NM_000053.4(ATP7B):c.2855G>A (p.Arg952Lys) AND Wilson disease

Germline classification:: Benign (9 submissions)
Last evaluated:: Feb 5, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000029357.39

Allele description [Variation Report for NM_000053.4(ATP7B):c.2855G>A (p.Arg952Lys)]

NM_000053.4(ATP7B):c.2855G>A (p.Arg952Lys)

Gene:

ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q14.3

Genomic location:

Preferred name:

NM_000053.4(ATP7B):c.2855G>A (p.Arg952Lys)

HGVS:

NC_000013.11:g.51949672C>T
NG_008806.1:g.66823G>A
NM_000053.4:c.2855G>AMANE SELECT
NM_001005918.3:c.2244+335G>A
NM_001243182.2:c.2522G>A
NM_001330578.2:c.2621G>A
NM_001330579.2:c.2603G>A
NP_000044.2:p.Arg952Lys
NP_000044.2:p.Arg952Lys
NP_001230111.1:p.Arg841Lys
NP_001317507.1:p.Arg874Lys
NP_001317508.1:p.Arg868Lys
NC_000013.10:g.52523808C>T
NM_000053.3:c.2855G>A
NM_001005918.2:c.2244+335G>A
P35670:p.Arg952Lys

Protein change:

R841K

Links:

UniProtKB: P35670#VAR_000746; dbSNP: rs732774

NCBI 1000 Genomes Browser:

rs732774

Molecular consequence:

NM_001005918.3:c.2244+335G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000053.4:c.2855G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2522G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2621G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2603G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

87249

Condition(s)

Name:: Wilson disease (WND)
Synonyms:: Wilson's disease; Hepatolenticular degeneration
Identifiers:: MONDO: MONDO:0010200; MedGen: C0019202; Orphanet: 905; OMIM: 277900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000052004	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	benign (Aug 18, 2011)	germline	curation, clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000384666	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV000602587	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Benign (Mar 8, 2022)	germline	clinical testing	Citation Link,
SCV000733358	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV001459717	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing
SCV001720717	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001750135	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 1, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004362480	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Mar 5, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004845464	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Feb 5, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing, curation
not provided	germline	unknown	87248	not provided	not provided	108544	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The Wilson disease gene: spectrum of mutations and their consequences.

Thomas GR, Forbes JR, Roberts EA, Walshe JM, Cox DW.

Nat Genet. 1995 Feb;9(2):210-7. Erratum in: Nat Genet 1995 Apr;9(4):451.

PubMed [citation]

PMID:: 7626145

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052004.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)
2	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
3	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
4	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
5	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
6	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
7	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
8	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
9	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
10	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
11	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
12	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
13	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
14	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
15	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
16	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
17	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
18	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
19	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
20	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
21	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
22	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
23	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
24	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
25	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
26	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
27	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
28	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
29	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
30	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
31	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
32	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
33	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
34	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
35	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
36	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
37	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
38	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
39	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
40	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
41	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
42	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
43	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
44	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
45	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
46	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
47	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
48	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
49	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
50	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
51	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
52	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
53	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
54	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
55	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
56	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
57	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
58	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
59	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
60	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
61	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
62	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
63	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)
64	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Converted during submission to Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	not provided
2	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 2
3	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 3
4	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 4
5	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 5
6	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 6
7	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 7
8	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 8
9	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 9
10	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 10
11	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 11
12	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 12
13	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 13
14	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 14
15	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 15
16	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 16
17	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 17
18	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 18
19	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 19
20	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 20
21	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 21
22	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 22
23	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 23
24	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 24
25	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 25
26	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 26
27	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 27
28	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 28
29	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 29
30	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 30
31	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 31
32	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 32
33	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 33
34	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 34
35	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 35
36	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 36
37	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 37
38	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 38
39	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 39
40	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 40
41	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 41
42	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 42
43	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 43
44	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 44
45	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 45
46	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 46
47	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 47
48	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 48
49	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 49
50	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 50
51	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 51
52	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 52
53	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 53
54	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 54
55	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 55
56	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 56
57	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 57
58	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 58
59	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 59
60	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 60
61	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 61
62	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 62
63	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 63
64	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 64

