ClinVar Miner

Variants in gene CTNS with conflicting interpretations

See also:
Y axis minimum submission review status: Y axis collection method:
X axis minimum submission review status: X axis collection method:
Minimum conflict level:
Gene type:
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
652 82 1 35 17 0 4 56

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.

pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 1 27 1 0 0
likely pathogenic 27 0 3 0 0
uncertain significance 1 3 0 15 2
likely benign 0 0 15 0 8
benign 0 0 2 8 0

All variants with conflicting interpretations #

Total variants: 56
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_004937.3(CTNS):c.124G>A (p.Val42Ile) rs35086888 0.01867
NM_004937.3(CTNS):c.108C>T (p.Asn36=) rs117404824 0.00664
NM_004937.3(CTNS):c.853-28C>T rs78671385 0.00563
NM_004937.3(CTNS):c.462-7C>A rs189632527 0.00259
NM_004937.3(CTNS):c.116C>T (p.Ser39Leu) rs144751390 0.00219
NM_004937.3(CTNS):c.327C>T (p.Thr109=) rs150554216 0.00141
NM_004937.3(CTNS):c.220G>A (p.Asp74Asn) rs139364393 0.00116
NM_004937.3(CTNS):c.834G>A (p.Leu278=) rs139519275 0.00094
NM_004937.3(CTNS):c.695G>A (p.Arg232His) rs142641674 0.00072
NM_004937.3(CTNS):c.534C>T (p.Ile178=) rs113967200 0.00058
NM_004937.3(CTNS):c.561+4C>T rs111256750 0.00040
NM_004937.3(CTNS):c.94G>A (p.Val32Ile) rs146684402 0.00036
NM_004937.3(CTNS):c.661G>A (p.Val221Met) rs138270433 0.00029
NM_004937.3(CTNS):c.123C>T (p.Asn41=) rs148084080 0.00019
NM_004937.3(CTNS):c.697G>A (p.Val233Met) rs201058200 0.00018
NM_004937.3(CTNS):c.364G>A (p.Ala122Thr) rs187396540 0.00005
NM_004937.3(CTNS):c.473T>C (p.Leu158Pro) rs113994206 0.00004
NM_004937.3(CTNS):c.589G>A (p.Gly197Arg) rs113994207 0.00004
NM_004937.3(CTNS):c.635C>T (p.Ala212Val) rs776658046 0.00004
NM_004937.3(CTNS):c.852+8C>T rs780856527 0.00004
NM_004937.3(CTNS):c.621C>T (p.Phe207=) rs749428707 0.00003
NM_004937.3(CTNS):c.198_218del (p.Ile67_Pro73del) rs113994204 0.00002
NM_004937.3(CTNS):c.270A>T (p.Thr90=) rs754247532 0.00001
NM_004937.3(CTNS):c.416C>T (p.Ser139Phe) rs267606754 0.00001
NM_004937.3(CTNS):c.612C>T (p.Asn204=) rs200170842 0.00001
NM_004937.3(CTNS):c.634G>A (p.Ala212Thr) rs768600603 0.00001
NM_004937.3(CTNS):c.822C>T (p.Leu274=) rs150773117 0.00001
NM_004937.3(CTNS):c.897T>C (p.Ile299=) rs199824920 0.00001
NM_004937.3(CTNS):c.922G>A (p.Gly308Arg) rs746307931 0.00001
GRCh38/hg38 17p13.2(chr17:3640170-3656795)x1
NM_004937.3(CTNS):c.1029C>A (p.Ile343=) rs147428183
NM_004937.3(CTNS):c.1082C>T (p.Pro361Leu) rs560868487
NM_004937.3(CTNS):c.225+5_225+8del rs1555561048
NM_004937.3(CTNS):c.286C>T (p.Gln96Ter)
NM_004937.3(CTNS):c.292dup (p.Thr98fs) rs786204434
NM_004937.3(CTNS):c.300T>A (p.Tyr100Ter) rs376042415
NM_004937.3(CTNS):c.323del (p.Gln108fs) rs879255615
NM_004937.3(CTNS):c.329+2T>C rs955833453
NM_004937.3(CTNS):c.382C>T (p.Gln128Ter) rs550254092
NM_004937.3(CTNS):c.40del (p.Pro13_Leu14insTer) rs1555558099
NM_004937.3(CTNS):c.422C>T (p.Ser141Phe) rs1436441738
NM_004937.3(CTNS):c.559_561+24del rs113994211
NM_004937.3(CTNS):c.561+1del rs786204667
NM_004937.3(CTNS):c.565C>T (p.Gln189Ter) rs1597654770
NM_004937.3(CTNS):c.611ACG[1] (p.Asp205del) rs760256854
NM_004937.3(CTNS):c.61_61+2del rs2075652654
NM_004937.3(CTNS):c.682-1G>T rs1057516771
NM_004937.3(CTNS):c.696_697dup (p.Val233fs) rs1555563982
NM_004937.3(CTNS):c.734G>A (p.Trp245Ter) rs763089013
NM_004937.3(CTNS):c.73A>T (p.Ser25Cys) rs777367316
NM_004937.3(CTNS):c.771_793del (p.Gly258fs) rs759623796
NM_004937.3(CTNS):c.809_811del (p.Ser270del) rs786204632
NM_004937.3(CTNS):c.839A>G (p.Lys280Arg) rs2150925451
NM_004937.3(CTNS):c.853-2A>G rs1475322504
NM_004937.3(CTNS):c.870C>G (p.Tyr290Ter) rs776842972
NM_004937.3(CTNS):c.926dup (p.Ser310fs) rs786204420

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