OSTM1 — 315 ClinVar variants
All ClinVar germline OSTM1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 75 flagged for review →
18 Pathogenic · 1 Pathogenic/Likely pathogenic · 4 Likely pathogenic · 7 Conflicting · 34 Benign · 4 Benign/Likely benign · 123 Likely benign · 124 Uncertain significance
Full OSTM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 75
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 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
OSTM1 p.Asn207Ser
Conflicting
Single submitter
Inborn genetic diseases
- OSTM1 p.Ser48Trp Conflicting Single submitter
Predictors lean, ClinVar uncertain 59
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
OSTM1 p.Arg144Lys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Arg225Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Arg225His
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Asn246Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Asp81Gly
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Glu56Lys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Gly69Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
- OSTM1 p.Leu175Ser Uncertain significance Multiple submitters
-
OSTM1 p.Pro117Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Pro3Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Pro82Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Ser139Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Ser141Asn
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Ser289Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Ser94Gly
Uncertain significance
Multiple submitters
autosomal recessive osteopetrosis 5
-
OSTM1 p.Thr99Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Tyr116Phe
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Val220Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Val277Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Val297Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
- OSTM1 p.Ala149Thr Uncertain significance Single submitter
- OSTM1 p.Ala149Val Uncertain significance Single submitter
-
OSTM1 p.Arg131Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Arg266Gln Uncertain significance Single submitter
- OSTM1 p.Asn177Ile Uncertain significance Single submitter
- OSTM1 p.Asn177Lys Uncertain significance Single submitter
- OSTM1 p.Asp127Ala Uncertain significance Single submitter
- OSTM1 p.Asp150Gly Uncertain significance Single submitter
-
OSTM1 p.Asp57Glu
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Gln50Arg Uncertain significance Single submitter
- OSTM1 p.Gln64Arg Uncertain significance Single submitter
-
OSTM1 p.Glu138Lys
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Glu168Gly Uncertain significance Single submitter
- OSTM1 p.Glu219Lys Uncertain significance Single submitter
- OSTM1 p.Gly134Arg Uncertain significance Single submitter
- OSTM1 p.Gly134Val Uncertain significance Single submitter
- OSTM1 p.Gly67Arg Uncertain significance Single submitter
-
OSTM1 p.His202Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.His253Tyr Uncertain significance Single submitter
- OSTM1 p.Ile157Phe Uncertain significance Single submitter
- OSTM1 p.Ile292Thr Uncertain significance Single submitter
- OSTM1 p.Ile329Leu Uncertain significance Single submitter
- OSTM1 p.Leu111Phe Uncertain significance Single submitter
-
OSTM1 p.Leu111Val
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Leu147Ser Uncertain significance Single submitter
-
OSTM1 p.Leu231Pro
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Leu316Pro Uncertain significance Single submitter
-
OSTM1 p.Leu80Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
OSTM1 p.Leu80Met
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Leu80Val Uncertain significance Single submitter
- OSTM1 p.Pro74Thr Uncertain significance Single submitter
-
OSTM1 p.Pro78Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Ser105Gly Uncertain significance Single submitter
-
OSTM1 p.Ser72Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
OSTM1 p.Thr136Ala
Uncertain significance
Single submitter
autosomal recessive osteopetrosis 5
- OSTM1 p.Thr164Ile Uncertain significance Single submitter
- OSTM1 p.Thr198Ile Uncertain significance Single submitter
-
OSTM1 p.Val187Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Val55Leu Uncertain significance Single submitter
Predictors split 14
The independent predictors disagree with each other — read with care.
