ClinVar Miner

Variants from ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel with conflicting interpretations

Location: United States  Primary collection method: curation
Minimum review status of the submission from ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel: Collection method of the submission from ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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 per condition Variants with at least 2 submissions on the same condition 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 conflict
143 152 0 76 80 0 52 190

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 submitters
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 19 26 1 0
likely pathogenic 5 0 17 0 0
uncertain significance 1 5 0 9 5
likely benign 0 0 26 0 13
benign 1 1 40 39 0

Submitter to submitter summary #

Total submitters: 39
Download table as spreadsheet
Submitter Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition 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 conflict
Labcorp Genetics (formerly Invitae), Labcorp 0 86 0 41 28 0 8 77
RettBASE 0 10 0 1 12 0 25 38
Centre for Population Genomics, CPG 0 125 0 14 10 0 7 31
Genetic Services Laboratory, University of Chicago 0 20 0 7 6 0 1 14
Baylor Genetics 0 11 0 2 11 0 0 13
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 4 0 0 3 0 1 4
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 10 0 2 2 0 0 4
Illumina Laboratory Services, Illumina 0 6 0 0 3 0 0 3
New York Genome Center 0 0 0 0 3 0 0 3
Revvity Omics, Revvity 0 1 0 0 2 0 1 3
3billion 0 12 0 1 0 0 1 2
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 5 0 0 1 0 1 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 2 0 0 0 2
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 2 0 1 1 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 11 0 0 0 0 2 2
Mendelics 0 6 0 0 1 0 1 2
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 3 0 1 1 0 0 2
Tgen's Center for Rare Childhood Disorders, Translational Genomics Research Institute (tgen) 0 0 0 1 1 0 0 2
Beijing Children’s hospital, National Center for Children’s Health 0 0 0 0 0 0 1 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 0 0 1 0 0 0 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 0 0 1 0 0 1
Center for Human Genetics, University of Leuven 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 0 1 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 1 0 0 0 1
Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine 0 0 0 0 0 0 1 1
Fulgent Genetics, Fulgent Genetics 0 1 0 0 1 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 1 0 0 0 1
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 2 0 1 0 0 0 1
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 0 0 0 0 0 1 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 3 0 0 0 0 1 1
Laboratory Cellgenetics, GMDL Cellgenetics 0 0 0 0 0 0 1 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 2 0 1 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 1 0 0 0 1
