ClinVar Miner

Variants with conflicting interpretations studied for Spastic paraplegia

Coded as:
Minimum review status of the submission for Spastic paraplegia: Y axis collection method of the submission for Spastic paraplegia:
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
370 127 1 117 68 0 8 169

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
Spastic paraplegia pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 1 7 2 0 0
likely pathogenic 3 0 0 0 0
uncertain significance 0 4 0 6 1
likely benign 0 0 22 0 3
benign 1 1 40 104 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 0 113 0 51 19 0 1 69
not provided 0 75 0 25 27 0 2 50
Spastic paraplegia, autosomal dominant 0 5 0 31 6 0 0 37
Spastic Paraplegia, Recessive 0 8 0 16 14 0 0 30
Spastic ataxia Charlevoix-Saguenay type 0 14 1 12 12 0 1 24
History of neurodevelopmental disorder 0 12 0 5 1 0 0 6
Congenital Bile Acid Synthesis Defect 0 2 0 2 2 0 1 5
Spastic paraplegia 35 0 2 0 2 2 0 0 4
Hereditary spastic paraplegia 0 3 0 0 2 0 0 2
Spastic paraplegia 10 0 3 0 2 0 0 0 2
Spastic paraplegia 15 0 7 0 1 1 0 0 2
Spastic paraplegia 33, autosomal dominant 0 0 0 1 0 0 1 2
Abnormality of brain morphology 0 0 0 0 0 0 1 1
Hydrocephalus due to aqueductal stenosis 0 1 0 0 1 0 0 1
Inborn genetic diseases 0 3 0 0 0 0 1 1
Spastic paraplegia 30, autosomal recessive; Hereditary sensory and autonomic neuropathy type IIC; Mental retardation, autosomal dominant 9 0 1 0 1 0 0 0 1
Spastic paraplegia 52, autosomal recessive 0 1 0 1 0 0 0 1
Spastic paraplegia 56, autosomal recessive 0 0 0 1 0 0 0 1
Spastic tetraparesis 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 169
Download table as spreadsheet
HGVS dbSNP
NM_000425.4(L1CAM):c.2211G>A (p.Pro737=) rs146782397
NM_000425.4(L1CAM):c.2302G>A (p.Val768Ile) rs36021462
NM_000425.4(L1CAM):c.256G>A (p.Val86Met) rs149309725
NM_000425.4(L1CAM):c.3081G>A (p.Ala1027=) rs139393266
NM_000425.4(L1CAM):c.338G>A (p.Arg113His) rs781908326
NM_000425.4(L1CAM):c.3412C>G (p.Leu1138Val) rs781860875
NM_000425.4(L1CAM):c.3519C>T (p.Phe1173=) rs142277193
NM_000425.4(L1CAM):c.3642C>T (p.Ser1214=) rs782341083
NM_000425.4(L1CAM):c.36C>A (p.Leu12=) rs140678848
NM_000425.4(L1CAM):c.400+9C>T rs201057718
NM_000425.4(L1CAM):c.984C>T (p.Thr328=) rs200638763
NM_001002261.3(ZFYVE27):c.126C>T (p.Leu42=) rs17419023
NM_001002261.3(ZFYVE27):c.244G>A (p.Val82Ile) rs17108378
NM_001002261.3(ZFYVE27):c.32C>T (p.Pro11Leu) rs112316490
NM_001002261.3(ZFYVE27):c.378G>A (p.Lys126=) rs75060573
NM_001002261.3(ZFYVE27):c.424C>T (p.Arg142Cys) rs145746084
NM_001002261.3(ZFYVE27):c.522G>A (p.Leu174=) rs143515214
NM_001002261.3(ZFYVE27):c.572G>T (p.Gly191Val) rs35077384
