ClinVar Miner

Variants with conflicting interpretations studied for Meckel-Gruber syndrome

Coded as:
Minimum review status of the submission for Meckel-Gruber syndrome: Y axis collection method of the submission for Meckel-Gruber 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
39 294 3 54 78 1 5 133

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
Meckel-Gruber syndrome pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 1 0 0 0 0
likely pathogenic 5 2 1 0 0 0
uncertain significance 2 0 0 66 33 0
likely benign 1 1 1 1 41 1
benign 0 0 0 7 0 0

Condition to condition summary #

Total conditions: 21
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 11 0 45 67 0 0 112
Joubert syndrome; Meckel-Gruber syndrome 0 10 0 8 21 0 1 30
Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis 0 6 0 6 13 0 0 19
not provided 0 70 1 5 7 0 2 15
Nephronophthisis 0 152 0 6 5 0 0 11
Cutis laxa, recessive 0 3 0 4 1 0 0 5
Joubert syndrome 0 314 0 1 1 0 3 5
Meckel syndrome type 8 0 1 0 2 0 0 0 2
Bardet-Biedl syndrome 13; Meckel syndrome type 1; Joubert syndrome 28 0 4 0 0 1 0 0 1
CC2D2A-Related Disorders 0 30 0 0 0 0 1 1
Iris coloboma; Nystagmus; Generalized hypotonia; Cerebellar vermis hypoplasia 0 0 0 1 0 0 0 1
Joubert syndrome 21 0 0 0 1 0 0 0 1
Joubert syndrome 5 0 2 0 1 0 0 0 1
Joubert syndrome 6 0 0 0 1 0 0 0 1
Joubert syndrome 9 0 0 0 0 0 0 1 1
Meckel syndrome type 1 0 0 1 1 0 0 0 1
Meckel syndrome type 3 0 0 1 0 0 0 0 1
Meckel syndrome type 6 0 0 0 0 0 0 1 1
Meckel syndrome, type 11 0 0 0 1 0 0 0 1
Retinitis pigmentosa in ciliopathies, modifier of 0 0 0 0 0 1 0 1
TMEM67-Related Disorders 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 133
Download table as spreadsheet
HGVS dbSNP
NM_001077416.2(TMEM231):c.823G>A (p.Val275Ile) rs397514753
NM_001080522.2(CC2D2A):c.*1T>A rs199945435
NM_001080522.2(CC2D2A):c.*21G>C rs1134634
NM_001080522.2(CC2D2A):c.-32G>A rs183968785
NM_001080522.2(CC2D2A):c.1041C>T (p.Asp347=) rs371086728
NM_001080522.2(CC2D2A):c.1127A>C (p.Glu376Ala) rs16892095
NM_001080522.2(CC2D2A):c.124-6C>T rs1861049
NM_001080522.2(CC2D2A):c.156C>T (p.Ser52=) rs1861050
NM_001080522.2(CC2D2A):c.1731G>A (p.Ser577=) rs376746356
NM_001080522.2(CC2D2A):c.1978G>C (p.Val660Leu) rs16892134
NM_001080522.2(CC2D2A):c.2804G>A (p.Arg935Gln) rs187003641
NM_001080522.2(CC2D2A):c.3046G>A (p.Glu1016Lys) rs373960465
NM_001080522.2(CC2D2A):c.3183-8T>C rs13121363
NM_001080522.2(CC2D2A):c.3201G>A (p.Ser1067=) rs73125627
NM_001080522.2(CC2D2A):c.3333T>C (p.Val1111=) rs753770061
NM_001080522.2(CC2D2A):c.355T>C (p.Leu119=) rs202150325
NM_001080522.2(CC2D2A):c.3872T>C (p.Ile1291Thr) rs370492044
NM_001080522.2(CC2D2A):c.4296T>C (p.Cys1432=) rs372671421
NM_001080522.2(CC2D2A):c.4438-9C>A rs117667651
NM_001080522.2(CC2D2A):c.4459C>T (p.Arg1487Cys) rs186486235
NM_001080522.2(CC2D2A):c.4667A>T (p.Asp1556Val) rs201502401
