ClinVar Miner

Variants with conflicting interpretations studied for Pitt-Hopkins-like syndrome 2

Coded as:
Minimum review status of the submission for Pitt-Hopkins-like syndrome 2: Y axis collection method of the submission for Pitt-Hopkins-like syndrome 2:
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
90 31 0 33 32 0 0 44

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 2 uncertain significance likely benign benign
uncertain significance 0 2 1
likely benign 16 0 15
benign 13 19 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 17 0 27 10 0 0 36
History of neurodevelopmental disorder 0 19 0 13 6 0 0 19
Pitt-Hopkins-like syndrome 0 3 0 4 15 0 0 19
not provided 0 18 0 5 14 0 0 19
Pitt-Hopkins-like syndrome 2; Schizophrenia 17 0 7 0 0 2 0 0 2
Pitt-Hopkins-like syndrome 2 164 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 44
Download table as spreadsheet
HGVS dbSNP
NM_001135659.2(NRXN1):c.105C>A (p.Gly35=) rs55640811
NM_001135659.2(NRXN1):c.1233+8C>T rs200448187
NM_001135659.2(NRXN1):c.1278+5A>T rs201802152
NM_001135659.2(NRXN1):c.1405C>T (p.Pro469Ser) rs78540316
NM_001135659.2(NRXN1):c.1446A>C (p.Val482=) rs201485014
NM_001135659.2(NRXN1):c.1485T>C (p.Leu495=) rs201727684
NM_001135659.2(NRXN1):c.1695A>G (p.Arg565=) rs201941844
NM_001135659.2(NRXN1):c.1808T>C (p.Ile603Thr) rs201837579
NM_001135659.2(NRXN1):c.1869C>T (p.Asp623=) rs199934259
NM_001135659.2(NRXN1):c.2065A>G (p.Ile689Val) rs200074974
NM_001135659.2(NRXN1):c.2157G>A (p.Pro719=) rs199714221
NM_001135659.2(NRXN1):c.222C>T (p.Gly74=) rs201592993
NM_001135659.2(NRXN1):c.2242C>A (p.Leu748Ile) rs56086732
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.2579G>A (p.Ser860Asn) rs80293130
NM_001135659.2(NRXN1):c.261C>A (p.Gly87=) rs587781102
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.2892C>T (p.Tyr964=) rs200182626
NM_001135659.2(NRXN1):c.3165C>T (p.Ala1055=) rs56402642
NM_001135659.2(NRXN1):c.3210A>C (p.Gly1070=) rs201886024
NM_001135659.2(NRXN1):c.322C>T (p.Pro108Ser) rs199784029
NM_001135659.2(NRXN1):c.3249A>G (p.Val1083=) rs200698497
NM_001135659.2(NRXN1):c.324G>A (p.Pro108=) rs199595253
NM_001135659.2(NRXN1):c.3369C>T (p.Pro1123=) rs116236999
NM_001135659.2(NRXN1):c.3528G>A (p.Thr1176=) rs80094872
NM_001135659.2(NRXN1):c.4053A>G (p.Ala1351=) rs79970751
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.4287C>G (p.Pro1429=) rs143446587
NM_001135659.2(NRXN1):c.4356C>T (p.Gly1452=) rs587781101
NM_001135659.2(NRXN1):c.4374A>G (p.Pro1458=) rs55923848
NM_001135659.2(NRXN1):c.4395G>T (p.Arg1465=) rs143495349
NM_001135659.2(NRXN1):c.4458T>C (p.Leu1486=) rs796052759
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.498G>A (p.Ala166=) rs201212909
NM_001135659.2(NRXN1):c.501C>G (p.Leu167=) rs200248561
NM_001135659.2(NRXN1):c.818A>G (p.Asp273Gly) rs144049982
NM_001135659.2(NRXN1):c.871+9G>A rs61658382
NM_001135659.2(NRXN1):c.897G>A (p.Ala299=) rs201027928
NM_001135659.2(NRXN1):c.932-5T>G rs199712573
NM_001135659.2(NRXN1):c.999C>T (p.Pro333=) rs2303298

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