NM_001002261.3(ZFYVE27):c.62C>T (p.Ala21Val) rs140812293
NM_001002261.3(ZFYVE27):c.79C>G (p.Pro27Ala) rs34979921
NM_001478.4(B4GALNT1):c.1385-10C>T rs200524912
NM_001478.4(B4GALNT1):c.793G>A (p.Gly265Arg) rs144922627
NM_001478.4(B4GALNT1):c.880G>A (p.Ala294Thr) rs147301375
NM_002156.4(HSPD1):c.1216-9C>T rs189395138
NM_002156.4(HSPD1):c.1360T>C (p.Leu454=) rs147135152
NM_002156.4(HSPD1):c.1446T>C (p.Asn482=) rs2303884
NM_002156.4(HSPD1):c.144C>T (p.Ala48=) rs11551346
NM_002156.4(HSPD1):c.1688G>C (p.Gly563Ala) rs41265953
NM_002156.4(HSPD1):c.18A>G (p.Thr6=) rs79630442
NM_002156.4(HSPD1):c.27C>G (p.Arg9=) rs11551349
NM_002156.4(HSPD1):c.425G>A (p.Arg142Lys) rs61755731
NM_002156.4(HSPD1):c.561T>C (p.Ser187=) rs141357756
NM_002156.4(HSPD1):c.603A>G (p.Val201=) rs146598485
NM_004187.3(KDM5C):c.1764G>A (p.Gln588=) rs61733871
NM_004187.3(KDM5C):c.1794C>T (p.Pro598=) rs35353912
NM_004187.3(KDM5C):c.2517-9_2517-7dupACT rs398124111
NM_004187.3(KDM5C):c.4637G>A (p.Arg1546Gln) rs139569882
NM_004321.7(KIF1A):c.38G>A (p.Arg13His) rs797045050
NM_004321.7(KIF1A):c.947G>A (p.Arg316Gln) rs749718096
NM_004733.3(SLC33A1):c.136G>A (p.Glu46Lys) rs149571533
NM_004733.3(SLC33A1):c.1525G>A (p.Gly509Ser) rs76440173
NM_004733.3(SLC33A1):c.327A>G (p.Gln109=) rs74578336
NM_004820.4(CYP7B1):c.1456C>T (p.Arg486Cys) rs116171274
NM_004820.4(CYP7B1):c.204G>A (p.Arg68=) rs377119798
NM_004820.4(CYP7B1):c.522T>C (p.Ser174=) rs371522442
NM_004820.4(CYP7B1):c.56T>C (p.Leu19Pro) rs72554624
NM_004820.4(CYP7B1):c.971G>A (p.Arg324His) rs59035258
NM_004984.2(KIF5A):c.129+9C>T rs372131378
NM_004984.2(KIF5A):c.2272G>A (p.Glu758Lys) rs140281678
NM_004984.2(KIF5A):c.2769G>A (p.Arg923=) rs35225609
NM_004984.3(KIF5A):c.1105C>T (p.Arg369Trp) rs140929639
NM_004984.3(KIF5A):c.1150G>C (p.Gly384Arg) rs143326964
NM_004984.3(KIF5A):c.1176G>A (p.Glu392=) rs75907338
NM_004984.3(KIF5A):c.1293+9G>A rs201749114
NM_004984.3(KIF5A):c.2040G>A (p.Val680=) rs117670788
NM_004984.3(KIF5A):c.2199-4G>A rs201366820
NM_004984.3(KIF5A):c.2412C>T (p.Asp804=) rs145062338
NM_004984.3(KIF5A):c.2957C>T (p.Pro986Leu) rs113247976
NM_004984.3(KIF5A):c.714+8G>A rs199624091
NM_004984.3(KIF5A):c.750C>T (p.Asp250=) rs375693647
NM_004984.3(KIF5A):c.827A>G (p.Tyr276Cys) rs121434443
NM_005619.4(RTN2):c.1143G>A (p.Ala381=) rs45532933
NM_005619.4(RTN2):c.1312C>T (p.Arg438Cys) rs148270789
NM_006517.4(SLC16A2):c.1596C>T (p.Ser532=) rs199904356
NM_006517.4(SLC16A2):c.412C>G (p.Gln138Glu) rs145061343
NM_007077.4(AP4S1):c.289C>T (p.Arg97Ter) rs200440467
NM_007077.4(AP4S1):c.348G>A (p.Met116Ile) rs74807133
NM_007175.6(ERLIN2):c.123G>A (p.Leu41=) rs112575270
NM_007175.6(ERLIN2):c.318C>T (p.Asn106=) rs16887018
NM_007175.7(ERLIN2):c.696G>A (p.Lys232=) rs138164407