-
OSTM1 p.Arg85Pro
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Lys311Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Met238Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Ser323Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
OSTM1 p.Val109Met
Uncertain significance
Multiple submitters
Inborn genetic diseases
- OSTM1 p.Ala133Pro Uncertain significance Single submitter
- OSTM1 p.Arg319His Uncertain significance Single submitter
- OSTM1 p.Asn274Ser Uncertain significance Single submitter
- OSTM1 p.His306Tyr Uncertain significance Single submitter
- OSTM1 p.Ile256Thr Uncertain significance Single submitter
-
OSTM1 p.Lys125Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- OSTM1 p.Met262Ile Uncertain significance Single submitter
- OSTM1 p.Ser95Thr Uncertain significance Single submitter
-
OSTM1 p.Val285Leu
Uncertain significance
Single submitter
Inborn genetic diseases
All OSTM1 variants
Pathogenic 18
- p.Gln140fs Multiple submitters autosomal recessive osteopetrosis 5
- p.Ser232fs Multiple submitters autosomal recessive osteopetrosis 5
- c.402_402+1dup Single submitter
- c.783+5G>T Single submitter autosomal recessive osteopetrosis 5
- p.Arg271Ter Single submitter autosomal recessive osteopetrosis 5
- p.Asn184fs Single submitter
- p.Gln120Ter Single submitter
- p.Glu86Ter Single submitter
- p.Leu118fs Single submitter
- p.Met148fs Single submitter
- p.Phe162fs Single submitter autosomal recessive osteopetrosis 5
- p.Ser137Ter Single submitter
- p.Ser141fs Single submitter
- p.Ser183Ter Single submitter
- p.Trp166Ter Single submitter
- p.Tyr188Ter Single submitter
- p.Val187fs Single submitter
- c.949+5G>A No assertion criteria autosomal recessive osteopetrosis 5
Pathogenic/Likely pathogenic 1
- p.Arg266Ter Multiple submitters
Likely pathogenic 4
- c.402+1G>A Single submitter
- c.517+1G>T Single submitter
- p.Glu83Ter Single submitter
- p.Glu86fs Single submitter osteopetrosis
Conflicting classifications of pathogenicity 7
- c.784-10C>G Single submitter autosomal recessive osteopetrosis 5
- c.950-12T>C Single submitter autosomal recessive osteopetrosis 5
- p.Asn207Ser Single submitter Inborn genetic diseases ⚠
- p.Asn93= Single submitter autosomal recessive osteopetrosis 5
- p.Lys311= Single submitter autosomal recessive osteopetrosis 5
- p.Ser48Trp Single submitter ⚠
- p.Thr186= Single submitter autosomal recessive osteopetrosis 5
Benign 34
- p.Leu52Phe Multiple submitters autosomal recessive osteopetrosis 5
- p.Pro74Arg Multiple submitters autosomal recessive osteopetrosis 5
- c.402+267G>C Single submitter
- c.518-255G>A Single submitter
- c.615+113A>G Single submitter
- c.615+21A>G Single submitter
- c.615+226A>C Single submitter
- c.616-3del Single submitter
- c.783+27C>G Single submitter
- c.950-166G>C Single submitter
- c.*1038A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1082G>A Single submitter autosomal recessive osteopetrosis 5
- c.*1161G>A Single submitter autosomal recessive osteopetrosis 5
- c.*1334T>C Single submitter autosomal recessive osteopetrosis 5
- c.*1352A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1367G>A Single submitter autosomal recessive osteopetrosis 5
- c.*1407A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1427A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1574A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1883T>C Single submitter autosomal recessive osteopetrosis 5
- c.*2053C>T Single submitter autosomal recessive osteopetrosis 5
- c.*212A>G Single submitter autosomal recessive osteopetrosis 5
- c.*2138G>T Single submitter autosomal recessive osteopetrosis 5
- c.*2283T>C Single submitter autosomal recessive osteopetrosis 5
- c.*2301A>G Single submitter autosomal recessive osteopetrosis 5