Neurogenetics Laboratory - MEYER, AOU Meyer 0 1 0 0 0 0 1 1
OMIM 0 11 0 0 0 0 1 1
Pediatric Genetics Clinic, Sheba Medical Center 0 0 0 1 0 0 0 1
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 0 0 0 0 0 1 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 8 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 190
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_130839.5(UBE3A):c.477A>T (p.Ala159=) rs28528079 0.02826
NM_130839.5(UBE3A):c.373T>C (p.Leu125=) rs61734190 0.02311
NM_130839.5(UBE3A):c.2124+9T>C rs79328837 0.00454
NM_001110792.2(MECP2):c.1225G>A (p.Glu409Lys) rs56268439 0.00308
NM_001110792.2(MECP2):c.638C>T (p.Ala213Val) rs61748381 0.00150
NM_005249.5(FOXG1):c.447C>T (p.Ala149=) rs112803404 0.00126
NM_130839.5(UBE3A):c.618A>T (p.Ala206=) rs143484751 0.00121
NM_130839.5(UBE3A):c.1269C>T (p.Asp423=) rs149506027 0.00117
NM_001110792.2(MECP2):c.1162C>T (p.Pro388Ser) rs61752387 0.00108
NM_130839.5(UBE3A):c.1767C>T (p.Tyr589=) rs139082033 0.00094
NM_001083962.2(TCF4):c.944C>T (p.Ala315Val) rs147445499 0.00064
NM_130839.5(UBE3A):c.1404A>G (p.Thr468=) rs150331504 0.00054
NM_005249.5(FOXG1):c.503G>C (p.Gly168Ala) rs148157138 0.00048
NM_001083962.2(TCF4):c.341G>A (p.Arg114Lys) rs139876825 0.00043
NM_001110792.2(MECP2):c.*14G>A rs199963992 0.00037
NM_001083962.2(TCF4):c.504A>G (p.Val168=) rs370160994 0.00036
NM_001083962.2(TCF4):c.790-9T>C rs373434281 0.00029
NM_005249.5(FOXG1):c.201G>T (p.Pro67=) rs587780944 0.00029
NM_005249.5(FOXG1):c.209A>C (p.Gln70Pro) rs587783633 0.00026
NM_005249.5(FOXG1):c.245C>A (p.Pro82Gln) rs796052453 0.00026
NM_001110792.2(MECP2):c.1174G>A (p.Val392Met) rs267608572 0.00023
NM_005249.5(FOXG1):c.1323C>T (p.Ser441=) rs144434028 0.00023
NM_005249.5(FOXG1):c.456G>T (p.Gly152=) rs587783637 0.00020
NM_005249.5(FOXG1):c.218A>C (p.Gln73Pro) rs760663911 0.00018
NM_001083962.2(TCF4):c.1487-5G>A rs749176054 0.00015
NM_005249.5(FOXG1):c.594C>G (p.Pro198=) rs141088742 0.00010
NM_130839.5(UBE3A):c.1338T>C (p.Phe446=) rs371154816 0.00009
NM_130839.5(UBE3A):c.815A>G (p.Asn272Ser) rs139928148 0.00009
NM_130839.5(UBE3A):c.1064G>C (p.Ser355Thr) rs141984760 0.00007
NM_130839.5(UBE3A):c.2096A>C (p.Lys699Thr) rs202161423 0.00007
NM_001110792.2(MECP2):c.1066C>T (p.Arg356Trp) rs61752361 0.00006
NM_001110792.2(MECP2):c.1198C>T (p.Pro400Ser) rs61753000 0.00006
NM_001110792.2(MECP2):c.1097G>T (p.Arg366Leu) rs61748387 0.00005
NM_130839.5(UBE3A):c.1179T>C (p.Asp393=) rs143000400 0.00005
NM_001083962.2(TCF4):c.1283G>T (p.Gly428Val) rs186508321 0.00004
NM_001083962.2(TCF4):c.466C>A (p.Pro156Thr) rs200889338 0.00004
NM_001110792.2(MECP2):c.1250C>T (p.Pro417Leu) rs61753016 0.00004
NM_001110792.2(MECP2):c.915C>G (p.Ile305Met) rs587783140 0.00004
NM_001110792.2(MECP2):c.968C>T (p.Thr323Met) rs61751445 0.00004
NM_001379110.1(SLC9A6):c.2021C>T (p.Thr674Met) rs886044780 0.00004
NM_005249.5(FOXG1):c.1045T>G (p.Ser349Ala) rs796052472 0.00004
