ClinVar Miner

Variants with conflicting interpretations studied for Rett syndrome

Coded as:
Minimum review status of the submission for Rett syndrome: Y axis collection method of the submission for Rett 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
378 107 2 29 10 1 22 55

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
Rett syndrome pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 2 14 7 1 1 1
likely pathogenic 16 0 4 0 0 1
uncertain significance 14 5 0 6 4 0
likely benign 1 0 1 0 6 0
benign 1 0 2 6 0 0

Condition to condition summary #

Total conditions: 15
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 provided 0 67 2 16 2 0 13 29
Rett syndrome 474 44 2 13 1 0 8 22
Severe neonatal-onset encephalopathy with microcephaly 0 25 2 12 4 0 4 19
not specified 0 12 0 10 8 0 3 19
Mental retardation, X-linked, syndromic 13 0 17 2 5 1 0 2 8
History of neurodevelopmental disorder 0 6 1 5 1 0 1 7
Inborn genetic diseases 0 6 1 3 0 0 1 4
Angelman syndrome 0 4 1 1 0 0 1 3
Autism, susceptibility to, X-linked 3 0 3 0 2 0 1 1 3
Severe neonatal-onset encephalopathy with microcephaly; MECP2 duplication syndrome; Mental retardation, X-linked, syndromic 13; Rett syndrome; Autism, susceptibility to, X-linked 3 0 3 0 3 0 0 0 3
Angelman syndrome; Mental retardation, X-linked, syndromic 13; Rett syndrome 0 2 0 1 1 0 0 2
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 64 0 0 0 1 0 0 0 1
Early infantile epileptic encephalopathy 2 0 1 0 1 0 0 0 1
Motor delay; Micrognathia; Hearing impairment; Downslanted palpebral fissures; Microcephaly; Stenosis of the external auditory canal; Intellectual disability; Postnatal growth retardation 0 0 0 1 0 0 0 1
Rett syndrome, zappella variant 0 0 1 0 0 0 0 1

All variants with conflicting interpretations #

Total variants: 55
Download table as spreadsheet
HGVS dbSNP
NM_001110792.1(MECP2):c.1A>G (p.Met1Val) rs587783132
NM_001110792.1(MECP2):c.1A>T (p.Met1Leu) rs587783132
NM_001110792.1(MECP2):c.42_47dupAGGAGG (p.Gly16_Glu17insGlyGly) rs587783744
NM_001110792.1(MECP2):c.5C>T (p.Ala2Val) rs179363901
NM_001110792.1(MECP2):c.62+1G>A rs786205048
NM_001110792.1(MECP2):c.916C>T (p.Arg306Ter) rs61751362
NM_001160036.1(RHOBTB2):c.1531C>T (p.Arg511Trp) rs1554504681
NM_003159.2(CDKL5):c.199C>T (p.Leu67Phe) rs267608437
NM_004992.3(MECP2):c.*14G>A rs199963992
NM_004992.3(MECP2):c.-143_-138dup rs398123566
NM_004992.3(MECP2):c.1072G>A (p.Ala358Thr) rs147017239
NM_004992.3(MECP2):c.1101_1106delCCACCA (p.His371_His372del) rs61752381
NM_004992.3(MECP2):c.1126C>T (p.Pro376Ser) rs61752387
NM_004992.3(MECP2):c.1129_1198del70 (p.Lys377Profs) rs1557135353
NM_004992.3(MECP2):c.1138G>A (p.Val380Met) rs267608572
NM_004992.3(MECP2):c.1155_1200del46 (p.Leu386Alafs) rs267608329
NM_004992.3(MECP2):c.1162C>G (p.Pro388Ala) rs61753000
NM_004992.3(MECP2):c.1163_1197del35 (p.Pro388Hisfs) rs267608589
NM_004992.3(MECP2):c.1168_1173delCCACCT (p.Pro390_Pro391del) rs61753008
NM_004992.3(MECP2):c.1180G>A (p.Glu394Lys) rs63094662
NM_004992.3(MECP2):c.1189G>A (p.Glu397Lys) rs56268439
NM_004992.3(MECP2):c.1214C>T (p.Pro405Leu) rs61753016
NM_004992.3(MECP2):c.1330G>A (p.Ala444Thr) rs61753975
NM_004992.3(MECP2):c.298C>G (p.Leu100Val) rs28935168
NM_004992.3(MECP2):c.301C>T (p.Pro101Ser) rs61754452
NM_004992.3(MECP2):c.302C>G (p.Pro101Arg) rs61754453
NM_004992.3(MECP2):c.316C>T (p.Arg106Trp) rs28934907
NM_004992.3(MECP2):c.364G>A (p.Val122Met) rs267608455
NM_004992.3(MECP2):c.378-17delT rs61753982
NM_004992.3(MECP2):c.378-3C>G rs267608465
NM_004992.3(MECP2):c.380C>T (p.Pro127Leu) rs267608387
NM_004992.3(MECP2):c.397C>T (p.Arg133Cys) rs28934904
NM_004992.3(MECP2):c.398G>A (p.Arg133His) rs61748389
NM_004992.3(MECP2):c.401C>G (p.Ser134Cys) rs61748390
NM_004992.3(MECP2):c.401C>T (p.Ser134Phe) rs61748390
NM_004992.3(MECP2):c.403A>G (p.Lys135Glu) rs61748391
NM_004992.3(MECP2):c.419C>T (p.Ala140Val) rs28934908
NM_004992.3(MECP2):c.452A>G (p.Asp151Gly) rs61748403
NM_004992.3(MECP2):c.455C>G (p.Pro152Arg) rs61748404
NM_004992.3(MECP2):c.472A>G (p.Thr158Ala) rs61748411
NM_004992.3(MECP2):c.473C>T (p.Thr158Met) rs28934906
NM_004992.3(MECP2):c.499C>T (p.Arg167Trp) rs61748420
NM_004992.3(MECP2):c.568C>T (p.Arg190Cys) rs587783137
NM_004992.3(MECP2):c.574A>T (p.Lys192Ter) rs193922679
NM_004992.3(MECP2):c.590C>T (p.Thr197Met) rs61749714
NM_004992.3(MECP2):c.602C>T (p.Ala201Val) rs61748381
NM_004992.3(MECP2):c.763C>T (p.Arg255Ter) rs61749721
NM_004992.3(MECP2):c.832G>A (p.Ala278Thr) rs782086416
NM_004992.3(MECP2):c.840delC (p.Ala281Profs) rs1557136332
NM_004992.3(MECP2):c.859G>C (p.Ala287Pro) rs61750257
NM_004992.3(MECP2):c.905C>T (p.Pro302Leu) rs61749723
NM_004992.3(MECP2):c.917G>A (p.Arg306His) rs61751443
NM_004992.3(MECP2):c.925C>T (p.Arg309Trp) rs61751444
NM_004992.3(MECP2):c.932C>T (p.Thr311Met) rs61751445
NM_004992.3(MECP2):c.965C>T (p.Pro322Leu) rs61751450

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