ClinVar Miner

Variants with conflicting interpretations studied for Pitt-Hopkins-like syndrome

Coded as:
Minimum review status of the submission for Pitt-Hopkins-like syndrome: Y axis collection method of the submission for Pitt-Hopkins-like 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
103 130 0 18 33 0 0 51

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
Pitt-Hopkins-like syndrome likely benign benign
uncertain significance 27 25
likely benign 0 12
benign 6 0

Condition to condition summary #

Total conditions: 5
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 9 0 18 29 0 0 47
History of neurodevelopmental disorder 0 14 0 4 17 0 0 21
Pitt-Hopkins-like syndrome 2 0 3 0 4 15 0 0 19
Pitt-Hopkins-like syndrome 1 0 136 0 5 7 0 0 12
not provided 0 17 0 2 2 0 0 4

All variants with conflicting interpretations #

Total variants: 51
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HGVS dbSNP
NM_001135659.2(NRXN1):c.-34C>A rs200335720
NM_001135659.2(NRXN1):c.-922+7A>C rs200115353
NM_001135659.2(NRXN1):c.1278+5A>T rs201802152
NM_001135659.2(NRXN1):c.1485T>C (p.Leu495=) rs201727684
NM_001135659.2(NRXN1):c.222C>T (p.Gly74=) rs201592993
NM_001135659.2(NRXN1):c.2505C>G (p.Pro835=) rs147984237
NM_001135659.2(NRXN1):c.2541C>T (p.Asn847=) rs115211871
NM_001135659.2(NRXN1):c.2725C>A (p.Leu909Met) rs201818223
NM_001135659.2(NRXN1):c.2850G>A (p.Lys950=) rs192909520
NM_001135659.2(NRXN1):c.3210A>C (p.Gly1070=) rs201886024
NM_001135659.2(NRXN1):c.3369C>T (p.Pro1123=) rs116236999
NM_001135659.2(NRXN1):c.3504T>C (p.Phe1168=) rs751894635
NM_001135659.2(NRXN1):c.3528G>A (p.Thr1176=) rs80094872
NM_001135659.2(NRXN1):c.4180A>T (p.Thr1394Ser) rs202006815
NM_001135659.2(NRXN1):c.4188G>A (p.Thr1396=) rs74714098
NM_001135659.2(NRXN1):c.4356C>T (p.Gly1452=) rs587781101
NM_001135659.2(NRXN1):c.4368G>A (p.Pro1456=) rs151195816
NM_001135659.2(NRXN1):c.4395G>T (p.Arg1465=) rs143495349
NM_001135659.2(NRXN1):c.4512T>C (p.His1504=) rs112536447
NM_001135659.2(NRXN1):c.4593G>A (p.Ala1531=) rs113380721
NM_001135659.2(NRXN1):c.501C>G (p.Leu167=) rs200248561
NM_001135659.2(NRXN1):c.511C>T (p.Leu171=) rs1045874
NM_001135659.2(NRXN1):c.818A>G (p.Asp273Gly) rs144049982
NM_001135659.2(NRXN1):c.871+9G>A rs61658382
NM_001135659.2(NRXN1):c.999C>T (p.Pro333=) rs2303298
NM_014141.5(CNTNAP2):c.-49T>G rs549396215
NM_014141.5(CNTNAP2):c.1311C>T (p.Ile437=) rs56356283
NM_014141.5(CNTNAP2):c.1659G>A (p.Ala553=) rs34592169
NM_014141.5(CNTNAP2):c.1710G>A (p.Ser570=) rs2286128
NM_014141.5(CNTNAP2):c.1777+10A>G rs2286127
NM_014141.5(CNTNAP2):c.1777+7G>A rs770951811
NM_014141.5(CNTNAP2):c.1854C>T (p.Gly618=) rs61732849
NM_014141.5(CNTNAP2):c.209-11C>T rs369056998
NM_014141.5(CNTNAP2):c.2099-15T>C rs75858942
NM_014141.5(CNTNAP2):c.2190C>T (p.Cys730=) rs74354654
NM_014141.5(CNTNAP2):c.2256-6A>T rs10240482
NM_014141.5(CNTNAP2):c.2280A>G (p.Ser760=) rs10240503
NM_014141.5(CNTNAP2):c.2356G>T (p.Val786Leu) rs138517537
NM_014141.5(CNTNAP2):c.2460C>T (p.Ser820=) rs144496909
NM_014141.5(CNTNAP2):c.2508T>C (p.Phe836=) rs149185385
NM_014141.5(CNTNAP2):c.2554+14G>T rs546437079
NM_014141.5(CNTNAP2):c.318C>T (p.Ser106=) rs61732853
NM_014141.5(CNTNAP2):c.3247+15A>G rs201602527
NM_014141.5(CNTNAP2):c.3248-4A>G rs3779031
NM_014141.5(CNTNAP2):c.3476-15C>A rs77706740
NM_014141.5(CNTNAP2):c.3522A>T (p.Gly1174=) rs141078449
NM_014141.5(CNTNAP2):c.3723G>A (p.Ala1241=) rs9648691
NM_014141.5(CNTNAP2):c.3797-6C>T rs79777576
NM_014141.5(CNTNAP2):c.561T>C (p.Val187=) rs201200400
NM_014141.5(CNTNAP2):c.681C>T (p.His227=) rs142984073
NM_014141.5(CNTNAP2):c.837G>A (p.Val279=) rs143507886

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