- c.*2329G>T Single submitter autosomal recessive osteopetrosis 5
- c.*2344C>G Single submitter autosomal recessive osteopetrosis 5
- c.*2547G>A Single submitter autosomal recessive osteopetrosis 5
- c.*2755A>G Single submitter autosomal recessive osteopetrosis 5
- c.*2887G>A Single submitter autosomal recessive osteopetrosis 5
- c.*3319T>G Single submitter autosomal recessive osteopetrosis 5
- c.*331A>G Single submitter autosomal recessive osteopetrosis 5
- c.*3329A>G Single submitter autosomal recessive osteopetrosis 5
- c.*355A>G Single submitter autosomal recessive osteopetrosis 5
Benign/Likely benign 4
- c.615+8A>G Multiple submitters autosomal recessive osteopetrosis 5
- p.Gly100= Multiple submitters autosomal recessive osteopetrosis 5
- p.Leu320= Multiple submitters autosomal recessive osteopetrosis 5
- p.Ser59= Multiple submitters
Likely benign 123
- p.Arg104= Multiple submitters
- p.Gly66= Multiple submitters autosomal recessive osteopetrosis 5
- p.His253= Multiple submitters
- p.Leu63= Multiple submitters
- c.402+16C>T Single submitter
- c.402+19_402+26del Single submitter
- c.402+19C>T Single submitter
- c.402+20C>T Single submitter
- c.402+8C>G Single submitter
- c.402+8C>T Single submitter
- c.403-13C>A Single submitter
- c.403-17T>C Single submitter
- c.517+10T>C Single submitter
- c.517+11C>G Single submitter
- c.517+11C>T Single submitter
- c.517+7_517+10del Single submitter
- c.518-11T>C Single submitter
- c.518-11T>G Single submitter
- c.518-17T>C Single submitter
- c.518-18T>C Single submitter
- c.518-20T>C Single submitter
- c.518-20T>G Single submitter
- c.615+15A>G Single submitter
- c.615+16T>C Single submitter
- c.615+17A>G Single submitter
- c.615+18T>C Single submitter
- c.615+7T>C Single submitter
- c.616-10G>T Single submitter
- c.616-14del Single submitter
- c.616-19T>C Single submitter
- c.616-20A>G Single submitter
- c.616-8C>T Single submitter
- c.783+11dup Single submitter
- c.783+15dup Single submitter
- c.783+18G>A Single submitter
- c.783+20T>A Single submitter
- c.783+8C>A Single submitter
- c.783+8C>T Single submitter
- c.784-10C>T Single submitter
- c.784-16T>C Single submitter
- c.784-17G>T Single submitter
- c.784-18T>C Single submitter
- c.784-20_784-18del Single submitter
- c.784-4C>G Single submitter
- c.949+12A>G Single submitter
- c.949+13C>T Single submitter
- c.949+14A>G Single submitter
- c.949+15A>G Single submitter
- c.950-12T>G Single submitter
- c.950-16C>A Single submitter
- c.950-16C>G Single submitter
- c.950-20A>T Single submitter
- c.950-4C>G Single submitter
- c.950-6A>G Single submitter
- c.*2276C>A Single submitter autosomal recessive osteopetrosis 5
- c.*2366A>G Single submitter autosomal recessive osteopetrosis 5
- c.*3192A>C Single submitter autosomal recessive osteopetrosis 5
- p.Ala106= Single submitter
- p.Ala149= Single submitter
- p.Ala227= Single submitter
- p.Ala287= Single submitter
- p.Ala92= Single submitter
- p.Arg107= Single submitter
- p.Arg266= Single submitter
- p.Asn163= Single submitter
- p.Asn177= Single submitter
- p.Asn203= Single submitter
- p.Asn207= Single submitter
- p.Asn263= Single submitter
- p.Asp260= Single submitter
- p.Cys224= Single submitter
- p.Cys279= Single submitter
- p.Cys84= Single submitter
- p.Gln120= Single submitter
- p.Gln239= Single submitter
- p.Glu259= Single submitter
- p.Glu54= Single submitter
- p.Gly206= Single submitter
- p.Gly67= Single submitter
- p.Gly69= Single submitter
- p.His195= Single submitter
- p.His209= Single submitter
- p.His306= Single submitter
- p.Ile129= Single submitter
- p.Leu102= Single submitter
- p.Leu175= Single submitter
- p.Leu182= Single submitter
- p.Leu190= Single submitter
- p.Leu211= Single submitter
- p.Leu234= Single submitter