NM_001080522.2(CC2D2A):c.4675-14T>A rs766203266
NM_001080522.2(CC2D2A):c.501G>T (p.Lys167Asn) rs190694237
NM_001080522.2(CC2D2A):c.685_687delGAA (p.Glu229del) rs386833764
NM_001080522.2(CC2D2A):c.717+11T>C rs184351317
NM_001080522.2(CC2D2A):c.762A>G (p.Leu254=) rs116198081
NM_001080522.2(CC2D2A):c.777C>T (p.His259=) rs2286976
NM_001173990.2(TMEM216):c.-24C>T rs59493015
NM_001173990.2(TMEM216):c.358A>G (p.Met120Val) rs200289511
NM_001173990.2(TMEM216):c.420T>C (p.Ala140=) rs749351351
NM_001173991.2(TMEM216):c.*21A>G rs111371929
NM_001173991.2(TMEM216):c.-24C>G rs59493015
NM_001173991.2(TMEM216):c.-2G>T rs7107543
NM_001173991.2(TMEM216):c.264G>A (p.Pro88=) rs3741265
NM_012463.3(ATP6V0A2):c.-14C>T rs1139320
NM_012463.3(ATP6V0A2):c.-222C>G rs71458814
NM_015272.4(RPGRIP1L):c.1341G>A (p.Leu447=) rs61743997
NM_015272.4(RPGRIP1L):c.1960G>A (p.Glu654Lys) rs141979202
NM_015272.4(RPGRIP1L):c.2231G>A (p.Arg744Gln) rs2302677
NM_015272.4(RPGRIP1L):c.2240G>A (p.Arg747Gln) rs142349647
NM_015272.4(RPGRIP1L):c.2658G>A (p.Ser886=) rs775153934
NM_015272.4(RPGRIP1L):c.2682A>G (p.Ser894=) rs141608712
NM_015272.4(RPGRIP1L):c.2925A>G (p.Val975=) rs144313291
NM_015272.4(RPGRIP1L):c.2959-15T>C rs11863101
NM_015272.4(RPGRIP1L):c.3073G>A (p.Gly1025Ser) rs2111119
NM_015272.4(RPGRIP1L):c.3312C>T (p.Pro1104=) rs568801926
NM_015272.4(RPGRIP1L):c.3428C>G (p.Thr1143Ser) rs111775292
NM_015272.4(RPGRIP1L):c.3624C>T (p.Tyr1208=) rs138724933
NM_015272.4(RPGRIP1L):c.3790G>A (p.Asp1264Asn) rs3213758
NM_015272.4(RPGRIP1L):c.3936C>T (p.Asp1312=) rs4784320
NM_015272.4(RPGRIP1L):c.685G>A (p.Ala229Thr) rs61747071
NM_015681.4(B9D1):c.-110G>A rs117169107
NM_015681.4(B9D1):c.-70G>A rs2296978
NM_015681.4(B9D1):c.376T>A (p.Ser126Thr) rs201299216
NM_015681.4(B9D1):c.580T>C (p.Leu194=) rs7212549
NM_017777.3(MKS1):c.-18C>G rs116514023
NM_017777.3(MKS1):c.1014G>A (p.Leu338=) rs201998680
NM_017777.3(MKS1):c.1066C>T (p.Gln356Ter) rs786205508
NM_017777.3(MKS1):c.1388G>A (p.Arg463Gln) rs201619500
NM_017777.3(MKS1):c.1671G>C (p.Leu557=) rs11548967
NM_017777.3(MKS1):c.213C>G (p.Asp71Glu) rs142813109
NM_017777.3(MKS1):c.27C>T (p.Asp9=) rs369488349
NM_017777.3(MKS1):c.417G>A (p.Glu139=) rs386834048
NM_017777.3(MKS1):c.644+8G>T rs370117125
NM_017777.3(MKS1):c.80+14C>G rs761061379
NM_017777.3(MKS1):c.858+9A>G rs3826300
NM_024790.6(CSPP1):c.2244_2247delAAGA (p.Glu750Lysfs) rs587777145
NM_024809.4(TCTN2):c.*155G>A rs12811354
NM_024809.4(TCTN2):c.*45G>A rs142969969
NM_024809.4(TCTN2):c.*468C>T rs7398298
NM_024809.4(TCTN2):c.1117G>A (p.Gly373Arg) rs187433682
NM_024809.4(TCTN2):c.1128T>C (p.Pro376=) rs7966867
NM_024809.4(TCTN2):c.1393+7C>T rs7298440
NM_024809.4(TCTN2):c.225C>T (p.Asn75=) rs73416301
NM_024809.4(TCTN2):c.635A>G (p.Asn212Ser) rs139927033
NM_024809.4(TCTN2):c.654C>T (p.Leu218=) rs138897437
NM_024809.4(TCTN2):c.810C>T (p.Asp270=) rs144567556
NM_024809.4(TCTN2):c.83-4C>T rs73416299
