ClinVar Miner

Variants with conflicting interpretations studied for Severe neonatal-onset encephalopathy with microcephaly

Coded as:
Minimum review status of the submission for Severe neonatal-onset encephalopathy with microcephaly: Y axis collection method of the submission for Severe neonatal-onset encephalopathy with microcephaly:
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
45 44 2 38 18 0 8 52

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
Severe neonatal-onset encephalopathy with microcephaly pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 2 7 3 1 1
likely pathogenic 1 0 2 0 0
uncertain significance 1 0 0 4 4
likely benign 0 0 2 0 4
benign 1 0 12 26 0

Condition to condition summary #

Total conditions: 9
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 30 0 23 10 0 2 33
Rett syndrome 0 25 2 12 4 0 4 19
not provided 0 31 0 6 7 0 1 13
History of neurodevelopmental disorder 0 17 0 6 3 0 0 9
Mental retardation, X-linked, syndromic 13 0 10 0 2 4 0 1 7
Severe neonatal-onset encephalopathy with microcephaly 135 4 0 0 2 0 0 2
Attention deficit hyperactivity disorder 0 0 0 1 0 0 0 1
Autism, susceptibility to, X-linked 3 0 3 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

All variants with conflicting interpretations #

Total variants: 52
Download table as spreadsheet
HGVS dbSNP
NM_001110792.1(MECP2):c.45_47dupAGG (p.Gly16dup) rs587783744
NM_001110792.1(MECP2):c.62+1G>A rs786205048
NM_004992.3(MECP2):c.-140_-138dup rs398123566
NM_004992.3(MECP2):c.-143_-138delCGCCGC rs398123566
NM_004992.3(MECP2):c.-143_-138dup rs398123566
NM_004992.3(MECP2):c.1071C>T (p.Ser357=) rs61750236
NM_004992.3(MECP2):c.1072G>A (p.Ala358Thr) rs147017239
NM_004992.3(MECP2):c.1075T>C (p.Ser359Pro) rs61752371
NM_004992.3(MECP2):c.1126C>T (p.Pro376Ser) rs61752387
NM_004992.3(MECP2):c.1133C>T (p.Ala378Val) rs201314910
NM_004992.3(MECP2):c.1138G>A (p.Val380Met) rs267608572
NM_004992.3(MECP2):c.1140G>A (p.Val380=) rs201711454
NM_004992.3(MECP2):c.1160C>T (p.Pro387Leu) rs63390262
NM_004992.3(MECP2):c.1162C>G (p.Pro388Ala) rs61753000
NM_004992.3(MECP2):c.1162_1179del18 (p.Pro388_Pro393del) rs267608406
NM_004992.3(MECP2):c.1188C>T (p.Ser396=) rs781816931
NM_004992.3(MECP2):c.1189G>A (p.Glu397Lys) rs56268439
NM_004992.3(MECP2):c.1197C>T (p.Pro399=) rs61753012
NM_004992.3(MECP2):c.1205C>T (p.Pro402Leu) rs61753014
NM_004992.3(MECP2):c.1215C>T (p.Pro405=) rs61753964
NM_004992.3(MECP2):c.1282G>A (p.Gly428Ser) rs61753971
NM_004992.3(MECP2):c.1315G>A (p.Ala439Thr) rs61753973
NM_004992.3(MECP2):c.1327G>A (p.Ala443Thr) rs193922677
NM_004992.3(MECP2):c.1330G>A (p.Ala444Thr) rs61753975
NM_004992.3(MECP2):c.1339G>A (p.Ala447Thr) rs267608626
NM_004992.3(MECP2):c.225G>A (p.Pro75=) rs61754442
NM_004992.3(MECP2):c.276A>G (p.Gly92=) rs140191561
NM_004992.3(MECP2):c.316C>T (p.Arg106Trp) rs28934907
NM_004992.3(MECP2):c.375C>A (p.Ile125=) rs146107517
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.401C>G (p.Ser134Cys) rs61748390
NM_004992.3(MECP2):c.419C>T (p.Ala140Val) rs28934908
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.590C>T (p.Thr197Met) rs61749714
NM_004992.3(MECP2):c.591G>A (p.Thr197=) rs61749716
NM_004992.3(MECP2):c.596C>G (p.Pro199Arg) rs267608502
NM_004992.3(MECP2):c.602C>T (p.Ala201Val) rs61748381
NM_004992.3(MECP2):c.603G>A (p.Ala201=) rs267608504
NM_004992.3(MECP2):c.633G>C (p.Arg211Ser) rs61749731
NM_004992.3(MECP2):c.686C>T (p.Ser229Leu) rs61749739
NM_004992.3(MECP2):c.750C>A (p.Arg250=) rs61748424
NM_004992.3(MECP2):c.750C>T (p.Arg250=) rs61748424
NM_004992.3(MECP2):c.753C>T (p.Pro251=) rs63582063
NM_004992.3(MECP2):c.763C>T (p.Arg255Ter) rs61749721
NM_004992.3(MECP2):c.840delC (p.Ala281Profs) rs1557136332
NM_004992.3(MECP2):c.897C>T (p.Thr299=) rs61748423
NM_004992.3(MECP2):c.905C>T (p.Pro302Leu) rs61749723
NM_004992.3(MECP2):c.932C>T (p.Thr311Met) rs61751445
NM_004992.3(MECP2):c.942C>T (p.Ile314=) rs61751446

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