ClinVar Miner

Variants with conflicting interpretations studied for Leigh syndrome

Coded as:
Minimum review status of the submission for Leigh syndrome: Y axis collection method of the submission for Leigh syndrome:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission Variants with at least 2 submissions and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any kind of conflict
121 334 3 92 53 0 9 153

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All conditions
Leigh syndrome pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 3 7 5 1 0
likely pathogenic 6 0 1 0 0
uncertain significance 1 3 0 37 27
likely benign 0 0 1 0 71
benign 0 0 1 13 0

Condition to condition summary #

Total conditions: 19
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any kind of conflict
not specified 0 16 0 72 44 0 1 117
not provided 0 47 0 49 15 0 7 70
Hereditary cancer-predisposing syndrome 0 5 0 22 4 0 0 26
Mitochondrial complex II deficiency; Paragangliomas 5 0 6 0 13 2 0 0 15
Leigh syndrome 591 9 0 5 2 0 1 8
Deficiency of guanidinoacetate methyltransferase 0 3 0 4 0 0 0 4
Leigh syndrome, French Canadian type 0 9 0 0 4 0 0 4
Leber's optic atrophy 0 0 3 0 0 0 0 3
Maple syrup urine disease, type 3 0 2 0 0 2 0 0 2
Mitochondrial complex I deficiency, nuclear type 1 0 2 0 1 0 0 1 2
Mitochondrial short-chain enoyl-coa hydratase 1 deficiency 0 0 0 2 0 0 0 2
Osteopetrosis 0 0 0 1 1 0 0 2
Cockayne syndrome 0 2 0 1 0 0 0 1
Combined oxidative phosphorylation deficiency 32 0 1 0 1 0 0 0 1
History of neurodevelopmental disorder 0 0 0 1 0 0 0 1
Leigh syndrome due to mitochondrial complex IV deficiency 0 2 0 1 0 0 0 1
MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 2 0 0 0 1 0 0 0 1
Mitochondrial complex I deficiency 0 208 0 1 0 0 0 1
Paragangliomas 5 0 2 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 153
Download table as spreadsheet
HGVS dbSNP
NC_012920.1:m.14484T>C rs199476104
NC_012920.1:m.3460G>A rs199476118
NM_000108.4(DLD):c.1351C>T (p.Leu451=) rs1803921
NM_000108.4(DLD):c.249T>C (p.Val83=) rs2228664
NM_000108.4(DLD):c.34G>A (p.Ala12Thr) rs75077312
NM_000108.4(DLD):c.439-7T>C rs10263341
NM_000108.4(DLD):c.543A>T (p.Ile181=) rs61749952
NM_000108.4(DLD):c.684+7G>A rs75123588
NM_000108.4(DLD):c.685-14T>A rs80111449
NM_000156.5(GAMT):c.*146A>C rs659455
NM_000156.5(GAMT):c.571-6G>A rs2074899
NM_000156.5(GAMT):c.626C>T (p.Thr209Met) rs17851582
NM_001199981.1(NDUFS1):c.1143A>G (p.Arg381=) rs1801318
NM_001199981.1(NDUFS1):c.858G>T (p.Ala286=) rs1127566
NM_001303.3(COX10):c.1038G>A (p.Ser346=) rs2230355
NM_001303.3(COX10):c.184A>T (p.Thr62Ser) rs2230351
NM_001303.3(COX10):c.290A>G (p.Tyr97Cys) rs16948986
NM_001303.3(COX10):c.33C>T (p.Arg11=) rs8076787
NM_001303.3(COX10):c.83C>T (p.Thr28Ile) rs16948978
NM_001303.3(COX10):c.928+12G>A rs200573622
NM_001303.3(COX10):c.929-7C>T rs62052075
NM_001303.3(COX10):c.981C>T (p.Asn327=) rs146175179
NM_002495.2(NDUFS4):c.198A>C (p.Gly66=) rs31304
NM_002495.3(NDUFS4):c.102G>A (p.Ser34=) rs138941073
NM_002495.3(NDUFS4):c.12G>C (p.Val4=) rs2279516
NM_002495.3(NDUFS4):c.312A>G (p.Arg104=) rs31303
NM_002495.3(NDUFS4):c.351-11_351-8delGTTT rs375549253