NM_024809.4(TCTN2):c.873A>G (p.Ala291=) rs73418153
NM_024809.4(TCTN2):c.891+7G>A rs7313032
NM_025114.3(CEP290):c.-41C>T rs759820573
NM_025114.3(CEP290):c.1092T>G (p.Ile364Met) rs201988582
NM_025114.3(CEP290):c.1624-5T>C rs142742071
NM_025114.3(CEP290):c.1991A>G (p.Asp664Gly) rs79705698
NM_025114.3(CEP290):c.2055T>C (p.Ala685=) rs45465996
NM_025114.3(CEP290):c.2484-8_2484-4dupGTTTT rs745522483
NM_025114.3(CEP290):c.251-10A>T rs190383141
NM_025114.3(CEP290):c.2512A>G (p.Lys838Glu) rs11104738
NM_025114.3(CEP290):c.2616G>A (p.Ser872=) rs776360559
NM_025114.3(CEP290):c.2717T>G (p.Leu906Trp) rs7970228
NM_025114.3(CEP290):c.3465G>A (p.Leu1155=) rs150138016
NM_025114.3(CEP290):c.3654T>C (p.Leu1218=) rs201838492
NM_025114.3(CEP290):c.3710G>A (p.Arg1237His) rs7307793
NM_025114.3(CEP290):c.3790C>T (p.Arg1264Cys) rs139998038
NM_025114.3(CEP290):c.4087C>T (p.Arg1363Trp) rs181121175
NM_025114.3(CEP290):c.4119A>G (p.Lys1373=) rs117122459
NM_025114.3(CEP290):c.4151G>A (p.Arg1384His) rs143152287
NM_025114.3(CEP290):c.4237G>C (p.Asp1413His) rs183655276
NM_025114.3(CEP290):c.4806G>A (p.Thr1602=) rs201614215
NM_025114.3(CEP290):c.503G>A (p.Arg168His) rs200063017
NM_025114.3(CEP290):c.5199A>G (p.Gln1733=) rs79644671
NM_025114.3(CEP290):c.5237G>A (p.Arg1746Gln) rs61941020
NM_025114.3(CEP290):c.5322C>T (p.Leu1774=) rs117370446
NM_025114.3(CEP290):c.5506A>G (p.Ile1836Val) rs11104729
NM_025114.3(CEP290):c.5764A>C (p.Ile1922Leu) rs746949236
NM_025114.3(CEP290):c.6116A>G (p.Asp2039Gly) rs192259143
NM_025114.3(CEP290):c.7186G>T (p.Asp2396Tyr) rs189556433
NM_030578.3(B9D2):c.*18G>A rs1800468
NM_030578.3(B9D2):c.195C>T (p.Phe65=) rs34088631
NM_153240.4(NPHP3):c.105G>A (p.Lys35=) rs377060857
NM_153240.4(NPHP3):c.1525-5delT rs762115717
NM_153240.4(NPHP3):c.189G>C (p.Gly63=) rs750280281
NM_153240.4(NPHP3):c.1986G>A (p.Arg662=) rs77533254
NM_153240.4(NPHP3):c.2571-7T>C rs62292468
NM_153240.4(NPHP3):c.2610G>A (p.Pro870=) rs16839515
NM_153240.4(NPHP3):c.2769C>T (p.Phe923=) rs116174472
NM_153240.4(NPHP3):c.3550G>A (p.Ala1184Thr) rs34391943
NM_153240.4(NPHP3):c.3913C>T (p.Arg1305Cys) rs35485382
NM_153240.4(NPHP3):c.408G>A (p.Thr136=) rs141410951
NM_153240.4(NPHP3):c.450G>A (p.Ala150=) rs78527322
NM_153240.4(NPHP3):c.57G>C (p.Thr19=) rs192633696
NM_153240.4(NPHP3):c.670+13C>T rs202228115
NM_153240.4(NPHP3):c.864T>A (p.Thr288=) rs147932449
NM_153704.5(TMEM67):c.-33delG rs145334032
NM_153704.5(TMEM67):c.1046T>C (p.Leu349Ser) rs386834180
NM_153704.5(TMEM67):c.1066-3C>T rs3097427
NM_153704.5(TMEM67):c.120T>C (p.Ser40=) rs767999682
NM_153704.5(TMEM67):c.1810A>G (p.Ile604Val) rs3134031
NM_153704.5(TMEM67):c.186T>C (p.Cys62=) rs115660279
NM_153704.5(TMEM67):c.2448G>A (p.Leu816=) rs886038738
NM_153704.5(TMEM67):c.2892A>C (p.Thr964=) rs16916221
NM_153704.5(TMEM67):c.514C>T (p.Arg172Ter) rs765468645
NM_153704.5(TMEM67):c.869+9A>G rs372597584

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