medullary stenosis-bone malignancy syndrome
- MTAP p.Ala216Thr Uncertain significance Single submitter
- MTAP p.Arg187Cys Uncertain significance Single submitter
- MTAP p.Arg29Thr Uncertain significance Single submitter
- MTAP p.Asn195Thr Uncertain significance Single submitter
- MTAP p.Glu228Lys Uncertain significance Single submitter
- MTAP p.Gly105Ser Uncertain significance Single submitter
- MTAP p.Lys11Gln Uncertain significance Single submitter
- MTAP p.Pro37Ala Uncertain significance Single submitter
- MTAP p.Ser123Phe Uncertain significance Single submitter
- MTAP p.Thr148Met Uncertain significance Single submitter
-
MTAP p.Arg187His
Likely benign
No assertion criteria
MTAP-related disorder
All MTAP variants
Conflicting classifications of pathogenicity 1
- p.Trp263Leu Single submitter diaphyseal medullary stenosis-bone malignancy syndrome ⚠
Benign 67
- c.120+279C>T Multiple submitters
- c.121-10T>C Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.121-140G>A Multiple submitters
- c.121-185A>G Multiple submitters
- c.121-67A>G Multiple submitters
- c.121-76T>C Multiple submitters
- c.180-23C>T Multiple submitters
- c.347+109C>T Multiple submitters
- c.450+136A>G Multiple submitters
- c.450+170C>A Multiple submitters
- c.690+169G>A Multiple submitters
- c.691-108G>T Multiple submitters
- c.814-72T>G Multiple submitters
- c.*2085G>A Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2365C>T Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2522A>G Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*258A>C Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*259C>A Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3093T>C Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3829T>C Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3916C>T Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3946A>C Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*536G>A Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.*884T>A Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- p.Arg187= Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- p.Trp189Leu Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome ⚠
- p.Val56Ile Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- c.120+83_120+85dup Single submitter
- c.120+84_120+85dup Single submitter
- c.180-257T>C Single submitter
- c.180-280A>G Single submitter
- c.34-266G>T Single submitter
- c.348-208C>T Single submitter
- c.690+227G>T Single submitter
- c.691-13A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.-5C>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1038A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1065A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1181A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1225G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1341C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*15C>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1643G>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1729G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*17A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1936C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2188C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2238C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2255A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2279T>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2539A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2873C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3144G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*328T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3307G>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3851C>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3862C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*393G>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*606A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*657T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*707A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*797C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*804T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*895G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- p.Ala218Val Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- p.Gly105= Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- p.Pro37= Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
Benign/Likely benign 5
- c.179+12T>A Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- p.Glu201= Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- p.Gly13= Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- p.Ile46Leu Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- p.Pro256= Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
Likely benign 4
- c.451-6T>C Single submitter
- p.Thr8= Single submitter
- p.Val34= Single submitter
- p.Arg187His No assertion criteria MTAP-related disorder ⚠
Uncertain significance 101
- c.*1453C>T Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome
- p.Gln75Arg Multiple submitters diaphyseal medullary stenosis-bone malignancy syndrome ⚠
- c.347+3A>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.-52G>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*102A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1093G>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1140A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1197C>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1384G>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1399C>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1482A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1558G>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1621_*1622del Single submitter
- c.*1668T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1760A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1831T>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*1836C>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2033G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2111A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2171G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2183T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2269A>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2286A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2333C>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2383C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2481T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*254A>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2606G>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2638G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2651G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2660C>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2693G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2740G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2837T>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2912G>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2937C>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*2968T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*303G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3052C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3057T>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3060A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3072G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3160T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3206C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3276A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3361C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3389T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3501T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3656A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3692G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3766C>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3774A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*378T>C Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*3943G>A Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*395A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*730A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*795A>T Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- c.*912A>G Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- p.Ala191Val Single submitter diaphyseal medullary stenosis-bone malignancy syndrome ⚠
- p.Ala216Thr Single submitter ⚠
- p.Ala244Thr Single submitter ⚠
- p.Ala76Val Single submitter ⚠
- p.Arg176Cys Single submitter ⚠
- p.Arg176His Single submitter ⚠
- p.Arg187Cys Single submitter ⚠
- p.Arg235Gln Single submitter ⚠
- p.Arg235Trp Single submitter ⚠
- p.Arg29Lys Single submitter ⚠
- p.Arg29Thr Single submitter ⚠
- p.Arg63Gly Single submitter diaphyseal medullary stenosis-bone malignancy syndrome ⚠
- p.Asn195Thr Single submitter ⚠
- p.Asn52Asp Single submitter ⚠
- p.Asp126Asn Single submitter ⚠
- p.Cys145Phe Single submitter ⚠
- p.Cys223Arg Single submitter ⚠
- p.Gln257Arg Single submitter ⚠
- p.Glu100= Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- p.Glu228Lys Single submitter ⚠
- p.Glu83Ala Single submitter ⚠
- p.Glu84Asp Single submitter
- p.Gly105Ser Single submitter ⚠
- p.Gly39Val Single submitter ⚠
- p.His61Arg Single submitter ⚠
- p.Leu159Val Single submitter ⚠
- p.Lys11Gln Single submitter ⚠
- p.Lys225Glu Single submitter
- p.Lys40Arg Single submitter diaphyseal medullary stenosis-bone malignancy syndrome ⚠
- p.Lys40Gln Single submitter ⚠
- p.Pro143Leu Single submitter ⚠
- p.Pro37Ala Single submitter ⚠
- p.Ser123Phe Single submitter ⚠
- p.Ser232Ter Single submitter diaphyseal medullary stenosis-bone malignancy syndrome
- p.Thr118Ala Single submitter ⚠
- p.Thr148Met Single submitter ⚠
- p.Thr253Ser Single submitter ⚠
- p.Thr36Ser Single submitter ⚠
- p.Thr5Ile Single submitter ⚠
- p.Thr6Ser Single submitter ⚠
- p.Thr93Ile Single submitter diaphyseal medullary stenosis-bone malignancy syndrome ⚠
- p.Trp224Arg Single submitter ⚠
- p.Val203Ile Single submitter ⚠