Leber Hereditary Optic Neuropathy (LHON) Resources at MSeqDR.org
I. General Introduction
Leber hereditary optic neuropathy (LHON, OMIM# 535000) presents in midlife and mainly characterized by bilateral, painless subacute loss of central vision during young adult life. LHON is transmitted by maternal inheritance, and affects approximately 1:50,000 people.
Synonyms of Leber Hereditary Optic Neuropathy:
- hereditary optic neuroretinopathy
- Leber hereditary optic atrophy
- Leber optic atrophy
- Leber's hereditary optic neuropathy
- Leber's optic atrophy
- Leber's optic neuropathy
- LHON
There is a LHON With Dystonia subtype ( Marsden syndrome, OMIM# 50001).
Only approximately 50% of male and 10% of female mutation carriers develop symptoms (Newman, 2002). There are inconclusive findings from genealogic data suggest that more males than females in the maternal lineages have optic atrophy. The phenotype-only locus is OMIM# 308905, susceptibility (modifier) to leber optic atrophy (Location Xp11).
LHON has been associated with missense mtDNA mutations that can act autonomously or in association with each other to cause the disease. The three primary mitochondrial DNA LHON-causing mutations are m.11778G>A (69% patients), m.3460G>A(13% patients), and m.14484T>C(14% patients), which account for over 90% of LHON patients. The most common LHON-causing mutation is m.11778G>A. The penetrance (chance of a carrier to lose vision) order is for m.3460G>A, m.11778G>A and the least is for m.14484T>C. There are reports regarding the heteroplasmy and penetrance of LHON.
II. LHON Gene Cards (Add more LHON diseases genes associations to work list)
Known LHON Genes:
Mutation in the ATP synthase 6 gene MT-ATP6,
Mutation in the mitochondrial complex I: MT-ND1, MT-ND2, MT-ND3, MT-ND4 MT-ND4L, MT-ND5, MT-ND6
Mutation in the mitochondrial complex III: MT-CO3, MT-CYB,
Mutation in the mitochondrial complex IV: MT-CO1
III. Pathogenic variant submission, using VCF/HGVS input format, then manage and complete annotations per variant.
IV. LHON (OMIM# 535000):
Name: |
Optic Atrophy, Hereditary, Leber |
Definition: |
A maternally linked genetic disorder that presents in mid-life as acute or subacute central vision loss leading to central scotoma and blindness. The disease has been associated with missense mutations in the mtDNA, in genes for Complex I, III, and IV polypeptides, that can act autonomously or in association with each other to cause the disease. (from Online Mendelian Inheritance in Man, http://www.ncbi.nlm.nih.gov/Omim/, MIM#535000 (April 17, 2001)) |
Alternative IDs: |
OMIM:308905|OMIM:535000 |
ParentIDs: |
MESH:D015418|MESH:D028361 |
TreeNumbers: |
C10.292.700.225.500.400 |C10.574.500.662.400 |C11.270.564.400 |C11.640.451.451.400 |C16.320.290.564.400 |C16.320.400.630.400 |C18.452.660.670 |
Synonyms: |
Disease, Leber’s |Diseases, Leber’s |Hereditary Optic Neuroretinopathies |Hereditary Optic Neuroretinopathy |Leber Disease |Leber Hereditary Optic Atrophy |Leber Hereditary Optic Neuropathy |LEBER HEREDITARY OPTIC NEUROPATHY, MODIFIER OF |Leber Optic Atrophy |Leb |
Slim Mappings: |
Eye disease|Genetic disease (inborn)|Metabolic disease|Nervous system disease |
Reference: |
MedGen: D029242
MeSH: D029242
OMIM: 53500;
MSeqDR : LHON 00072; LDYT 00149;
Genes:(Add more LHON disease-gene associations to MSeqDR)
Mutation in the ATP synthase 6 gene MT-ATP6,
Mutation in the mitochondrial complex I: MT-ND1, MT-ND2, MT-ND4, MT-ND4L, MT-ND5, MT-ND6
Mutation in the mitochondrial complex III: MT-CO3, MT-CYB,
Mutation in the mitochondrial complex IV: MT-CO1
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Phenotypes:
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HEAD & NECK
NEUROLOGIC
Peripheral Nervous System
