LRTOMT — 238 ClinVar variants
All ClinVar germline LRTOMT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 58 flagged for review →
12 Pathogenic · 3 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 16 Conflicting · 13 Benign · 2 Benign/Likely benign · 46 Likely benign · 137 Uncertain significance
Full LRTOMT gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 58
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 7
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
LRTOMT p.Ala133Pro
Conflicting
Single submitter
autosomal recessive nonsyndromic hearing loss 63
- LRTOMT p.Ala232Val Conflicting Single submitter
-
LRTOMT p.Arg108His
Conflicting
Single submitter
Inborn genetic diseases
-
LRTOMT p.Ile282Leu
Conflicting
Single submitter
Inborn genetic diseases
-
LRTOMT p.Thr168Met
Conflicting
Single submitter
Inborn genetic diseases
-
LRTOMT p.Thr63Met
Conflicting
Single submitter
Inborn genetic diseases
-
LRTOMT p.Val118Ile
Conflicting
Single submitter
autosomal recessive nonsyndromic hearing loss 63
Predictors lean, ClinVar uncertain 43
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
LRTOMT p.Ala133Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Arg125Gln
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Arg164Gln
Uncertain significance
Multiple submitters
autosomal recessive nonsyndromic hearing loss 63
-
LRTOMT p.Arg167Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Arg217Gln
Uncertain significance
Multiple submitters
autosomal recessive nonsyndromic hearing loss 63
-
LRTOMT p.Arg217Pro
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Arg217Trp
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Arg252His
Uncertain significance
Multiple submitters
Inborn genetic diseases
- LRTOMT p.Arg52Gln Uncertain significance Multiple submitters
- LRTOMT p.Arg58Gln Uncertain significance Multiple submitters
-
LRTOMT p.Cys21Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Leu66Val
Uncertain significance
Multiple submitters
autosomal recessive nonsyndromic hearing loss 63
- LRTOMT p.Pro155Ala Uncertain significance Multiple submitters
-
LRTOMT p.Pro198Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
- LRTOMT p.Val127Ala Uncertain significance Multiple submitters
-
LRTOMT c.*1225T>A
Uncertain significance
Single submitter
autosomal recessive nonsyndromic hearing loss 63
-
LRTOMT p.Ala131Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Ala133Asp
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.Ala152Thr Uncertain significance Single submitter
-
LRTOMT p.Arg164Trp
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Arg167His
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Arg208Trp
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.Arg219Gln Uncertain significance Single submitter
-
LRTOMT p.Arg262His
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Arg62His
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.Arg77Gln Uncertain significance Single submitter
- LRTOMT p.Asp18Ala Uncertain significance Single submitter
-
LRTOMT p.Asp18Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.Gln26His Uncertain significance Single submitter
-
LRTOMT p.Gly32Glu
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.His231Arg Uncertain significance Single submitter
-
LRTOMT p.Ile122Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.Leu19Met Uncertain significance Single submitter
- LRTOMT p.Leu246Ile Uncertain significance Single submitter
-
LRTOMT p.Met115Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Met185Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Phe181Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Pro154Ala
Uncertain significance
Single submitter
autosomal recessive nonsyndromic hearing loss 63
-
LRTOMT p.Pro198Ser
Uncertain significance
Single submitter
autosomal recessive nonsyndromic hearing loss 63
-
LRTOMT p.Thr168Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.Thr168Arg Uncertain significance Single submitter
-
LRTOMT p.Val190Ala
Uncertain significance
Single submitter
Inborn genetic diseases
-
LRTOMT p.Val51Leu
Uncertain significance
Single submitter
Inborn genetic diseases
Predictors split 8
The independent predictors disagree with each other — read with care.