- p.Leu254= Single submitter
- p.Leu268= Single submitter
- p.Leu316= Single submitter
- p.Leu47= Single submitter
- p.Leu53= Single submitter
- p.Leu62= Single submitter
- p.Leu77= Single submitter
- p.Leu89= Single submitter
- p.Lys313= Single submitter
- p.Phe273= Single submitter
- p.Phe291= Single submitter
- p.Pro108= Single submitter
- p.Pro117= Single submitter
- p.Ser124Asn Single submitter Inborn genetic diseases
- p.Ser183= Single submitter
- p.Ser218= Single submitter
- p.Ser270= Single submitter
- p.Ser322= Single submitter
- p.Ser48= Single submitter
- p.Ser61= Single submitter
- p.Ser94= Single submitter
- p.Thr114= Single submitter
- p.Thr136= Single submitter
- p.Thr165= Single submitter
- p.Thr196= Single submitter
- p.Thr252= Single submitter
- p.Thr272= Single submitter
- p.Tyr217= Single submitter
- p.Tyr235= Single submitter
- p.Tyr300= Single submitter
- p.Val155= Single submitter
- p.Val187= Single submitter
- p.Val298= Single submitter
Uncertain significance 124
- c.*147G>T Multiple submitters autosomal recessive osteopetrosis 5
- c.*2362A>G Multiple submitters autosomal recessive osteopetrosis 5
- p.Arg144Lys Multiple submitters Inborn genetic diseases ⚠
- p.Arg225Cys Multiple submitters Inborn genetic diseases ⚠
- p.Arg225His Multiple submitters Inborn genetic diseases ⚠
- p.Arg85Pro Multiple submitters Inborn genetic diseases ⚠
- p.Asn246Ser Multiple submitters Inborn genetic diseases ⚠
- p.Asp81Gly Multiple submitters Inborn genetic diseases ⚠
- p.Glu56Lys Multiple submitters Inborn genetic diseases ⚠
- p.Gly69Ala Multiple submitters Inborn genetic diseases ⚠
- p.Leu175Ser Multiple submitters ⚠
- p.Lys311Thr Multiple submitters Inborn genetic diseases ⚠
- p.Met238Ile Multiple submitters Inborn genetic diseases ⚠
- p.Pro117Leu Multiple submitters Inborn genetic diseases ⚠
- p.Pro3Leu Multiple submitters Inborn genetic diseases ⚠
- p.Pro82Leu Multiple submitters Inborn genetic diseases ⚠
- p.Ser139Thr Multiple submitters Inborn genetic diseases ⚠
- p.Ser141Asn Multiple submitters Inborn genetic diseases ⚠
- p.Ser289Thr Multiple submitters Inborn genetic diseases ⚠
- p.Ser323Arg Multiple submitters Inborn genetic diseases ⚠
- p.Ser94Gly Multiple submitters autosomal recessive osteopetrosis 5 ⚠
- p.Thr99Ala Multiple submitters Inborn genetic diseases ⚠
- p.Tyr116Phe Multiple submitters Inborn genetic diseases ⚠
- p.Val109Met Multiple submitters Inborn genetic diseases ⚠
- p.Val220Ile Multiple submitters Inborn genetic diseases ⚠
- p.Val277Ile Multiple submitters Inborn genetic diseases ⚠
- p.Val297Ile Multiple submitters Inborn genetic diseases ⚠
- c.615+4T>C Single submitter
- c.616-5T>C Single submitter
- c.949+1G>C Single submitter
- c.-52G>T Single submitter autosomal recessive osteopetrosis 5
- c.*1007G>A Single submitter autosomal recessive osteopetrosis 5
- c.*1023A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1045T>C Single submitter autosomal recessive osteopetrosis 5
- c.*1085T>G Single submitter autosomal recessive osteopetrosis 5
- c.*1166A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1205C>G Single submitter autosomal recessive osteopetrosis 5
- c.*1399T>A Single submitter autosomal recessive osteopetrosis 5
- c.*1455C>T Single submitter autosomal recessive osteopetrosis 5
- c.*1469G>A Single submitter autosomal recessive osteopetrosis 5
- c.*1634A>G Single submitter autosomal recessive osteopetrosis 5
- c.*168T>G Single submitter autosomal recessive osteopetrosis 5
- c.*177A>G Single submitter autosomal recessive osteopetrosis 5
- c.*1844T>G Single submitter autosomal recessive osteopetrosis 5
- c.*2035A>G Single submitter autosomal recessive osteopetrosis 5
- c.*2145A>T Single submitter autosomal recessive osteopetrosis 5