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V. LHON subtype Marsden syndrome (OMIM# 500001):
Name: |
Marsden syndrome |
Definition: |
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Alternative IDs: |
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ParentIDs: |
MESH:D004421|MESH:D029242 |
TreeNumbers: |
C10.292.700.225.500.400/C536024 |C10.574.500.662.400/C536024 |C10.597.350.300/C536024 |C11.270.564.400/C536024 |C11.640.451.451.400/C536024 |C16.320.290.564.400/C536024 |C16.320.400.630.400/C536024 |C18.452.660.670/C536024 |C23.888.592.350.300/C536024 |
Synonyms: |
Dystonia, familial, with visual failure and striatal lucencies |Leber Hereditary Optic Neuropathy With Dystonia |
Slim Mappings: |
Eye disease|Genetic disease (inborn)|Metabolic disease|Nervous system disease|Signs and symptoms |
Reference: |
MedGen: C536024
MeSH: C536024
OMIM:500001;
MSeqDR : LDYT 00149
Genes:(Add more LHON disease-gene associations to MSeqDR)
Mutation in the mitochondrial complex I: MT-ND1, MT-ND3, MT-ND4, MT-ND6 |
Phenotypes:
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OMIM Clinical Synopsis
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MSeqDR Portal |
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VI. Disease Causing Variants from ClinVar (Submit more pathogenic variant to MSeqDR):
Variant |
GeneID |
GeneSymbol |
Clinical Significance |
dbSNP |
RCVaccession |
PhenotypeIDs |
m.8686T>C |
4508 |
MT-ATP6 |
not provided |
-1 |
RCV000709918; RCV000709918; RCV000709918; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN043634; MedGen:C1328349,OMIM:551500, Orphanet:ORPHA644 |
m.9101T>C |
4508 |
MT-ATP6 |
Pathogenic |
199476134 |
RCV000010277; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.7444G>A |
4512 |
MT-CO1 |
Pathogenic |
199474822 |
RCV000010300; RCV000010301; RCV000010299; |
MedGen:C1838854,OMIM:580000, Orphanet:ORPHA168609; MedGen:C3151897,OMIM:500008; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.9438G>A |
4514 |
MT-CO3 |
Pathogenic |
267606611 |
RCV000010286; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.9804G>A |
4514 |
MT-CO3 |
Conflicting interpretations of pathogenicity |
200613617 |
RCV000010287; RCV000756352; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202 |
m.14831G>A |
4519 |
MT-CYB |
Pathogenic |
199795644 |
RCV000055706; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.15257G>A |
4519 |
MT-CYB |
Conflicting interpretations of pathogenicity |
41518645 |
RCV000010312; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.15437G>A |
4519 |
MT-CYB |
Uncertain significance |
878853058 |
RCV000764855; RCV000764855; RCV000224435; |
MedGen:C0162671,OMIM:540000, Orphanet:ORPHA550,SNOMED CT:39925003; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202 |
m.15812G>A |
4519 |
MT-CYB |
Pathogenic |
200336777 |
RCV000010313; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.3376G>A |
4535 |
MT-ND1 |
Pathogenic |
397515612 |
RCV000056167; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.3394T>C |
4535 |
MT-ND1 |
Pathogenic |
41460449 |
RCV000010375; RCV000507319; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202 |
m.3460G>A |
4535 |
MT-ND1 |
Pathogenic |
199476118 |
RCV000010370; RCV000143998; RCV000735416; RCV000757484; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C0023264,OMIM:256000, Orphanet:ORPHA506,SNOMED CT:29570005; na; MedGen:CN517202 |
m.3635G>A |
4535 |
MT-ND1 |
Pathogenic |
397515507 |
RCV000055707; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.3697G>A |
4535 |
MT-ND1 |
Pathogenic |
199476122 |
RCV000010385; RCV000010386; RCV000056168; |
MedGen:C0162671,OMIM:540000, Orphanet:ORPHA550,SNOMED CT:39925003; MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.3700G>A |
4535 |
MT-ND1 |
Pathogenic |
397515508 |
RCV000415448; RCV000055708; RCV000415448; RCV000415448; |