NM_005249.5(FOXG1):c.1273T>C (p.Ser425Pro) rs780242359 0.00004
NM_130839.5(UBE3A):c.1169A>G (p.Asn390Ser) rs147446244 0.00004
NM_001083962.2(TCF4):c.1113G>A (p.Ser371=) rs148308964 0.00003
NM_001083962.2(TCF4):c.1486+4G>C rs201274415 0.00003
NM_001083962.2(TCF4):c.1990G>A (p.Ala664Thr) rs755332116 0.00003
NM_001083962.2(TCF4):c.903C>T (p.Asn301=) rs781392344 0.00003
NM_001110792.2(MECP2):c.1477G>A (p.Val493Met) rs193922678 0.00003
NM_001110792.2(MECP2):c.260C>T (p.Pro87Leu) rs267608440 0.00003
NM_130839.5(UBE3A):c.582A>G (p.Ala194=) rs764101035 0.00003
NM_001083962.2(TCF4):c.1354G>A (p.Gly452Arg) rs138570124 0.00002
NM_001083962.2(TCF4):c.245G>A (p.Ser82Asn) rs773462232 0.00002
NM_001110792.2(MECP2):c.1187C>T (p.Pro396Leu) rs193922676 0.00002
NM_001110792.2(MECP2):c.1199C>T (p.Pro400Leu) rs61753006 0.00002
NM_001110792.2(MECP2):c.414-6C>G rs782482746 0.00002
NM_001110792.2(MECP2):c.490C>G (p.Pro164Ala) rs179363900 0.00002
NM_001110792.2(MECP2):c.553C>G (p.Pro185Ala) rs61748427 0.00002
NM_001110792.2(MECP2):c.727G>A (p.Gly243Arg) rs587783139 0.00002
NM_001323289.2(CDKL5):c.194G>A (p.Arg65Gln) rs267608436 0.00002
NM_001379110.1(SLC9A6):c.-56-25C>G rs782396686 0.00002
NM_001379110.1(SLC9A6):c.1269G>C (p.Lys423Asn) rs781918578 0.00002
NM_001083962.2(TCF4):c.1349T>C (p.Met450Thr) rs774283982 0.00001
NM_001083962.2(TCF4):c.1951C>G (p.Pro651Ala) rs549600113 0.00001
NM_001083962.2(TCF4):c.584A>G (p.Asn195Ser) rs148573556 0.00001
NM_001083962.2(TCF4):c.706C>G (p.Pro236Ala) rs139859596 0.00001
NM_001083962.2(TCF4):c.937G>A (p.Gly313Arg) rs767178395 0.00001
NM_001110792.2(MECP2):c.1018C>G (p.Leu340Val) rs267608556 0.00001
NM_001110792.2(MECP2):c.1286A>T (p.Lys429Met) rs61753968 0.00001
NM_001110792.2(MECP2):c.1466G>C (p.Ser489Thr) rs267608328 0.00001
NM_001110792.2(MECP2):c.289C>T (p.Arg97Cys) rs1064797047 0.00001
NM_001110792.2(MECP2):c.554C>G (p.Pro185Arg) rs267608492 0.00001
NM_001110792.2(MECP2):c.55G>A (p.Glu19Lys) rs782789719 0.00001
NM_001110792.2(MECP2):c.673C>G (p.Leu225Val) rs782473355 0.00001
NM_001110792.2(MECP2):c.895G>C (p.Ala299Pro) rs61750257 0.00001
NM_001323289.2(CDKL5):c.1196A>C (p.Asn399Thr) rs267608611 0.00001
NM_001323289.2(CDKL5):c.2684C>T (p.Pro895Leu) rs587783157 0.00001
NM_001379110.1(SLC9A6):c.1380C>T (p.Ser460=) rs782177396 0.00001
NM_001379110.1(SLC9A6):c.2001G>A (p.Pro667=) rs782708610 0.00001
NM_001379110.1(SLC9A6):c.452A>T (p.His151Leu) rs796053275 0.00001
NM_005249.5(FOXG1):c.1058A>G (p.Asn353Ser) rs749879411 0.00001
NM_005249.5(FOXG1):c.131A>C (p.His44Pro) rs1555321183 0.00001
NM_005249.5(FOXG1):c.256C>A (p.Gln86Lys) rs398124202 0.00001
NM_005249.5(FOXG1):c.263G>A (p.Arg88Gln) rs1046668279 0.00001
NM_005249.5(FOXG1):c.275C>T (p.Ala92Val) rs1057520147 0.00001
NM_005249.5(FOXG1):c.344C>T (p.Ala115Val) rs796052454 0.00001
NM_005249.5(FOXG1):c.382G>T (p.Gly128Cys) rs1029176730 0.00001
NM_130839.5(UBE3A):c.176G>A (p.Arg59His) rs587784511 0.00001