NM_007347.4(AP4E1):c.1085A>G (p.Tyr362Cys) rs58909326
NM_007347.4(AP4E1):c.1177-9T>C rs145851652
NM_007347.4(AP4E1):c.1276A>C (p.Ile426Leu) rs148817957
NM_007347.4(AP4E1):c.1283A>G (p.Asn428Ser) rs116796602
NM_007347.4(AP4E1):c.258T>C (p.Tyr86=) rs143624283
NM_007347.4(AP4E1):c.2755A>G (p.Met919Val) rs115188375
NM_007347.4(AP4E1):c.2905-8A>G rs56813592
NM_014363.5(SACS):c.10611A>G (p.Ala3537=) rs137856939
NM_014363.5(SACS):c.10668G>A (p.Leu3556=) rs139517699
NM_014363.5(SACS):c.10896A>G (p.Ile3632Met) rs35256065
NM_014363.5(SACS):c.10906C>T (p.Arg3636Ter) rs780247476
NM_014363.5(SACS):c.10982C>T (p.Ala3661Val) rs36061856
NM_014363.5(SACS):c.11032C>G (p.Pro3678Ala) rs17078601
NM_014363.5(SACS):c.11688G>A (p.Arg3896=) rs116791509
NM_014363.5(SACS):c.11703T>C (p.Asn3901=) rs146154135
NM_014363.5(SACS):c.12597A>G (p.Pro4199=) rs112630127
NM_014363.5(SACS):c.12649A>G (p.Asn4217Asp) rs35799469
NM_014363.5(SACS):c.13717A>C (p.Asn4573His) rs34382952
NM_014363.5(SACS):c.1373C>T (p.Thr458Ile) rs61729954
NM_014363.5(SACS):c.1839G>A (p.Gln613=) rs35840595
NM_014363.5(SACS):c.2080G>A (p.Ala694Thr) rs17325713
NM_014363.5(SACS):c.2146C>T (p.His716Tyr) rs146852400
NM_014363.5(SACS):c.2643G>C (p.Glu881Asp) rs200517685
NM_014363.5(SACS):c.2983G>T (p.Val995Phe) rs142967124
NM_014363.5(SACS):c.2988A>G (p.Leu996=) rs111846884
NM_014363.5(SACS):c.3129A>G (p.Ser1043=) rs148878361
NM_014363.5(SACS):c.3427C>A (p.Gln1143Lys) rs144267558
NM_014363.5(SACS):c.4117_4118delGCinsCT (p.Ala1373Leu) rs797045938
NM_014363.5(SACS):c.4188C>T (p.His1396=) rs61754477
NM_014363.5(SACS):c.4466A>G (p.Asn1489Ser) rs147099630
NM_014363.5(SACS):c.4744G>A (p.Asp1582Asn) rs1160357920
NM_014363.5(SACS):c.6267G>A (p.Ser2089=) rs9550956
NM_014363.5(SACS):c.6781C>A (p.Leu2261Ile) rs146722795
NM_014363.5(SACS):c.7273C>T (p.Arg2425Ter) rs145766983
NM_014363.5(SACS):c.7384C>T (p.Pro2462Ser) rs78239814
NM_014363.5(SACS):c.7528G>A (p.Ala2510Thr) rs111920492
NM_014363.5(SACS):c.8339T>G (p.Phe2780Cys) rs111540787
NM_014363.5(SACS):c.8344_8345delGCinsAT (p.Ala2782Ile) rs386768924
NM_014363.5(SACS):c.8393C>A (p.Pro2798Gln) rs140551762
NM_014363.5(SACS):c.8793delA (p.Lys2931Asnfs) rs767871841
NM_014363.5(SACS):c.8844delT (p.Ile2949Phefs) rs281865117
NM_014363.5(SACS):c.909A>G (p.Ala303=) rs41315020
NM_014363.5(SACS):c.972C>A (p.Asp324Glu) rs546652936
NM_014846.3(WASHC5):c.2100G>A (p.Val700=) rs148936723
NM_014846.3(WASHC5):c.2771-7T>C rs142685897
NM_014846.3(WASHC5):c.732G>A (p.Pro244=) rs146320386
NM_015346.3(ZFYVE26):c.1184G>T (p.Gly395Val) rs35512910
NM_015346.3(ZFYVE26):c.1224G>T (p.Gly408=) rs17104689
NM_015346.3(ZFYVE26):c.1844C>T (p.Ser615Phe) rs117228915
NM_015346.3(ZFYVE26):c.2067C>T (p.Leu689=) rs141880939