Human Phenotype Ontology:HP:0000512,MedGen:C0476397; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; Human Phenotype Ontology:HP:0001138,MedGen:C3887709; Human Phenotype Ontology:HP:0000572,MedGen:C3665 |
m.3733G>A |
4535 |
MT-ND1 |
Pathogenic |
199476125 |
RCV000010389; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.4025C>T |
4535 |
MT-ND1 |
Pathogenic |
397515509 |
RCV000055709; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.4136A>G |
4535 |
MT-ND1 |
Pathogenic |
199476121 |
RCV000010378; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.4160T>C |
4535 |
MT-ND1 |
Pathogenic |
199476119 |
RCV000010372; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.4171C>A |
4535 |
MT-ND1 |
Pathogenic |
28616230 |
RCV000010384; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.4216T>C |
4535 |
MT-ND1 |
Conflicting interpretations of pathogenicity |
1599988 |
RCV000010373; RCV000709875; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202 |
m.4640C>A |
4536 |
MT-ND2 |
Pathogenic |
387906426 |
RCV000010366; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.4917A>G |
4536 |
MT-ND2 |
Uncertain significance |
28357980 |
RCV000010364; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.5244G>A |
4536 |
MT-ND2 |
Pathogenic |
199476115 |
RCV000010365; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.10237T>C |
4537 |
MT-ND3 |
Pathogenic |
1556423787 |
RCV000055695; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.11253T>C |
4538 |
MT-ND4 |
Pathogenic |
200145866 |
RCV000055696; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.11360A>G |
4538 |
MT-ND4 |
Uncertain significance |
878928689 |
RCV000764854; RCV000626558; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; Human Phenotype Ontology:HP:0001250,MedGen:C0036572 |
m.11696G>A |
4538 |
MT-ND4 |
Pathogenic |
200873900 |
RCV000010356; RCV000055697; |
MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.11778G>A |
4538 |
MT-ND4 |
Pathogenic |
199476112 |
RCV000010354; RCV000224219; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202 |
m.10663T>C |
4539 |
MT-ND4L |
Pathogenic |
1556423844 |
RCV000010353; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.12338T>C |
4540 |
MT-ND5 |
Pathogenic |
201863060 |
RCV000022893; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.12811T>C |
4540 |
MT-ND5 |
Uncertain significance |
199974018 |
RCV000055698; RCV000507393; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202 |
m.12848C>T |
4540 |
MT-ND5 |
Pathogenic |
267606899 |
RCV000010350; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.13045A>C |
4540 |
MT-ND5 |
Pathogenic |
267606895 |
RCV000010340; RCV000010341; RCV000010342; |
MedGen:C0162671,OMIM:540000, Orphanet:ORPHA550,SNOMED CT:39925003; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C1838951 |
m.13637A>G |
4540 |
MT-ND5 |
Pathogenic |
200855215 |
RCV000055699; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.13708G>A |
4540 |
MT-ND5 |
Conflicting interpretations of pathogenicity |
28359178 |
RCV000010336; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.13730G>A |
4540 |
MT-ND5 |
Pathogenic |
387906425 |
RCV000010337; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14279G>A |
4541 |
MT-ND6 |
Pathogenic |
869025187 |
RCV000055705; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14325T>C |
4541 |
MT-ND6 |
Pathogenic |
397515505 |
RCV000055700; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14459G>A |
4541 |
MT-ND6 |
Pathogenic |
199476105 |
RCV000010326; RCV000010327; RCV000144019; RCV000010328; |
MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C0023264,OMIM:256000, Orphanet:ORPHA506,SNOMED CT:29570005; MedGen:C1838951 |
m.14482C>A |
4541 |
MT-ND6 |
Pathogenic |
199476108 |