NM_130839.5(UBE3A):c.1881T>C (p.Asp627=) rs587784522 0.00001
NM_130839.5(UBE3A):c.2415T>C (p.Phe805=) rs587780991 0.00001
NM_001083962.2(TCF4):c.1739G>A (p.Arg580Gln) rs121909121
NM_001083962.2(TCF4):c.1741G>T (p.Val581Phe) rs587784460
NM_001083962.2(TCF4):c.1744C>T (p.Arg582Cys) rs2047109965
NM_001083962.2(TCF4):c.1817C>T (p.Thr606Ile) rs2144403104
NM_001083962.2(TCF4):c.1965dup (p.Gly656fs) rs797046035
NM_001083962.2(TCF4):c.305G>A (p.Ser102Asn) rs796053413
NM_001083962.2(TCF4):c.413C>G (p.Thr138Ser) rs796053416
NM_001083962.2(TCF4):c.759C>G (p.Ser253Arg) rs1555796785
NM_001083962.2(TCF4):c.8A>G (p.His3Arg) rs2097656766
NM_001083962.2(TCF4):c.990G>A (p.Ser330=) rs587784469
NM_001110792.2(MECP2):c.1001C>T (p.Pro334Leu) rs61751450
NM_001110792.2(MECP2):c.1097G>A (p.Arg366His) rs61748387
NM_001110792.2(MECP2):c.1134CCA[1] (p.His383_His384del) rs61752381
NM_001110792.2(MECP2):c.1165_1234del (p.Lys389fs) rs1557135353
NM_001110792.2(MECP2):c.1168G>T (p.Ala390Ser) rs587783106
NM_001110792.2(MECP2):c.1169C>G (p.Ala390Gly) rs201314910
NM_001110792.2(MECP2):c.1174_1199del (p.Val392fs) rs267608382
NM_001110792.2(MECP2):c.1191_1202del (p.Leu398_Pro401del) rs782174572
NM_001110792.2(MECP2):c.1490_1493del (p.Val497fs) rs267608640
NM_001110792.2(MECP2):c.1497A>G (p.Ter499Trp) rs267608642
NM_001110792.2(MECP2):c.189C>G (p.His63Gln) rs267608432
NM_001110792.2(MECP2):c.1A>T (p.Met1Leu) rs587783132
NM_001110792.2(MECP2):c.334C>G (p.Leu112Val) rs28935168
NM_001110792.2(MECP2):c.337C>T (p.Pro113Ser) rs61754452
NM_001110792.2(MECP2):c.338C>G (p.Pro113Arg) rs61754453
NM_001110792.2(MECP2):c.33AGG[7] (p.Gly15_Gly16dup) rs587783744
NM_001110792.2(MECP2):c.400G>A (p.Val134Met) rs267608455
NM_001110792.2(MECP2):c.408G>C (p.Leu136Phe) rs61755763
NM_001110792.2(MECP2):c.408G>T (p.Leu136Phe) rs61755763
NM_001110792.2(MECP2):c.414-3C>G rs267608465
NM_001110792.2(MECP2):c.416C>T (p.Pro139Leu) rs267608387
NM_001110792.2(MECP2):c.428C>A (p.Ala143Asp) rs267608470
NM_001110792.2(MECP2):c.434G>A (p.Arg145His) rs61748389
NM_001110792.2(MECP2):c.434G>T (p.Arg145Leu) rs61748389
NM_001110792.2(MECP2):c.437C>T (p.Ser146Phe) rs61748390
NM_001110792.2(MECP2):c.439A>G (p.Lys147Glu) rs61748391
NM_001110792.2(MECP2):c.488A>G (p.Asp163Gly) rs61748403
NM_001110792.2(MECP2):c.503A>G (p.Asp168Gly) rs61748407
NM_001110792.2(MECP2):c.505T>A (p.Phe169Ile) rs61748410
NM_001110792.2(MECP2):c.507C>G (p.Phe169Leu) rs267608484
NM_001110792.2(MECP2):c.508A>G (p.Thr170Ala) rs61748411
NM_001110792.2(MECP2):c.535C>T (p.Arg179Trp) rs61748420
NM_001110792.2(MECP2):c.553C>A (p.Pro185Thr) rs61748427
NM_001110792.2(MECP2):c.62+1G>A rs786205048
NM_001110792.2(MECP2):c.6CGC[4] (p.Ala7_Ala8del) rs398123566
NM_001110792.2(MECP2):c.6CGC[8] (p.Ala7_Ala8dup) rs398123566
NM_001110792.2(MECP2):c.6CGC[9] (p.Ala6_Ala8dup) rs398123566
NM_001110792.2(MECP2):c.872C>T (p.Ala291Val) rs61750249
NM_001110792.2(MECP2):c.907_1080del (p.Ile305_Ser362del) rs1557136013
NM_001110792.2(MECP2):c.916C>T (p.Arg306Ter) rs61751362
