ClinVar Miner

Variants with conflicting interpretations studied for Spastic Paraplegia, Recessive

Coded as:
Minimum review status of the submission for Spastic Paraplegia, Recessive: Y axis collection method of the submission for Spastic Paraplegia, Recessive:
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
275 112 0 65 105 0 1 167

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, Recessive likely pathogenic uncertain significance likely benign benign
pathogenic 1 1 0 0
uncertain significance 0 0 74 52
likely benign 0 3 0 61
benign 0 0 3 0

Condition to condition summary #

Total conditions: 13
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 18 0 51 72 0 0 122
Spastic paraplegia 30, autosomal recessive; Hereditary sensory and autonomic neuropathy type IIC; Mental retardation, autosomal dominant 9 0 4 0 14 20 0 0 34
Spastic paraplegia 0 8 0 16 14 0 0 30
not provided 0 19 0 11 19 0 0 30
Spastic paraplegia 11, autosomal recessive 0 8 0 6 16 0 0 22
History of neurodevelopmental disorder 0 2 0 12 9 0 0 21
Spastic paraplegia 48, autosomal recessive 0 5 0 5 10 0 0 15
Spastic paraplegia 7 0 2 0 4 8 0 0 12
Spastic paraplegia 39 0 0 0 3 5 0 0 8
Mast syndrome 0 1 0 0 1 0 0 1
Optic nerve hypoplasia 0 0 0 0 0 0 1 1
Spastic paraplegia 15 0 1 0 1 0 0 0 1
Spastic paraplegia 30, autosomal recessive 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 167
Download table as spreadsheet
HGVS dbSNP
NM_003119.2(SPG7):c.1529C>T rs61755320
NM_003119.3(SPG7):c.1032C>T (p.Gly344=) rs116319889
NM_003119.3(SPG7):c.1324+10C>T rs202070075
NM_003119.3(SPG7):c.1359G>A (p.Ala453=) rs115448299
NM_003119.3(SPG7):c.1457G>A (p.Arg486Gln) rs111475461
NM_003119.3(SPG7):c.1507A>G (p.Thr503Ala) rs2292954
NM_003119.3(SPG7):c.1663+13C>T rs80324518
NM_003119.3(SPG7):c.1770C>T (p.Ala590=) rs60488729
NM_003119.3(SPG7):c.1780-16_1780-14del rs863224213
NM_003119.3(SPG7):c.1936+12C>T rs112379588
NM_003119.3(SPG7):c.199C>T (p.Leu67=) rs148315471
NM_003119.3(SPG7):c.2037G>A (p.Ala679=) rs79756036
NM_003119.3(SPG7):c.2063G>A (p.Arg688Gln) rs12960
NM_003119.3(SPG7):c.2188A>G (p.Asn730Asp) rs35749032
NM_003119.3(SPG7):c.2280G>A (p.Pro760=) rs11559075
NM_003119.3(SPG7):c.2295C>T (p.Asp765=) rs61747712
NM_003119.3(SPG7):c.656T>C (p.Ile219Thr) rs114255772
NM_003119.3(SPG7):c.9G>T (p.Val3=) rs553241838
NM_004321.7(KIF1A):c.-13G>A rs140017120
NM_004321.7(KIF1A):c.-55C>T rs886055838
NM_004321.7(KIF1A):c.1194G>A (p.Leu398=) rs201242759
NM_004321.7(KIF1A):c.1476A>G (p.Pro492=) rs35663732
NM_004321.7(KIF1A):c.183+15C>T rs73102676
NM_004321.7(KIF1A):c.183+7C>T rs74469870
NM_004321.7(KIF1A):c.184-10C>T rs7594776
NM_004321.7(KIF1A):c.204G>T (p.Ala68=) rs141052770
NM_004321.7(KIF1A):c.2089+12C>T rs192836330
NM_004321.7(KIF1A):c.2208C>T (p.Ala736=) rs35945835
NM_004321.7(KIF1A):c.234C>T (p.Gly78=) rs61744930
NM_004321.7(KIF1A):c.2358C>T (p.Ala786=) rs62637652
NM_004321.7(KIF1A):c.2448C>T (p.Tyr816=) rs199996308
NM_004321.7(KIF1A):c.2555+4G>A rs572013653