-
LRTOMT p.Asp224Asn
Uncertain significance
Multiple submitters
Inborn genetic diseases
- LRTOMT p.Asp243Glu Uncertain significance Multiple submitters
-
LRTOMT p.Gly180Ser
Uncertain significance
Multiple submitters
autosomal recessive nonsyndromic hearing loss 63
-
LRTOMT p.Pro251Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Val64Gly
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
LRTOMT p.Ala230Pro
Uncertain significance
Single submitter
Inborn genetic diseases
- LRTOMT p.Asp224Glu Uncertain significance Single submitter
- LRTOMT p.Lys258Asn Uncertain significance Single submitter
All LRTOMT variants
Pathogenic 12
- p.Arg70Ter Multiple submitters
- p.Ser207fs Multiple submitters Inborn genetic diseases
- c.358+1G>A Single submitter
- c.555+2T>G Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Arg67Ter Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Asp103fs Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Cys142Ter Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Trp105Ter Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Val46_Val47insTer Single submitter
- p.Glu110Lys No assertion criteria autosomal recessive nonsyndromic hearing loss 63
- p.Trp105Arg No assertion criteria autosomal recessive nonsyndromic hearing loss 63
- p.Tyr111Ter No assertion criteria autosomal recessive nonsyndromic hearing loss 63
Pathogenic/Likely pathogenic 3
- c.358+4A>C Multiple submitters Rare genetic deafness
- p.Arg81Gln Multiple submitters LRTOMT-related disorders
- p.Thr33fs Multiple submitters LRTOMT-related disorders
Likely pathogenic 9
- p.Arg58Ter Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Arg81Pro Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Gln284fs Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Gly116Glu Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Ile189fs Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Leu159Arg Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Leu214Pro Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Ser68fs Single submitter
- p.Glu129fs No assertion criteria autosomal recessive nonsyndromic hearing loss 63
Conflicting classifications of pathogenicity 16
- c.-289C>T Single submitter
- c.-602G>A Single submitter
- p.Ala133Pro Single submitter autosomal recessive nonsyndromic hearing loss 63 ⚠
- p.Ala232Val Single submitter ⚠
- p.Arg108His Single submitter Inborn genetic diseases ⚠
- p.Arg219Ter Single submitter LRTOMT-related disorders
- p.Arg52Trp Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Arg70Gln Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Asp195= Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Cys109= Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.His55Gln Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Ile282Leu Single submitter Inborn genetic diseases ⚠
- p.Ser74= Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Thr168Met Single submitter Inborn genetic diseases ⚠
- p.Thr63Met Single submitter Inborn genetic diseases ⚠
- p.Val118Ile Single submitter autosomal recessive nonsyndromic hearing loss 63 ⚠
Benign 13
- c.34+1914T>C Multiple submitters
- c.83+161G>A Multiple submitters
- c.83+34T>A Multiple submitters
- c.34+594del Single submitter
- c.34+594dup Single submitter
- c.35-44T>C Single submitter
- c.359-51G>A Single submitter
- c.-115-261GA[4] Single submitter
- c.-321-29G>A Single submitter
- c.-321-4577T>C Single submitter
- c.-321-4874A>C Single submitter
- c.-321-5438G>A Single submitter
- p.Asp85Asn Single submitter
Benign/Likely benign 2
- c.-116+19G>C Multiple submitters
- p.Leu23= Multiple submitters
Likely benign 46
- c.34+1684C>T Multiple submitters
- c.34+373A>G Multiple submitters
- c.35-4G>A Multiple submitters
- c.35-5C>T Multiple submitters
- p.Pro198= Multiple submitters
- c.84-216G>C Multiple submitters
- p.Ala39= Multiple submitters
- c.34+18G>A Single submitter
- c.34+309G>A Single submitter
- c.34+387A>C Single submitter
- c.34+446C>T Single submitter
- c.34+461A>G Single submitter
- c.35-16G>C Single submitter
- c.358+16C>A Single submitter
- c.358+26C>T Single submitter
- c.437+8C>T Single submitter
- c.555+122G>A Single submitter
- c.556-11del Single submitter
- c.84-18T>C Single submitter
- c.84-234_84-232del Single submitter
- c.-113C>T Single submitter
- c.-321-109A>G Single submitter
- c.-321-4662A>G Single submitter
- c.-321-4940C>T Single submitter
- c.-743G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*877T>C Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Ala152= Single submitter
- p.Ala179= Single submitter
- p.Ala236= Single submitter
- p.Ala29Thr Single submitter Inborn genetic diseases
- p.Arg62Cys Single submitter
- p.Gly156= Single submitter
- p.Gly281= Single submitter
- p.Ile189= Single submitter
- p.Ile78= Single submitter
- p.Leu102= Single submitter
- p.Leu225= Single submitter
- p.Leu40= Single submitter
- p.Pro154= Single submitter
- p.Pro17= Single submitter
- p.Pro198= Single submitter
- p.Ser68= Single submitter
- p.Thr168= Single submitter
- p.Thr202= Single submitter
- p.Tyr287= Single submitter
- p.Ala133= No assertion criteria LRTOMT-related disorder
Uncertain significance 137
- c.-123T>C Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- c.-254G>T Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- c.*1488T>G Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- p.Ala133Thr Multiple submitters Inborn genetic diseases ⚠
- p.Ala250Val Multiple submitters Inborn genetic diseases
- p.Arg125Gln Multiple submitters Inborn genetic diseases ⚠
- p.Arg125Trp Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- p.Arg164Gln Multiple submitters autosomal recessive nonsyndromic hearing loss 63 ⚠
- p.Arg167Cys Multiple submitters Inborn genetic diseases ⚠
- p.Arg217Gln Multiple submitters autosomal recessive nonsyndromic hearing loss 63 ⚠
- p.Arg217Pro Multiple submitters Inborn genetic diseases ⚠
- p.Arg217Trp Multiple submitters Inborn genetic diseases ⚠
- p.Arg252Cys Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- p.Arg252His Multiple submitters Inborn genetic diseases ⚠
- p.Arg262Cys Multiple submitters Inborn genetic diseases
- p.Arg264Cys Multiple submitters Inborn genetic diseases
- p.Arg266Cys Multiple submitters Inborn genetic diseases
- p.Arg52Gln Multiple submitters ⚠