NM_015346.3(ZFYVE26):c.2332+7delT rs145183291
NM_015346.3(ZFYVE26):c.2692A>T (p.Thr898Ser) rs17192170
NM_015346.3(ZFYVE26):c.2852C>T (p.Thr951Met) rs35471427
NM_015346.3(ZFYVE26):c.2887G>C (p.Val963Leu) rs116890187
NM_015346.3(ZFYVE26):c.3118T>A (p.Ser1040Thr) rs112787369
NM_015346.3(ZFYVE26):c.3210C>G (p.Pro1070=) rs7156492
NM_015346.3(ZFYVE26):c.3308C>T (p.Pro1103Leu) rs3742885
NM_015346.3(ZFYVE26):c.3365C>T (p.Ala1122Val) rs3742884
NM_015346.3(ZFYVE26):c.3722G>A (p.Arg1241Gln) rs140756827
NM_015346.3(ZFYVE26):c.3757C>T (p.Leu1253=) rs34296097
NM_015346.3(ZFYVE26):c.4066T>G (p.Cys1356Gly) rs149276487
NM_015346.3(ZFYVE26):c.4197C>T (p.Thr1399=) rs35018134
NM_015346.3(ZFYVE26):c.4293G>C (p.Gln1431His) rs373740172
NM_015346.3(ZFYVE26):c.4324G>A (p.Asp1442Asn) rs534497092
NM_015346.3(ZFYVE26):c.4502C>T (p.Thr1501Met) rs201034965
NM_015346.3(ZFYVE26):c.453C>T (p.Ser151=) rs75391113
NM_015346.3(ZFYVE26):c.4734C>T (p.Ile1578=) rs200243306
NM_015346.3(ZFYVE26):c.4854C>T (p.Leu1618=) rs151287975
NM_015346.3(ZFYVE26):c.5121A>C (p.Gly1707=) rs143981992
NM_015346.3(ZFYVE26):c.5485-1delG rs878855013
NM_015346.3(ZFYVE26):c.5784T>C (p.Tyr1928=) rs34852231
NM_015346.3(ZFYVE26):c.6135C>T (p.Ala2045=) rs146209388
NM_015346.3(ZFYVE26):c.6405G>A (p.Leu2135=) rs76327447
NM_015346.3(ZFYVE26):c.6819G>A (p.Arg2273=) rs144007962
NM_015346.3(ZFYVE26):c.6921C>T (p.Ser2307=) rs35917338
NM_015346.3(ZFYVE26):c.6987-3C>T rs76728509
NM_015346.3(ZFYVE26):c.7055C>T (p.Thr2352Ile) rs151166497
NM_015346.3(ZFYVE26):c.7232G>A (p.Arg2411His) rs34373049
NM_015346.3(ZFYVE26):c.7407T>C (p.Asp2469=) rs35106153
NM_015346.3(ZFYVE26):c.7417-5G>C rs201771769
NM_015346.3(ZFYVE26):c.7533C>T (p.Ser2511=) rs147494935
NM_015346.3(ZFYVE26):c.7586C>G (p.Pro2529Arg) rs143198225
NM_020435.3(GJC2):c.108C>T (p.Ile36=) rs75469429
NM_020435.3(GJC2):c.147C>T (p.Asp49=) rs139992251
NM_020435.3(GJC2):c.575C>G (p.Pro192Arg) rs375318012
NM_020435.3(GJC2):c.947C>T (p.Pro316Leu) rs760502262
NM_020944.2(GBA2):c.33C>T (p.Thr11=) rs34312177
NM_024306.4(FA2H):c.1113G>C (p.Thr371=) rs140017632
NM_024306.4(FA2H):c.289C>G (p.Pro97Ala) rs35874850
NM_024306.4(FA2H):c.338G>A (p.Arg113Gln) rs147632811
NM_024306.4(FA2H):c.443C>T (p.Pro148Leu) rs372350326
NM_024306.4(FA2H):c.570C>A (p.Thr190=) rs138892784
NM_024306.4(FA2H):c.691T>C (p.Tyr231His) rs878855081
NM_024306.4(FA2H):c.933T>C (p.Tyr311=) rs11554620
NM_183075.2(CYP2U1):c.1151G>T (p.Arg384Ile) rs142676629
NM_183075.2(CYP2U1):c.947A>T (p.Asp316Val) rs397514513
NM_183075.2(CYP2U1):c.992A>G (p.Asn331Ser) rs148983337
NM_206900.2(RTN2):c.1374C>T (p.Ala458=) rs148630935
NM_206900.2(RTN2):c.949G>A (p.Gly317Ser) rs143937661

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