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: 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 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
1609 39 0 8 29 0 1 38

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 likely pathogenic uncertain significance likely benign benign
likely pathogenic 0 1 0 0
uncertain significance 1 0 24 5
likely benign 0 24 0 8
benign 0 5 8 0

Condition to condition summary #

Total conditions: 1
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
Pitt-Hopkins-like syndrome 2 1609 39 0 8 29 0 1 38

All variants with conflicting interpretations #

Total variants: 38
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001330078.2(NRXN1):c.1285C>T (p.Pro429Ser) rs78540316 0.00323
NM_001330078.2(NRXN1):c.4473G>A (p.Ala1491=) rs113380721 0.00191
NM_001330078.2(NRXN1):c.2385C>G (p.Pro795=) rs147984237 0.00166
NM_001330078.2(NRXN1):c.772+1078A>G rs144049982 0.00153
NM_001330078.2(NRXN1):c.501C>G (p.Leu167=) rs200248561 0.00145
NM_001330078.2(NRXN1):c.322C>T (p.Pro108Ser) rs199784029 0.00138
NM_001330078.2(NRXN1):c.222C>T (p.Gly74=) rs201592993 0.00135
NM_001330078.2(NRXN1):c.3045C>T (p.Ala1015=) rs56402642 0.00109
NM_001330078.2(NRXN1):c.4254A>G (p.Pro1418=) rs55923848 0.00109
NM_001330078.2(NRXN1):c.4275G>T (p.Arg1425=) rs143495349 0.00096
NM_001330078.2(NRXN1):c.3201C>T (p.Ser1067=) rs75275592 0.00069
NM_001330078.2(NRXN1):c.2533C>T (p.His845Tyr) rs199784139 0.00064
NM_001330078.2(NRXN1):c.1945A>G (p.Ile649Val) rs200074974 0.00062
NM_001330078.2(NRXN1):c.-995T>C rs200865985 0.00061
NM_001330078.2(NRXN1):c.105C>A (p.Gly35=) rs55640811 0.00059
NM_001330078.2(NRXN1):c.1365T>C (p.Leu455=) rs201727684 0.00051
NM_001330078.2(NRXN1):c.2605C>A (p.Leu869Met) rs201818223 0.00044
NM_001330078.2(NRXN1):c.4392T>C (p.His1464=) rs112536447 0.00035
NM_001330078.2(NRXN1):c.3489C>T (p.Ala1163=) rs147580960 0.00011
NM_001330078.2(NRXN1):c.772+1040A>T rs201741449 0.00011
NM_001330078.2(NRXN1):c.3090A>C (p.Gly1030=) rs201886024 0.00010
NM_001330078.2(NRXN1):c.3364+9C>T rs200767650 0.00008
NM_001330078.2(NRXN1):c.2253A>G (p.Ala751=) rs199648817 0.00006
NM_001330078.2(NRXN1):c.2730G>A (p.Lys910=) rs192909520 0.00006
NM_001330078.2(NRXN1):c.4004C>T (p.Thr1335Ile) rs200672080 0.00006
NM_001330078.2(NRXN1):c.4248G>A (p.Pro1416=) rs151195816 0.00006
NM_001330078.2(NRXN1):c.3219C>T (p.Asn1073=) rs563089155 0.00005
NM_001330078.2(NRXN1):c.1857A>G (p.Pro619=) rs1324701043 0.00004
NM_001330078.2(NRXN1):c.3384T>C (p.Phe1128=) rs751894635 0.00004
NM_001330078.2(NRXN1):c.4236C>T (p.Gly1412=) rs587781101 0.00004
NM_001330078.2(NRXN1):c.492C>T (p.Ala164=) rs201180707 0.00004
NM_001330078.2(NRXN1):c.772+1032G>A rs771759988 0.00004
NM_001330078.2(NRXN1):c.600C>T (p.Gly200=) rs201481698 0.00003
NM_001330078.2(NRXN1):c.1760-13C>G rs886056171 0.00001
NM_001330078.2(NRXN1):c.2698A>C (p.Arg900=) rs574531814 0.00001
NM_001330078.2(NRXN1):c.3012G>A (p.Lys1004=) rs201118246 0.00001
NM_001330078.2(NRXN1):c.3237A>G (p.Gly1079=) rs886056170 0.00001
NM_001330078.2(NRXN1):c.543G>A (p.Lys181=) rs1670775186

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