- p.Arg54Gln Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- p.Arg58Gln Multiple submitters ⚠
- p.Asp224Asn Multiple submitters Inborn genetic diseases ⚠
- p.Asp243Glu Multiple submitters ⚠
- p.Cys21Arg Multiple submitters Inborn genetic diseases ⚠
- p.Cys260Trp Multiple submitters Inborn genetic diseases
- p.Glu129del Multiple submitters
- p.Gly180Ser Multiple submitters autosomal recessive nonsyndromic hearing loss 63 ⚠
- p.His114Tyr Multiple submitters Inborn genetic diseases
- p.His268Tyr Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- p.His89Arg Multiple submitters
- p.Leu66Val Multiple submitters autosomal recessive nonsyndromic hearing loss 63 ⚠
- p.Phe83Leu Multiple submitters hearing loss disorder
- p.Pro155Ala Multiple submitters ⚠
- p.Pro198Leu Multiple submitters Inborn genetic diseases ⚠
- p.Pro251Ser Multiple submitters Inborn genetic diseases ⚠
- p.Thr63= Multiple submitters autosomal recessive nonsyndromic hearing loss 63
- p.Val127Ala Multiple submitters ⚠
- p.Val240Met Multiple submitters Inborn genetic diseases
- p.Val64Gly Multiple submitters Inborn genetic diseases ⚠
- c.34+331T>G Single submitter
- c.34+347G>A Single submitter
- c.-288G>A Single submitter
- c.-305G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-322+5G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-344G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-379T>C Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-409G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-422T>C Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-453A>G Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-481G>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-554G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-57G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-703C>G Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-705A>G Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-725T>G Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-761C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-762C>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-816C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.-885C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1116G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1160T>C Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1225T>A Single submitter autosomal recessive nonsyndromic hearing loss 63 ⚠
- c.*1363C>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1544A>G Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1608G>C Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1773C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1788C>G Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*1810A>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*205C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*244C>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*336C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*400C>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*437T>C Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*580C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*601A>C Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*622C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*638C>T Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*851G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- c.*860G>A Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Ala131Ser Single submitter Inborn genetic diseases ⚠
- p.Ala133Asp Single submitter Inborn genetic diseases ⚠
- p.Ala152Thr Single submitter ⚠
- p.Ala230Pro Single submitter Inborn genetic diseases ⚠
- p.Ala90Pro Single submitter
- p.Arg164Trp Single submitter Inborn genetic diseases ⚠
- p.Arg167His Single submitter Inborn genetic diseases ⚠
- p.Arg177Cys Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Arg201Cys Single submitter Inborn genetic diseases
- p.Arg208Trp Single submitter Inborn genetic diseases ⚠
- p.Arg219Gln Single submitter ⚠
- p.Arg252= Single submitter
- p.Arg262His Single submitter Inborn genetic diseases ⚠
- p.Arg266His Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Arg54Trp Single submitter Inborn genetic diseases
- p.Arg62His Single submitter Inborn genetic diseases ⚠
- p.Arg67Gln Single submitter Inborn genetic diseases
- p.Arg77Gln Single submitter ⚠
- p.Arg8Ter Single submitter
- p.Asp182His Single submitter Inborn genetic diseases
- p.Asp18Ala Single submitter ⚠
- p.Asp18Asn Single submitter Inborn genetic diseases ⚠
- p.Asp210Glu Single submitter
- p.Asp224Glu Single submitter ⚠
- p.Asp224Tyr Single submitter
- p.Gln26His Single submitter ⚠
- p.Glu129Gly Single submitter Inborn genetic diseases
- p.Glu229Lys Single submitter
- p.Gly291Asp Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Gly32Glu Single submitter Inborn genetic diseases ⚠
- p.Gly93Ser Single submitter Inborn genetic diseases
- p.His231Arg Single submitter ⚠
- p.His268Arg Single submitter
- p.His77Arg Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Ile122Leu Single submitter Inborn genetic diseases ⚠
- p.Leu153= Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Leu19Met Single submitter ⚠
- p.Leu246Ile Single submitter ⚠
- p.Leu60Pro Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Lys258Asn Single submitter ⚠
- p.Met115Thr Single submitter Inborn genetic diseases ⚠
- p.Met185Val Single submitter Inborn genetic diseases ⚠
- p.Phe181Ser Single submitter Inborn genetic diseases ⚠
- p.Pro154Ala Single submitter autosomal recessive nonsyndromic hearing loss 63 ⚠
- p.Pro198Ser Single submitter autosomal recessive nonsyndromic hearing loss 63 ⚠
- p.Pro92= Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Ser105= Single submitter
- p.Thr168Ala Single submitter Inborn genetic diseases ⚠
- p.Thr168Arg Single submitter ⚠
- p.Tyr256His Single submitter Inborn genetic diseases
- p.Tyr287Cys Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Tyr85Phe Single submitter Inborn genetic diseases
- p.Val135_Leu136insGluGluLysAlaProAlaCysVal Single submitter
- p.Val162Met Single submitter Inborn genetic diseases
- p.Val190Ala Single submitter Inborn genetic diseases ⚠
- p.Val190Met Single submitter autosomal recessive nonsyndromic hearing loss 63
- p.Val51Leu Single submitter Inborn genetic diseases ⚠
- p.Val61Ala Single submitter Inborn genetic diseases
- p.Val86Met Single submitter Inborn genetic diseases