- c.*2195T>G Single submitter autosomal recessive osteopetrosis 5
- c.*2276C>T Single submitter autosomal recessive osteopetrosis 5
- c.*2277G>A Single submitter autosomal recessive osteopetrosis 5
- c.*2317A>C Single submitter autosomal recessive osteopetrosis 5
- c.*2364A>G Single submitter autosomal recessive osteopetrosis 5
- c.*2370dup Single submitter
- c.*2371G>A Single submitter autosomal recessive osteopetrosis 5
- c.*2487T>A Single submitter autosomal recessive osteopetrosis 5
- c.*2515_*2516del Single submitter
- c.*262C>G Single submitter autosomal recessive osteopetrosis 5
- c.*2707C>T Single submitter autosomal recessive osteopetrosis 5
- c.*2769G>T Single submitter autosomal recessive osteopetrosis 5
- c.*2773G>A Single submitter autosomal recessive osteopetrosis 5
- c.*2799A>G Single submitter autosomal recessive osteopetrosis 5
- c.*2858A>G Single submitter autosomal recessive osteopetrosis 5
- c.*291A>G Single submitter autosomal recessive osteopetrosis 5
- c.*2990T>C Single submitter autosomal recessive osteopetrosis 5
- c.*3060G>A Single submitter autosomal recessive osteopetrosis 5
- c.*3186T>C Single submitter autosomal recessive osteopetrosis 5
- c.*3256A>G Single submitter autosomal recessive osteopetrosis 5
- c.*3280T>C Single submitter autosomal recessive osteopetrosis 5
- c.*432T>G Single submitter autosomal recessive osteopetrosis 5
- c.*751C>T Single submitter autosomal recessive osteopetrosis 5
- c.*778T>G Single submitter autosomal recessive osteopetrosis 5
- c.*835G>T Single submitter autosomal recessive osteopetrosis 5
- c.*872T>C Single submitter autosomal recessive osteopetrosis 5
- c.*873A>G Single submitter autosomal recessive osteopetrosis 5
- c.*953C>T Single submitter autosomal recessive osteopetrosis 5
- p.Ala133Pro Single submitter ⚠
- p.Ala149Thr Single submitter ⚠
- p.Ala149Val Single submitter ⚠
- p.Arg131Gln Single submitter Inborn genetic diseases ⚠
- p.Arg266Gln Single submitter ⚠
- p.Arg319His Single submitter ⚠
- p.Asn177Ile Single submitter ⚠
- p.Asn177Lys Single submitter ⚠
- p.Asn274Ser Single submitter ⚠
- p.Asp127Ala Single submitter ⚠
- p.Asp150Gly Single submitter ⚠
- p.Asp57Glu Single submitter Inborn genetic diseases ⚠
- p.Gln50Arg Single submitter ⚠
- p.Gln64Arg Single submitter ⚠
- p.Glu138Lys Single submitter Inborn genetic diseases ⚠
- p.Glu168Gly Single submitter ⚠
- p.Glu219Lys Single submitter ⚠
- p.Gly134= Single submitter
- p.Gly134Arg Single submitter ⚠
- p.Gly134Val Single submitter ⚠
- p.Gly67Arg Single submitter ⚠
- p.His202Arg Single submitter Inborn genetic diseases ⚠
- p.His253Tyr Single submitter ⚠
- p.His306Tyr Single submitter ⚠
- p.Ile157Phe Single submitter ⚠
- p.Ile256Thr Single submitter ⚠
- p.Ile292Thr Single submitter ⚠
- p.Ile329Leu Single submitter ⚠
- p.Leu111Phe Single submitter ⚠
- p.Leu111Val Single submitter Inborn genetic diseases ⚠
- p.Leu147Ser Single submitter ⚠
- p.Leu231Pro Single submitter Inborn genetic diseases ⚠
- p.Leu316Pro Single submitter ⚠
- p.Leu80Arg Single submitter Inborn genetic diseases ⚠
- p.Leu80Met Single submitter Inborn genetic diseases ⚠
- p.Leu80Val Single submitter ⚠
- p.Lys125Asn Single submitter Inborn genetic diseases ⚠
- p.Met262Ile Single submitter ⚠
- p.Phe291fs Single submitter
- p.Pro74Thr Single submitter ⚠
- p.Pro78Arg Single submitter Inborn genetic diseases ⚠
- p.Ser105Gly Single submitter ⚠
- p.Ser72Leu Single submitter Inborn genetic diseases ⚠
- p.Ser95Thr Single submitter ⚠
- p.Thr136Ala Single submitter autosomal recessive osteopetrosis 5 ⚠
- p.Thr164Ile Single submitter ⚠
- p.Thr198Ile Single submitter ⚠
- p.Val187Ala Single submitter Inborn genetic diseases ⚠
- p.Val285Leu Single submitter Inborn genetic diseases ⚠
- p.Val55Leu Single submitter ⚠