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

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: Report conflict between different conditions
Show significances as they were submitted (without aggregation into standard terms)

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
1483	96	0	20	58	0	0	76

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	16	2
	likely benign	48	0	8
	benign	6	15	0

Condition to condition summary #

Total conditions: 2

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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	87	0	19	50	0	0	67
Menkes kinky-hair syndrome; Cutis laxa, X-linked; X-linked distal spinal muscular atrophy type 3	1622	18	0	3	12	0	0	15

All variants with conflicting interpretations #

Total variants: 76

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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	0.00044
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	0.00024
NM_000052.7(ATP7A):c.1954C>T (p.Arg652Trp)	rs377714939	0.00016
NM_000052.7(ATP7A):c.2530C>T (p.Arg844Cys)	rs374162669	0.00014
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.1615C>A (p.Pro539Thr)	rs781817601	0.00008
NM_000052.7(ATP7A):c.4364G>A (p.Arg1455Gln)	rs147848649	0.00008
NM_000052.7(ATP7A):c.3565A>G (p.Ile1189Val)	rs368917354	0.00007
NM_000052.7(ATP7A):c.207G>A (p.Met69Ile)	rs782290331	0.00006
NM_000052.7(ATP7A):c.3632G>A (p.Arg1211Gln)	rs782166627	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.824A>G (p.Asn275Ser)	rs368147403	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.15G>A (p.Met5Ile)	rs781952393	0.00003
NM_000052.7(ATP7A):c.2111A>G (p.Gln704Arg)	rs782577253	0.00003
NM_000052.7(ATP7A):c.2725G>A (p.Ala909Thr)	rs146119866	0.00003
NM_000052.7(ATP7A):c.4424A>G (p.Asn1475Ser)	rs782774219	0.00003
NM_000052.7(ATP7A):c.475G>A (p.Ala159Thr)	rs188836609	0.00003
NM_000052.7(ATP7A):c.844A>G (p.Ile282Val)	rs782237314	0.00003
NM_000052.7(ATP7A):c.2251G>A (p.Val751Met)	rs1384495572	0.00002
NM_000052.7(ATP7A):c.3116A>G (p.Lys1039Arg)	rs781968399	0.00002
NM_000052.7(ATP7A):c.3434C>T (p.Ala1145Val)	rs374154862	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.4241C>T (p.Thr1414Ile)	rs782198884	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.761G>A (p.Arg254His)	rs782363269	0.00002
NM_000052.7(ATP7A):c.1286A>G (p.Glu429Gly)	rs2077660217	0.00001
NM_000052.7(ATP7A):c.1327A>G (p.Thr443Ala)	rs1227094533	0.00001
NM_000052.7(ATP7A):c.1376C>T (p.Ser459Leu)	rs1557232786	0.00001
NM_000052.7(ATP7A):c.1384C>G (p.Pro462Ala)	rs781964005	0.00001
NM_000052.7(ATP7A):c.1574C>G (p.Ala525Gly)	rs368355216	0.00001
NM_000052.7(ATP7A):c.1618C>G (p.Pro540Ala)	rs896151271	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.281C>T (p.Ala94Val)	rs1557231591	0.00001
NM_000052.7(ATP7A):c.3488T>A (p.Met1163Lys)	rs1557237460	0.00001
NM_000052.7(ATP7A):c.3595G>A (p.Val1199Ile)	rs782026169	0.00001
NM_000052.7(ATP7A):c.3701C>G (p.Pro1234Arg)	rs1557238254	0.00001
NM_000052.7(ATP7A):c.4066C>T (p.Arg1356Trp)	rs370736173	0.00001
NM_000052.7(ATP7A):c.415A>T (p.Ile139Leu)	rs1557231629	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.56G>A (p.Cys19Tyr)	rs782127182	0.00001
NM_000052.7(ATP7A):c.1126A>G (p.Thr376Ala)	rs782616685
NM_000052.7(ATP7A):c.1127C>A (p.Thr376Lys)	rs2077659011
NM_000052.7(ATP7A):c.121-2del	rs1287511385
NM_000052.7(ATP7A):c.1558C>T (p.Leu520Phe)	rs1331470313
NM_000052.7(ATP7A):c.1835T>G (p.Ile612Ser)	rs1569549840
NM_000052.7(ATP7A):c.1856T>C (p.Ile619Thr)	rs1569549841
NM_000052.7(ATP7A):c.1857C>G (p.Ile619Met)	rs782818837
NM_000052.7(ATP7A):c.2453C>T (p.Thr818Ile)	rs1557234937
NM_000052.7(ATP7A):c.2464A>G (p.Ile822Val)	rs1050354930
NM_000052.7(ATP7A):c.278C>G (p.Thr93Arg)	rs539177302
NM_000052.7(ATP7A):c.3358A>C (p.Ser1120Arg)	rs781914030
NM_000052.7(ATP7A):c.3533A>G (p.Tyr1178Cys)	rs1557238006
NM_000052.7(ATP7A):c.368G>A (p.Arg123Lys)	rs782664232
NM_000052.7(ATP7A):c.410A>G (p.Asn137Ser)	rs2149082684
NM_000052.7(ATP7A):c.4267C>T (p.Arg1423Trp)	rs149079962
NM_000052.7(ATP7A):c.83A>T (p.Gln28Leu)	rs782146244
NM_000052.7(ATP7A):c.924A>G (p.Ile308Met)	rs2522293888

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