NM_002496.2(NDUFS8):c.236C>T (p.Pro79Leu) rs28939679
NM_002496.3(NDUFS8):c.*14C>T rs1051806
NM_002496.3(NDUFS8):c.*40A>G rs61329983
NM_002496.3(NDUFS8):c.299C>T (p.Ala100Val) rs748754134
NM_002496.3(NDUFS8):c.459C>T (p.Cys153=) rs149201273
NM_002496.3(NDUFS8):c.502-10C>T rs369961682
NM_002496.3(NDUFS8):c.502-13C>T rs199793417
NM_002496.3(NDUFS8):c.597C>T (p.Ile199=) rs1804688
NM_002496.3(NDUFS8):c.64C>T (p.Pro22Ser) rs369602258
NM_003172.3(SURF1):c.-11_13del24 rs863224229
NM_003172.3(SURF1):c.211G>C (p.Val71Leu) rs147993882
NM_003172.3(SURF1):c.280T>C (p.Leu94=) rs28615629
NM_003172.3(SURF1):c.54+10G>A rs587598397
NM_003172.3(SURF1):c.54+9C>G rs587675928
NM_003172.3(SURF1):c.543C>T (p.Phe181=) rs62637580
NM_003172.3(SURF1):c.573C>G (p.Thr191=) rs28715079
NM_003172.3(SURF1):c.586C>T (p.Gln196Ter) rs147816470
NM_003172.3(SURF1):c.604G>C (p.Asp202His) rs72619327
NM_003172.3(SURF1):c.745A>G (p.Asn249Asp) rs587669420
NM_003172.3(SURF1):c.758_759delCA (p.Thr253Serfs) rs782349178
NM_003172.3(SURF1):c.809_826dup (p.Ile275_Val276insGluHisLeuGlnTyrIle)
NM_003172.3(SURF1):c.883C>T (p.Arg295Cys) rs147312193
NM_004092.3(ECHS1):c.2T>G (p.Met1Arg) rs587776497
NM_004092.3(ECHS1):c.5C>T (p.Ala2Val) rs587776498
NM_004168.3(SDHA):c.-4A>G rs377134185
NM_004168.3(SDHA):c.113A>T (p.Asp38Val) rs34635677
NM_004168.3(SDHA):c.1170C>T (p.Phe390=) rs35277230
NM_004168.3(SDHA):c.1305G>T (p.Leu435=) rs35964044
NM_004168.3(SDHA):c.133G>A (p.Ala45Thr) rs140736646
NM_004168.3(SDHA):c.163T>C (p.Tyr55His) rs142926807
NM_004168.3(SDHA):c.1664-8G>A rs199790689
NM_004168.3(SDHA):c.1776T>C (p.His592=) rs1126538
NM_004168.3(SDHA):c.17G>A (p.Gly6Asp) rs187964306
NM_004168.3(SDHA):c.1886A>T (p.Tyr629Phe) rs6960
NM_004168.3(SDHA):c.1908+15C>T rs34504623
NM_004168.3(SDHA):c.1909-12_1909-11delCT rs372662724
NM_004168.3(SDHA):c.1911C>T (p.Val637=) rs11557098
NM_004168.3(SDHA):c.441C>T (p.Pro147=) rs201453889
NM_004168.3(SDHA):c.549C>T (p.Gly183=) rs61733344
NM_004168.3(SDHA):c.550G>A (p.Gly184Arg) rs148246073
NM_004168.3(SDHA):c.723C>T (p.Asp241=) rs146653693
NM_004168.3(SDHA):c.771-11A>G rs2288461
NM_004168.3(SDHA):c.822C>T (p.Gly274=) rs34771391
NM_004168.3(SDHA):c.891T>C (p.Pro297=) rs1126417
NM_004168.3(SDHA):c.969C>T (p.Gly323=) rs142849100
NM_004168.4(SDHA):c.1038C>G (p.Ser346=) rs1041949
NM_004168.4(SDHA):c.1680G>A (p.Thr560=) rs1139449
NM_004168.4(SDHA):c.1752A>G (p.Ala584=) rs13070
NM_004168.4(SDHA):c.1932G>A (p.Val644=) rs6961
NM_004168.4(SDHA):c.1969G>A (p.Val657Ile) rs6962
NM_004168.4(SDHA):c.309A>G (p.Ala103=) rs1139424
NM_004168.4(SDHA):c.619A>C (p.Arg207=) rs6555055
NM_004168.4(SDHA):c.684T>C (p.Asn228=) rs2115272
NM_004328.4(BCS1L):c.-14G>A rs367721351
NM_004328.4(BCS1L):c.-43G>A rs145989550
NM_004328.4(BCS1L):c.1017T>C (p.Pro339=) rs35843327
NM_004328.4(BCS1L):c.628G>A (p.Asp210Asn) rs58447305
NM_004328.4(BCS1L):c.822G>A (p.Pro274=) rs112329020
NM_004328.4(BCS1L):c.996C>T (p.Asn332=) rs33946522
NM_004376.6(COX15):c.452C>G (p.Ser151Ter) rs149718203
NM_004544.3(NDUFA10):c.1000-3C>G rs199648872
NM_004544.3(NDUFA10):c.1000-5delC rs138479490
NM_004544.3(NDUFA10):c.105A>G (p.Lys35=) rs2083411
NM_004544.3(NDUFA10):c.24G>A (p.Leu8=) rs113012830
