ClinVar Miner

Variants with conflicting interpretations studied for MECP2-related condition

Minimum review status of the submission for MECP2-related condition: Collection method of the submission for MECP2-related condition:
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 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
31 31 0 53 30 0 1 75

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
MECP2-related condition pathogenic uncertain significance likely benign benign
uncertain significance 0 0 4 3
likely benign 1 25 0 50
benign 0 0 3 0

Condition to condition summary #

Total conditions: 5
Download table as spreadsheet
Condition 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
not specified 0 13 0 48 9 0 0 56
not provided 0 44 0 20 25 0 1 45
History of neurodevelopmental disorder 0 4 0 5 0 0 0 5
Severe neonatal-onset encephalopathy with microcephaly; Syndromic X-linked intellectual disability Lubs type; X-linked intellectual disability-psychosis-macroorchidism syndrome; Rett syndrome; Autism, susceptibility to, X-linked 3 0 11 0 2 1 0 0 3
See cases 0 1 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 75
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001110792.2(MECP2):c.618C>T (p.Ser206=) rs61749711 0.00189
NM_001110792.2(MECP2):c.246C>T (p.Ser82=) rs61754439 0.00119
NM_001110792.2(MECP2):c.*9G>A rs144008995 0.00080
NM_001110792.2(MECP2):c.644C>T (p.Thr215Met) rs61749720 0.00070
NM_001110792.2(MECP2):c.626C>T (p.Thr209Met) rs61749714 0.00064
NM_001110792.2(MECP2):c.855G>T (p.Gly285=) rs61750245 0.00046
NM_001110792.2(MECP2):c.885C>G (p.Ala295=) rs61750253 0.00042
NM_001110792.2(MECP2):c.870C>T (p.Ala290=) rs61750248 0.00041
NM_001110792.2(MECP2):c.*14G>A rs199963992 0.00037
NM_001110792.2(MECP2):c.312A>G (p.Gly104=) rs140191561 0.00035
NM_001110792.2(MECP2):c.623C>G (p.Thr208Ser) rs61749713 0.00034
NM_001110792.2(MECP2):c.1108G>A (p.Ala370Thr) rs147017239 0.00030
NM_001110792.2(MECP2):c.1174G>A (p.Val392Met) rs267608572 0.00022
NM_001110792.2(MECP2):c.876C>T (p.Ala292=) rs61750251 0.00022
NM_001110792.2(MECP2):c.1020C>T (p.Leu340=) rs61751442 0.00021
NM_001110792.2(MECP2):c.1173C>T (p.Pro391=) rs61752980 0.00020
NM_001110792.2(MECP2):c.1224C>T (p.Ser408=) rs781816931 0.00019
NM_001110792.2(MECP2):c.429C>G (p.Ala143=) rs61748385 0.00018
NM_001110792.2(MECP2):c.621C>T (p.Gly207=) rs61749712 0.00017
NM_001110792.2(MECP2):c.1176G>A (p.Val392=) rs201711454 0.00015
NM_001110792.2(MECP2):c.1409G>A (p.Arg470His) rs185957513 0.00015
NM_001110792.2(MECP2):c.771C>G (p.Val257=) rs782027467 0.00013
NM_001110792.2(MECP2):c.897C>T (p.Ala299=) rs139378224 0.00013
NM_001110792.2(MECP2):c.1032C>T (p.Ser344=) rs148744894 0.00012
NM_001110792.2(MECP2):c.669G>C (p.Arg223Ser) rs61749731 0.00012
NM_001110792.2(MECP2):c.1318G>A (p.Gly440Ser) rs61753971 0.00011
NM_001110792.2(MECP2):c.639G>A (p.Ala213=) rs267608504 0.00010
NM_001110792.2(MECP2):c.731G>C (p.Gly244Ala) rs61748422 0.00010