NM_001110792.2(MECP2):c.937C>G (p.Leu313Val) rs1557136251
NM_001110792.2(MECP2):c.941C>T (p.Pro314Leu) rs61749723
NM_001110792.2(MECP2):c.946A>G (p.Lys316Glu) rs61751440
NM_001110792.2(MECP2):c.947A>G (p.Lys316Arg) rs267608550
NM_001110792.2(MECP2):c.961C>T (p.Arg321Trp) rs61751444
NM_001323289.2(CDKL5):c.146-1G>A rs587783399
NM_001323289.2(CDKL5):c.1612A>G (p.Thr538Ala)
NM_001323289.2(CDKL5):c.2152G>A (p.Val718Met) rs267608653
NM_001323289.2(CDKL5):c.220G>T (p.Glu74Ter) rs587783073
NM_001323289.2(CDKL5):c.351T>A (p.Tyr117Ter) rs587783077
NM_001323289.2(CDKL5):c.372_385del (p.His124fs) rs2518849265
NM_001323289.2(CDKL5):c.545T>C (p.Leu182Pro) rs2147145603
NM_001323289.2(CDKL5):c.578A>T (p.Asp193Val) rs267608500
NM_001323289.2(CDKL5):c.656A>C (p.Gln219Pro) rs786204963
NM_001379110.1(SLC9A6):c.370-9_370-5del rs796053290
NM_001379110.1(SLC9A6):c.81G>A (p.Leu27=) rs2089324822
NM_005249.5(FOXG1):c.141CCA[4] (p.His55_His57del) rs587783630
NM_005249.5(FOXG1):c.194CGC[6] (p.Pro69dup) rs761703699
NM_005249.5(FOXG1):c.209AGC[5] (p.Gln73dup) rs398124201
NM_005249.5(FOXG1):c.209_229del (p.Gln70_Pro76del) rs1466028633
NM_005249.5(FOXG1):c.209_232del (p.Gln70_Pro77del) rs794726920
NM_005249.5(FOXG1):c.209_235del (p.Gln70_Pro78del) rs587783634
NM_005249.5(FOXG1):c.209_235dup (p.Gln70_Pro78dup) rs587783634
NM_005249.5(FOXG1):c.219GCC[7] (p.Pro80dup) rs786200975
NM_005249.5(FOXG1):c.219GCC[8] (p.Pro79_Pro80dup) rs786200975
NM_005249.5(FOXG1):c.227C>T (p.Pro76Leu) rs1381438340
NM_005249.5(FOXG1):c.237_239del (p.Pro80del) rs796052474
NM_005249.5(FOXG1):c.313_314insAGCCGC (p.Leu104_Pro105insGlnPro) rs1004546223
NM_005249.5(FOXG1):c.460GAG[1] (p.Glu155del) rs1175471807
NM_005249.5(FOXG1):c.471G>T (p.Lys157Asn) rs398124205
NM_005249.5(FOXG1):c.475G>A (p.Ala159Thr) rs1436573424
NM_005249.5(FOXG1):c.565C>G (p.Leu189Val) rs1555321308
NM_005249.5(FOXG1):c.620T>C (p.Ile207Thr) rs1881803464
NM_005249.5(FOXG1):c.670G>A (p.Gly224Ser) rs727503935
NM_005249.5(FOXG1):c.672C>G (p.Gly224=) rs587783639
NM_005249.5(FOXG1):c.681C>G (p.Asn227Lys) rs786205012
NM_005249.5(FOXG1):c.699G>T (p.Leu233=) rs2138661396
NM_005249.5(FOXG1):c.701C>T (p.Ser234Phe) rs1555321334
NM_005249.5(FOXG1):c.706A>G (p.Asn236Asp) rs2502226349
NM_005249.5(FOXG1):c.748G>A (p.Gly250Ser) rs2138661461
NM_005249.5(FOXG1):c.799G>A (p.Gly267Ser) rs587783643
NM_005249.5(FOXG1):c.953A>T (p.His318Leu) rs2138661790
NM_005249.5(FOXG1):c.95A>G (p.Asn32Ser) rs1429160286
NM_005249.5(FOXG1):c.977G>A (p.Ser326Asn) rs748001255
NM_130839.5(UBE3A):c.1007T>C (p.Met336Thr) rs863225071
NM_130839.5(UBE3A):c.1609-8A>G rs2077891986
NM_130839.5(UBE3A):c.1802CTT[1] (p.Ser602del) rs587781234
NM_130839.5(UBE3A):c.1865A>G (p.Asn622Ser) rs587784521
NM_130839.5(UBE3A):c.2444G>A (p.Gly815Glu) rs1595375255
NM_130839.5(UBE3A):c.2567_2570del (p.Lys856fs) rs587784527
NM_130839.5(UBE3A):c.377C>A (p.Thr126Lys) rs587781241

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