NM_004544.3(NDUFA10):c.548-9A>G rs147876332
NM_004544.3(NDUFA10):c.549T>C (p.Cys183=) rs149783296
NM_004544.3(NDUFA10):c.5C>G (p.Ala2Gly) rs11541494
NM_004544.3(NDUFA10):c.771A>G (p.Gln257=) rs13848
NM_004551.2(NDUFS3):c.628-7C>T rs11039306
NM_004551.2(NDUFS3):c.79C>T (p.Pro27Ser) rs368907187
NM_004551.2(NDUFS3):c.91T>C (p.Leu31=) rs770306617
NM_004589.3(SCO1):c.16C>G (p.Leu6Val) rs61753148
NM_004589.3(SCO1):c.172C>T (p.Pro58Ser) rs1802083
NM_004589.3(SCO1):c.297A>G (p.Ala99=) rs11538237
NM_004589.3(SCO1):c.594A>G (p.Pro198=) rs2271228
NM_005006.6(NDUFS1):c.123C>T (p.Val41=) rs2230888
NM_005006.6(NDUFS1):c.1371G>A (p.Ser457=) rs2230892
NM_005006.6(NDUFS1):c.154-10_154-9delTT rs568965659
NM_005006.6(NDUFS1):c.414T>C (p.Asp138=) rs11548670
NM_005006.6(NDUFS1):c.421-7A>G rs192949406
NM_005006.6(NDUFS1):c.551+14C>A rs10206644
NM_005006.6(NDUFS1):c.975C>T (p.Arg325=) rs2230890
NM_007103.3(NDUFV1):c.-45T>G rs373940385
NM_007103.3(NDUFV1):c.1056T>C (p.Ala352=) rs11227859
NM_007103.3(NDUFV1):c.150C>T (p.Asp50=) rs11540012
NM_007103.3(NDUFV1):c.205C>T (p.Leu69=) rs199543483
NM_007103.3(NDUFV1):c.366G>A (p.Pro122=) rs140445386
NM_007103.3(NDUFV1):c.549C>G (p.Gly183=) rs10896187
NM_007103.3(NDUFV1):c.72+15G>T rs187400726
NM_017547.3(FOXRED1):c.612_615dupAGTG (p.Ala206Serfs) rs398124308
NM_018060.3(IARS2):c.1821G>A (p.Trp607Ter) rs373436822
NM_018060.3(IARS2):c.2122G>A (p.Glu708Lys) rs143722284
NM_023936.1(MRPS34):c.37G>A (p.Glu13Lys) rs1131692037
NM_024407.4(NDUFS7):c.*13C>A rs11551663
NM_024407.4(NDUFS7):c.153C>T (p.Ala51=) rs140236960
NM_024407.4(NDUFS7):c.408+10G>T rs2074896
NM_024407.4(NDUFS7):c.68C>T (p.Pro23Leu) rs1142530
NM_133259.3(LRPPRC):c.-11A>G rs188424940
NM_133259.3(LRPPRC):c.1068A>G (p.Gln356=) rs4953042
NM_133259.3(LRPPRC):c.1156-8dupT rs747766605
NM_133259.3(LRPPRC):c.1262-12T>C rs149449510
NM_133259.3(LRPPRC):c.135C>T (p.Ala45=) rs886056061
NM_133259.3(LRPPRC):c.1419T>C (p.Asp473=) rs886056057
NM_133259.3(LRPPRC):c.1432A>G (p.Thr478Ala) rs35035668
NM_133259.3(LRPPRC):c.1583-14A>G rs372371276
NM_133259.3(LRPPRC):c.1888C>T (p.Leu630=) rs35881858
NM_133259.3(LRPPRC):c.1928A>G (p.His643Arg) rs148575027
NM_133259.3(LRPPRC):c.2118A>G (p.Glu706=) rs118188415
NM_133259.3(LRPPRC):c.2325A>G (p.Lys775=) rs139634347
NM_133259.3(LRPPRC):c.2385C>T (p.Gly795=) rs886056056
NM_133259.3(LRPPRC):c.246G>A (p.Gln82=) rs6741066
NM_133259.3(LRPPRC):c.2562A>G (p.Val854=) rs4494798
NM_133259.3(LRPPRC):c.2966G>A (p.Arg989His) rs774857058
NM_133259.3(LRPPRC):c.3595A>G (p.Asn1199Asp) rs113974315
NM_133259.3(LRPPRC):c.41C>G (p.Ala14Gly) rs114205971
NM_133259.3(LRPPRC):c.58C>T (p.Leu20Phe) rs184339274
NM_133259.3(LRPPRC):c.64C>G (p.Leu22Val) rs181626399
NM_133259.3(LRPPRC):c.79C>T (p.Leu27Phe) rs116727742
NM_133259.3(LRPPRC):c.96C>T (p.Gly32=) rs886056064
NM_139242.3(MTFMT):c.626C>T (p.Ser209Leu) rs201431517
NM_174889.4(NDUFAF2):c.-91C>T rs4647036
NM_174889.4(NDUFAF2):c.139C>T (p.Arg47Ter) rs137852863
NM_174889.4(NDUFAF2):c.462T>C (p.Phe154=) rs77878573
NM_174889.4(NDUFAF2):c.60G>A (p.Lys20=) rs158921
m.14459G>A rs199476105
m.8344A>G rs118192098

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