Co-occurrences

#	Zygosity	Alleles	Number of Observations
2	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
3	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.3045G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
4	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
5	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
6	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.3009G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
7	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
8	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3620A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C	1
9	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
10	Homozygote	ATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C, MEFV:c.942C>T, MEFV:c.495C>A, MEFV:c.306T>C, MEFV:c.1764G>A, MEFV:c.1530T>C, MEFV:c.1428A>G, MEFV:c.1422G>A	1
11	Homozygote	ATP7B:c.3009G>A, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C, ATP7B:c.3700G>T, ATP7B:c.4058G>A	1
12	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
13	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
14	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
15	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
16	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.3060+16G>T	1
17	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
18	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3054G>A	1
19	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.4414G>A	1
20	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
21	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
22	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.98T>C, ATP7B:c.2953T>C	1
23	Homozygote	ATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C	1
24	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.3009G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C	1
25	Homozygote	ATP7B:c.3009G>A, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
26	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
27	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
28	Homozygote	ATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C	1
29	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
30	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
31	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3557-6C>T	1
32	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.3045G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.2972C>T	1
33	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
34	Homozygote	ATP7B:c.3045G>A, ATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C	1
35	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2866-13G>C, ATP7B:c.2495A>G, ATP7B:c.3419T>C	1
36	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3207C>A	1
37	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
38	SingleHeterozygote	ATP7B:c.4302G>A, ATP7B:c.1707+9T>C, ATP7B:c.3620A>G, ATP7B:c.3419T>C, ATP7B:c.3366A>G	1
39	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
40	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
41	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
42	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C	1
43	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
44	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2866-13G>C, ATP7B:c.2495A>G, ATP7B:c.3419T>C	1
45	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
46	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
47	Homozygote	ATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.3060+16G>T	1
48	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2866-13G>C, ATP7B:c.2495A>G, ATP7B:c.3419T>C	1
49	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
50	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
51	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.1934T>G	1
52	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3489C>T, FBN1:c.6997+17C>G, FBN1:c.1415G>A, TGFBR2:c.263+7A>G	1
53	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2866-13G>C, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
54	Homozygote	ATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C	1
55	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3955C>T, ATP7B:c.2930C>T	1
56	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2866-13G>C, ATP7B:c.2495A>G, ATP7B:c.3620A>G, ATP7B:c.3419T>C, ATP7B:c.2305A>G	1
57	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
58	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.3009G>A, ATP7B:c.2973G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C	1
59	Homozygote	ATP7B:c.3009G>A, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C	1
60	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.1216T>G	1
61	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2866-13G>C, ATP7B:c.2495A>G, ATP7B:c.3419T>C	1
62	Homozygote	ATP7B:c.3588C>T, ATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1366G>C, ATP7B:c.1216T>G, ATP7B:c.3419T>C	1
63	SingleHeterozygote	ATP7B:c.3903+6C>T, ATP7B:c.2866-13G>C, ATP7B:c.2495A>G, ATP7B:c.1216T>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C, ATP7B:c.4301C>T	1
64	Homozygote	ATP7B:c.3903+6C>T, ATP7B:c.2495A>G, ATP7B:c.1216T>G, ATP7B:c.3419T>C, ATP7B:c.1366G>C	1

From Illumina Laboratory Services, Illumina, SCV000384666.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000602587.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733358.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV001459717.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001720717.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV001750135.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Color Diagnostics, LLC DBA Color Health, SCV004362480.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From All of Us Research Program, National Institutes of Health, SCV004845464.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	87185	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		87185	not provided	not provided	not provided

Last Updated: Oct 13, 2024

Relating variation to medicine