NM_004321.7(KIF1A):c.2595C>G (p.Pro865=) rs140783695
NM_004321.7(KIF1A):c.2676C>T (p.Ala892=) rs116297894
NM_004321.7(KIF1A):c.2769C>T (p.Ser923=) rs73102625
NM_004321.7(KIF1A):c.2782G>A (p.Val928Met) rs183359489
NM_004321.7(KIF1A):c.2943C>T (p.Ala981=) rs368682964
NM_004321.7(KIF1A):c.2944G>A (p.Ala982Thr) rs201793635
NM_004321.7(KIF1A):c.2979C>T (p.His993=) rs35664935
NM_004321.7(KIF1A):c.3365C>T (p.Thr1122Met) rs374873057
NM_004321.7(KIF1A):c.3369G>A (p.Arg1123=) rs371024769
NM_004321.7(KIF1A):c.3549T>C (p.His1183=) rs184931664
NM_004321.7(KIF1A):c.3585C>T (p.Arg1195=) rs144520412
NM_004321.7(KIF1A):c.3598+11T>C rs56847463
NM_004321.7(KIF1A):c.3840G>A (p.Pro1280=) rs2241683
NM_004321.7(KIF1A):c.393C>T (p.Asn131=) rs35139906
NM_004321.7(KIF1A):c.4005G>A (p.Ala1335=) rs370868080
NM_004321.7(KIF1A):c.4016-8C>T rs1529663
NM_004321.7(KIF1A):c.4162-10C>T rs750461872
NM_004321.7(KIF1A):c.423C>T (p.Ser141=) rs565992344
NM_004321.7(KIF1A):c.430-14G>A rs201456681
NM_004321.7(KIF1A):c.4301C>T (p.Ala1434Val) rs141441058
NM_004321.7(KIF1A):c.4441-5C>T rs117815481
NM_004321.7(KIF1A):c.4475C>T (p.Pro1492Leu) rs200902828
NM_004321.7(KIF1A):c.4509C>A (p.Thr1503=) rs76974316
NM_004321.7(KIF1A):c.4548C>T (p.Tyr1516=) rs202049905
NM_004321.7(KIF1A):c.4586G>A (p.Arg1529Gln) rs191428830
NM_004321.7(KIF1A):c.4722G>A (p.Pro1574=) rs148176695
NM_004321.7(KIF1A):c.4740G>A (p.Gly1580=) rs143815273
NM_004321.7(KIF1A):c.4761G>A (p.Pro1587=) rs527977882
NM_004321.7(KIF1A):c.714G>A (p.Thr238=) rs201970806
NM_004321.7(KIF1A):c.849C>T (p.Ser283=) rs187442951
NM_004321.7(KIF1A):c.882+8G>A rs376552408
NM_004321.7(KIF1A):c.991T>C (p.Leu331=) rs1063353
NM_004820.4(CYP7B1):c.204G>A (p.Arg68=) rs377119798
NM_004820.4(CYP7B1):c.260-5dupT rs8192896
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_006702.4(PNPLA6):c.1090G>C (p.Ala364Pro) rs17854645
NM_006702.4(PNPLA6):c.1136-6C>T rs574930
NM_006702.4(PNPLA6):c.1563C>T (p.Asp521=) rs761103593
NM_006702.4(PNPLA6):c.1954-15C>T rs7250363
NM_006702.4(PNPLA6):c.1977G>A (p.Pro659=) rs8107538
NM_006702.4(PNPLA6):c.198+13C>T rs200676307
NM_006702.4(PNPLA6):c.3381C>T (p.Ser1127=) rs138837774
NM_006702.4(PNPLA6):c.3435T>C (p.Val1145=) rs35770729
NM_006702.4(PNPLA6):c.3489G>A (p.Gln1163=) rs112133109
NM_006702.4(PNPLA6):c.3798C>T (p.Asp1266=) rs149871062
NM_006702.4(PNPLA6):c.3964G>A (p.Gly1322Ser) rs145178162
NM_006702.4(PNPLA6):c.56T>C (p.Val19Ala) rs188353745
NM_006702.4(PNPLA6):c.648C>T (p.Asn216=) rs591040
NM_006702.4(PNPLA6):c.64G>C (p.Val22Leu) rs112732576
NM_006702.4(PNPLA6):c.66G>A (p.Val22=) rs35732838
NM_014855.2(AP5Z1):c.1369C>T (p.Leu457=) rs111358719
NM_014855.2(AP5Z1):c.1529G>A (p.Arg510Gln) rs77890266
NM_014855.2(AP5Z1):c.1554C>T (p.Phe518=) rs77560694
NM_014855.2(AP5Z1):c.1557A>G (p.Gln519=) rs201687417
NM_014855.2(AP5Z1):c.1708-5C>T rs184752711
NM_014855.2(AP5Z1):c.1794C>T (p.Ala598=) rs374673921
NM_014855.2(AP5Z1):c.1939-9C>T rs73305392
NM_014855.2(AP5Z1):c.2400G>A (p.Arg800=) rs368571200
NM_014855.2(AP5Z1):c.366+5C>T rs143800095