NM_001110792.2(MECP2):c.*806G>A rs267608363 0.00009
NM_001110792.2(MECP2):c.1216G>A (p.Glu406Lys) rs63094662 0.00009
NM_001110792.2(MECP2):c.1363G>A (p.Ala455Thr) rs193922677 0.00009
NM_001110792.2(MECP2):c.1375G>A (p.Ala459Thr) rs267608626 0.00009
NM_001110792.2(MECP2):c.756C>T (p.Thr252=) rs61749746 0.00009
NM_001110792.2(MECP2):c.1097G>T (p.Arg366Leu) rs61748387 0.00008
NM_001110792.2(MECP2):c.1473G>A (p.Thr491=) rs587781033 0.00008
NM_001110792.2(MECP2):c.551C>T (p.Pro184Leu) rs267608491 0.00008
NM_001110792.2(MECP2):c.1066C>T (p.Arg356Trp) rs61752361 0.00006
NM_001110792.2(MECP2):c.1107C>T (p.Ser369=) rs61750236 0.00006
NM_001110792.2(MECP2):c.1198C>T (p.Pro400Ser) rs61753000 0.00006
NM_001110792.2(MECP2):c.737C>G (p.Ala246Gly) rs138211345 0.00006
NM_001110792.2(MECP2):c.90C>G (p.Leu30=) rs372500343 0.00006
NM_001110792.2(MECP2):c.1111T>C (p.Ser371Pro) rs61752371 0.00005
NM_001110792.2(MECP2):c.1232C>T (p.Pro411Leu) rs62915962 0.00005
NM_001110792.2(MECP2):c.1292C>T (p.Pro431Leu) rs376324027 0.00005
NM_001110792.2(MECP2):c.510G>A (p.Thr170=) rs61748413 0.00005
NM_001110792.2(MECP2):c.696C>T (p.Leu232=) rs267608512 0.00005
NM_001110792.2(MECP2):c.1250C>T (p.Pro417Leu) rs61753016 0.00004
NM_001110792.2(MECP2):c.1302C>T (p.Gly434=) rs61753970 0.00004
NM_001110792.2(MECP2):c.1291C>T (p.Pro431Ser) rs140258520 0.00003
NM_001110792.2(MECP2):c.260C>T (p.Pro87Leu) rs267608440 0.00003
NM_001110792.2(MECP2):c.968C>T (p.Thr323Met) rs61751445 0.00003
NM_001110792.2(MECP2):c.553C>G (p.Pro185Ala) rs61748427 0.00002
NM_001110792.2(MECP2):c.645G>A (p.Thr215=) rs61749722 0.00002
NM_001110792.2(MECP2):c.727G>A (p.Gly243Arg) rs587783139 0.00002
NM_001110792.2(MECP2):c.1089C>G (p.Pro363=) rs782242577 0.00001
NM_001110792.2(MECP2):c.1320C>T (p.Gly440=) rs267608621 0.00001
NM_001110792.2(MECP2):c.1482C>T (p.Thr494=) rs76895094 0.00001
NM_001110792.2(MECP2):c.474C>T (p.Gly158=) rs61748386 0.00001
NM_001110792.2(MECP2):c.723G>T (p.Ser241=) rs782461567 0.00001
NM_001110792.2(MECP2):c.860T>C (p.Val287Ala) rs143989769 0.00001
NM_001110792.2(MECP2):c.1169C>G (p.Ala390Gly) rs201314910
NM_001110792.2(MECP2):c.1169C>T (p.Ala390Val) rs201314910
NM_001110792.2(MECP2):c.1198CCACCT[1] (p.Pro402_Pro403del) rs61753008
NM_001110792.2(MECP2):c.1198_1215del (p.Pro400_Pro405del) rs267608406
NM_001110792.2(MECP2):c.1241C>T (p.Pro414Leu) rs61753014
NM_001110792.2(MECP2):c.1351G>A (p.Ala451Thr) rs61753973
NM_001110792.2(MECP2):c.33AGG[6] (p.Gly16dup) rs587783744
NM_001110792.2(MECP2):c.564C>G (p.Pro188=) rs61754420
NM_001110792.2(MECP2):c.6CGC[3] (p.Ala6_Ala8del) rs398123566
NM_001110792.2(MECP2):c.6CGC[5] (p.Ala8del) rs398123566
NM_001110792.2(MECP2):c.6CGC[7] (p.Ala8dup) rs398123566
NM_001110792.2(MECP2):c.6CGC[8] (p.Ala7_Ala8dup) rs398123566
NM_001110792.2(MECP2):c.784C>T (p.Arg262Cys) rs141382970
NM_001110792.2(MECP2):c.785G>A (p.Arg262His) rs61750227
NM_001110792.2(MECP2):c.786C>T (p.Arg262=) rs61748424

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