ClinVar Miner

Variants with conflicting interpretations studied for Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3

Coded as:
Minimum review status of the submission for Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3: Collection method of the submission for Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3:
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
1338 69 0 16 42 0 0 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.

All conditions
Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 uncertain significance likely benign benign
uncertain significance 0 9 2
likely benign 36 0 8
benign 4 11 0

Condition to condition summary #

Total conditions: 2
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
Inborn genetic diseases 0 61 0 15 39 0 0 52
Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3 1436 17 0 3 7 0 0 10

All variants with conflicting interpretations #

Total variants: 56
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HGVS dbSNP gnomAD frequency
NM_000052.7(ATP7A):c.4201G>C (p.Val1401Leu) rs5959130 0.00500
NM_000052.7(ATP7A):c.1955G>A (p.Arg652Gln) rs143214563 0.00089
NM_000052.7(ATP7A):c.4006A>G (p.Asn1336Asp) rs146651049 0.00082
NM_000052.7(ATP7A):c.880A>T (p.Asn294Tyr) rs150526992 0.00060
NM_000052.7(ATP7A):c.2452A>G (p.Thr818Ala) rs201788154 0.00039
NM_000052.7(ATP7A):c.4389T>C (p.Ser1463=) rs371939448 0.00037
NM_000052.7(ATP7A):c.2131G>A (p.Val711Ile) rs782268170 0.00025
NM_000052.7(ATP7A):c.3613G>C (p.Glu1205Gln) rs782349186 0.00025
NM_000052.7(ATP7A):c.1954C>T (p.Arg652Trp) rs377714939 0.00016
NM_000052.7(ATP7A):c.2530C>T (p.Arg844Cys) rs374162669 0.00012
NM_000052.7(ATP7A):c.278C>T (p.Thr93Met) rs539177302 0.00012
NM_000052.7(ATP7A):c.1000G>A (p.Ala334Thr) rs368622356 0.00010
NM_000052.7(ATP7A):c.1385C>T (p.Pro462Leu) rs201999500 0.00009
NM_000052.7(ATP7A):c.3565A>G (p.Ile1189Val) rs368917354 0.00007
NM_000052.7(ATP7A):c.3632G>A (p.Arg1211Gln) rs782166627 0.00006
NM_000052.7(ATP7A):c.824A>G (p.Asn275Ser) rs368147403 0.00006
NM_000052.7(ATP7A):c.1721C>T (p.Thr574Met) rs782076879 0.00005
NM_000052.7(ATP7A):c.4312G>A (p.Val1438Ile) rs782682493 0.00005
NM_000052.7(ATP7A):c.1427C>T (p.Thr476Ile) rs782702847 0.00003
NM_000052.7(ATP7A):c.1561G>A (p.Val521Met) rs139902461 0.00003
NM_000052.7(ATP7A):c.2111A>G (p.Gln704Arg) rs782577253 0.00003
NM_000052.7(ATP7A):c.4424A>G (p.Asn1475Ser) rs782774219 0.00003
NM_000052.7(ATP7A):c.844A>G (p.Ile282Val) rs782237314 0.00003
NM_000052.7(ATP7A):c.15G>A (p.Met5Ile) rs781952393 0.00002
NM_000052.7(ATP7A):c.2725G>A (p.Ala909Thr) rs146119866 0.00002
NM_000052.7(ATP7A):c.3434C>T (p.Ala1145Val) rs374154862 0.00002
NM_000052.7(ATP7A):c.3533A>G (p.Tyr1178Cys) rs1557238006 0.00002
NM_000052.7(ATP7A):c.3736A>G (p.Met1246Val) rs1385333276 0.00002
NM_000052.7(ATP7A):c.3775A>G (p.Lys1259Glu) rs782428979 0.00002
NM_000052.7(ATP7A):c.4352G>A (p.Gly1451Asp) rs782232632 0.00002
NM_000052.7(ATP7A):c.4356G>C (p.Leu1452Phe) rs782364202 0.00002
NM_000052.7(ATP7A):c.1327A>G (p.Thr443Ala) rs1227094533 0.00001
NM_000052.7(ATP7A):c.1558C>T (p.Leu520Phe) rs1331470313 0.00001
NM_000052.7(ATP7A):c.1574C>G (p.Ala525Gly) rs368355216 0.00001
NM_000052.7(ATP7A):c.1907G>A (p.Arg636Gln) rs1557234412 0.00001
NM_000052.7(ATP7A):c.1947-5A>G rs1557234466 0.00001
NM_000052.7(ATP7A):c.2108G>A (p.Arg703His) rs2234936 0.00001
NM_000052.7(ATP7A):c.2279A>G (p.Tyr760Cys) rs782006661 0.00001
NM_000052.7(ATP7A):c.2287A>G (p.Ile763Val) rs2077837721 0.00001
NM_000052.7(ATP7A):c.3595G>A (p.Val1199Ile) rs782026169 0.00001
NM_000052.7(ATP7A):c.368G>A (p.Arg123Lys) rs782664232 0.00001
NM_000052.7(ATP7A):c.4066C>T (p.Arg1356Trp) rs370736173 0.00001
NM_000052.7(ATP7A):c.4363C>T (p.Arg1455Trp) rs1457236338 0.00001
NM_000052.7(ATP7A):c.4414C>T (p.Arg1472Cys) rs782062633 0.00001
NM_000052.7(ATP7A):c.4448A>C (p.Asp1483Ala) rs782799150 0.00001
NM_000052.7(ATP7A):c.83A>T (p.Gln28Leu) rs782146244 0.00001
NM_000052.7(ATP7A):c.121-2del rs1287511385
NM_000052.7(ATP7A):c.1618C>G (p.Pro540Ala)
NM_000052.7(ATP7A):c.1856T>C (p.Ile619Thr) rs1569549841
NM_000052.7(ATP7A):c.1857C>G (p.Ile619Met)
NM_000052.7(ATP7A):c.2251G>A (p.Val751Met)
NM_000052.7(ATP7A):c.2464A>G (p.Ile822Val)
NM_000052.7(ATP7A):c.281C>T (p.Ala94Val)
NM_000052.7(ATP7A):c.3116A>G (p.Lys1039Arg)
NM_000052.7(ATP7A):c.4267C>T (p.Arg1423Trp) rs149079962
NM_000052.7(ATP7A):c.56G>A (p.Cys19Tyr)

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