NM_014855.2(AP5Z1):c.512-7A>G rs73305371
NM_014855.2(AP5Z1):c.588C>T (p.Ser196=) rs146665638
NM_014855.2(AP5Z1):c.780C>A (p.Thr260=) rs377507553
NM_014855.3(AP5Z1):c.1197G>A (p.Glu399=) rs117666541
NM_014855.3(AP5Z1):c.379G>A (p.Glu127Lys) rs115454162
NM_014855.3(AP5Z1):c.481G>A (p.Val161Met) rs191971593
NM_014855.3(AP5Z1):c.759C>T (p.Ser253=) rs17135121
NM_014855.3(AP5Z1):c.881G>A (p.Arg294Gln) rs200957609
NM_015346.3(ZFYVE26):c.-70A>T rs17192296
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.2332+7delT rs145183291
NM_015346.3(ZFYVE26):c.2401+11T>A rs191741115
NM_015346.3(ZFYVE26):c.2427C>T (p.Gly809=) rs144063215
NM_015346.3(ZFYVE26):c.2559G>A (p.Leu853=) rs7143196
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.30T>G (p.Ala10=) rs141905183
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.3757C>T (p.Leu1253=) rs34296097
NM_015346.3(ZFYVE26):c.4035G>T (p.Val1345=) rs374530573
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.4370G>A (p.Cys1457Tyr) rs2235967
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.5121A>C (p.Gly1707=) rs143981992
NM_015346.3(ZFYVE26):c.5484+13G>A rs140117984
NM_015346.3(ZFYVE26):c.5672A>G (p.Asn1891Ser) rs3742883
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.677G>A (p.Arg226His) rs147919567
NM_015346.3(ZFYVE26):c.6819G>A (p.Arg2273=) rs144007962
NM_015346.3(ZFYVE26):c.6849A>G (p.Thr2283=) rs74935043
NM_015346.3(ZFYVE26):c.6921C>T (p.Ser2307=) rs35917338
NM_015346.3(ZFYVE26):c.6987-3C>T rs76728509
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_016630.6(SPG21):c.846G>A (p.Ala282=) rs146986015
NM_020533.2(MCOLN1):c.1360-13G>A rs2305888
NM_025137.3(SPG11):c.1347C>T (p.Thr449=) rs3759874
NM_025137.3(SPG11):c.1348A>G (p.Ile450Val) rs3759873
NM_025137.3(SPG11):c.1388T>C (p.Phe463Ser) rs3759871
NM_025137.3(SPG11):c.1698T>G (p.Asp566Glu) rs79708848
NM_025137.3(SPG11):c.16G>A (p.Gly6Arg) rs200573434
NM_025137.3(SPG11):c.1801C>A (p.Pro601Thr) rs775799559
NM_025137.3(SPG11):c.2169C>T (p.Gly723=) rs371338650
NM_025137.3(SPG11):c.257+13G>A rs201936649
NM_025137.3(SPG11):c.3146-6T>G rs777849932
NM_025137.3(SPG11):c.3420G>A (p.Leu1140=) rs36014111
NM_025137.3(SPG11):c.4001+9G>T rs141177255
NM_025137.3(SPG11):c.4687A>G (p.Arg1563Gly) rs75430389
NM_025137.3(SPG11):c.4744-6T>C rs147550048
NM_025137.3(SPG11):c.4810T>C (p.Phe1604Leu) rs116807842
NM_025137.3(SPG11):c.60G>C (p.Ala20=) rs544136842
NM_025137.3(SPG11):c.6258G>T (p.Leu2086=) rs150761878
NM_025137.3(SPG11):c.6330G>A (p.Gly2110=) rs35932349
NM_025137.3(SPG11):c.6477+13delC rs574960359
NM_025137.3(SPG11):c.64A>G (p.Met22Val) rs34255962
NM_025137.3(SPG11):c.6632G>A (p.Arg2211His) rs144165094
NM_025137.3(SPG11):c.6755-17_6755-15delCTT rs143026515
NM_025137.3(SPG11):c.6877C>T (p.Arg2293Trp) rs151317653
NM_025137.3(SPG11):c.7146C>T (p.Ser2382=) rs747227352
NM_025137.3(SPG11):c.833A>G (p.Asn278Ser) rs75309308
NM_025137.3(SPG11):c.993C>T (p.Ser331=) rs76823973

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