ClinVar Miner

Variants with conflicting interpretations studied for Non-syndromic X-linked intellectual disability

Coded as:
Minimum review status of the submission for Non-syndromic X-linked intellectual disability: Y axis collection method of the submission for Non-syndromic X-linked intellectual disability:
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
298 19 0 34 13 2 0 45

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
Non-syndromic X-linked intellectual disability pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 0 0 0 2
likely pathogenic 1 0 0 0 0
uncertain significance 0 0 2 0 0
likely benign 0 11 0 24 0
benign 0 0 9 0 0

Condition to condition summary #

Total conditions: 6
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 7 0 26 7 0 0 32
History of neurodevelopmental disorder 0 15 0 15 3 0 0 18
not provided 0 4 0 2 3 0 0 4
Autism, susceptibility to, X-linked 2 0 0 0 0 0 2 0 2
Mental retardation, X-linked 61 0 0 0 1 0 0 0 1
Mental retardation, syndromic 14, X-linked 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 45
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HGVS dbSNP
NM_001039891.2(ZNF674):c.1028C>T (p.Thr343Met) rs61730637
NM_001039891.2(ZNF674):c.601C>T (p.Arg201Ter) rs182004761
NM_001039891.2(ZNF674):c.707A>G (p.Lys236Arg) rs201621696
NM_002578.4(PAK3):c.483A>G (p.Ala161=) rs146801179
NM_002578.4(PAK3):c.531G>A (p.Glu177=) rs56270341
NM_003179.2(SYP):c.687C>T (p.Ala229=) rs201427270
NM_003179.2(SYP):c.868G>T (p.Gly290Trp) rs376222680
NM_003179.2(SYP):c.877G>A (p.Gly293Ser) rs139475570
NM_004458.2(ACSL4):c.1698-10G>A rs193072191
NM_004840.2(ARHGEF6):c.2007C>T (p.Ser669=) rs12008084
NM_004840.2(ARHGEF6):c.362G>A (p.Arg121His) rs35106300
NM_007137.3(ZNF81):c.1495A>G (p.Ile499Val) rs182239885
NM_007137.3(ZNF81):c.1911G>A (p.Pro637=) rs663514
NM_007137.3(ZNF81):c.350G>T (p.Gly117Val) rs17147793
NM_007137.3(ZNF81):c.417A>G (p.Ile139Met) rs189835360
NM_007137.3(ZNF81):c.470A>G (p.Asn157Ser) rs41312157
NM_007137.3(ZNF81):c.554C>T (p.Ser185Leu) rs186251256
NM_007137.3(ZNF81):c.638C>A (p.Ala213Glu) rs537825
NM_007137.3(ZNF81):c.8C>T (p.Ala3Val) rs183846665
NM_014271.3(IL1RAPL1):c.2067C>G (p.Thr689=) rs140330609
NM_014271.3(IL1RAPL1):c.36C>T (p.Tyr12=) rs148060509
NM_021998.4(ZNF711):c.-27+5C>T rs41311563
NM_021998.4(ZNF711):c.798A>G (p.Thr266=) rs72549428
NM_080632.2(UPF3B):c.-13G>C rs185511642
NM_080632.2(UPF3B):c.1121G>A (p.Arg374His) rs143538947
NM_153252.4(BRWD3):c.2184G>A (p.Ala728=) rs369118921
NM_153252.4(BRWD3):c.2325+5G>A rs186391561
NM_153252.4(BRWD3):c.33G>A (p.Glu11=) rs139071237
NM_153252.4(BRWD3):c.5100T>C (p.Gly1700=) rs140852252
NM_153252.4(BRWD3):c.5130G>T (p.Gly1710=) rs146425236
NM_153252.4(BRWD3):c.597A>C (p.Ser199=) rs142085721
NM_153252.4(BRWD3):c.813+10G>C rs55824836
NM_153380.3(ZNF41):c.1578T>A (p.Ala526=) rs148848609
NM_153380.3(ZNF41):c.1997C>T (p.Ala666Val) rs144970008
NM_153380.3(ZNF41):c.2114G>A (p.Arg705His) rs144904486
NM_153380.3(ZNF41):c.332C>T (p.Pro111Leu) rs104894955
NM_153380.3(ZNF41):c.374T>G (p.Ile125Arg) rs17147624
NM_153380.3(ZNF41):c.590A>G (p.Lys197Arg) rs148585367
NM_153380.3(ZNF41):c.660T>G (p.Asn220Lys) rs34301930
NM_153380.3(ZNF41):c.786G>A (p.Gln262=) rs2498490
NM_153380.3(ZNF41):c.945T>G (p.Asp315Glu) rs2498170
NM_171998.3(RAB39B):c.543A>G (p.Thr181=) rs369970931
NM_181332.2(NLGN4X):c.1254_1255del (p.Glu418Aspfs)
NM_183353.2(RLIM):c.1067A>G (p.Tyr356Cys) rs786205133
nsv513783

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