RCV000010332; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14482C>G |
4541 |
MT-ND6 |
Pathogenic |
199476108 |
RCV000055701; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14484T>C |
4541 |
MT-ND6 |
Pathogenic |
199476104 |
RCV000010325; RCV000144018; RCV000223709; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C0023264,OMIM:256000, Orphanet:ORPHA506,SNOMED CT:29570005; MedGen:CN517202 |
m.14495A>G |
4541 |
MT-ND6 |
Pathogenic |
199476106 |
RCV000010330; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14498T>C |
4541 |
MT-ND6 |
Pathogenic |
869025186 |
RCV000055702; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14568C>T |
4541 |
MT-ND6 |
Pathogenic |
397515506 |
RCV000055703; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.14596A>T |
4541 |
MT-ND6 |
Pathogenic |
387906424 |
RCV000010329; RCV000055704; |
MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
m.3275C>T |
4567 |
MT-TL1 |
Uncertain significance |
1057516057 |
RCV000408928; RCV000408950; RCV000408938; RCV000408938; RCV000408938; RCV000408925; RCV000408938; RCV000408950; |
MedGen:C0424605; MedGen:C0424605; MedGen:C0016059; Human Phenotype Ontology:HP:0001397,MedGen:C2711227; Human Phenotype Ontology:HP:0012115,MedGen:C0019158; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; |
NM_001166159.1(NDUFS2) :c.268G>A (p.Ala90Thr) |
4720 |
NDUFS2 |
Pathogenic |
1553249704 |
RCV000625868; |
Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003 |
VII. LHON Pseudo Cases:
1. 28314831___1 - MS01001288 ; 2. 28314831___2 - MS01001299 ; 3. 28314831___3 - MS01001308 ; 4. 28314831___4 - MS01001309 ; 5. 28314831___5 - MS01001310 ; 6. 28314831___6 - MS01001311 ; 7. 28314831___7 - MS01001312 ; 8. 28314831___8 - MS01001313 ; 9. 28314831___9 - MS01001314 ; 10. 28314831___10 - MS01001289 ; 11. 28314831___11 - MS01001290 ; 12. 28314831___12 - MS01001291 ; 13. 28314831___13 - MS01001292 ; 14. 28314831___14 - MS01001293 ; 15. 28314831___15 - MS01001294 ; 16. 28314831___16 - MS01001295 ; 17. 28314831___17 - MS01001296 ; 18. 28314831___18 - MS01001297 ; 19. 28314831___19 - MS01001298 ; 20. 28314831___20 - MS01001300 ; 21. 28314831___21 - MS01001301 ; 22. 28314831___22 - MS01001302 ; 23. 28314831___23 - MS01001303 ; 24. 28314831___24 - MS01001304 ; 25. 28314831___25 - MS01001305 ; 26. 28314831___26 - MS01001306 ; 27. 28314831___27 - MS01001307
Potential LHON Pseudo Cases: 1. 28081242___QT1470 - MS01001348 ; 2. 28081242___QT1470M - MS01001349 ; 3. 28081242___Le2424 - MS01001327 ; 4. 28081242___LE2424M - MS01001315 ; 5. 28081242___QT1325 - MS01001347 ; 6. 28081242___Le2643 - MS01001333 ; 7. 28081242___Le2174 - MS01001320 ; 8. 28081242___QT1319 - MS01001346 ; 9. 28081242___Le2458 - MS01001328 ; 10. 28081242___Le2973 - MS01001340 ; 11. 28081242___LE2974 - MS01001318 ; 12. 28081242___QT1752 - MS01001351 ; 13. 28081242___QT1657 - MS01001350 ; 14. 28081242___LE2799 - MS01001316 ; 15. 28081242___Le2934 - MS01001338 ; 16. 28081242___Le2532 - MS01001331 ; 17. 28081242___LE2904 - MS01001317 ; 18. 28081242___Le2519 - MS01001329 ; 19. 28081242___Le2519F - MS01001330 ; 20. 28081242___Le2198 - MS01001321 ; 21. 28081242___Le2198M - MS01001322 ; 22. 28081242___Le2198S - MS01001323 ; 23. 28081242___QT1292 - MS01001343 ; 24. 28081242___QT1292M - MS01001345 ; 25. 28081242___QT1292G - MS01001344 ; 26. 28081242___Le2726 - MS01001335 ; 27. 28081242___Le2379 - MS01001325 ; 28. 28081242___Le2883 - MS01001337 ; 29. 28081242___Le2779 - MS01001336 ; 30. 28081242___Le2411 - MS01001326 ; 31. 28081242___Le2637 - MS01001332 ; 32. 28081242___Le2217 - MS01001324 ; 33. 28081242___Le2661 - MS01001334 ; 34. 28081242___Le2961 - MS01001339 ; 35. 28081242___QT1063 - MS01001341 ; 36. 28081242___QT1063M - MS01001342 ; 37. 28081242___Le2103 - MS01001319
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