NM_000053.4(ATP7B):c.2634T>G (p.Asn878Lys) AND Wilson disease

Germline classification:: Uncertain significance (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003314446.1

Allele description [Variation Report for NM_000053.4(ATP7B):c.2634T>G (p.Asn878Lys)]

NM_000053.4(ATP7B):c.2634T>G (p.Asn878Lys)

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.2634T>G (p.Asn878Lys)

HGVS:

NC_000013.11:g.51950103A>C
NG_008806.1:g.66392T>G
NM_000053.4:c.2634T>GMANE SELECT
NM_001005918.3:c.2148T>G
NM_001243182.2:c.2301T>G
NM_001330578.2:c.2400T>G
NM_001330579.2:c.2382T>G
NM_001406511.1:c.2634T>G
NM_001406512.1:c.2634T>G
NM_001406513.1:c.2634T>G
NM_001406514.1:c.2601T>G
NM_001406515.1:c.2634T>G
NM_001406516.1:c.2634T>G
NM_001406517.1:c.2538T>G
NM_001406518.1:c.2538T>G
NM_001406519.1:c.2634T>G
NM_001406520.1:c.2490T>G
NM_001406521.1:c.2490T>G
NM_001406522.1:c.2490T>G
NM_001406523.1:c.2634T>G
NM_001406524.1:c.2457T>G
NM_001406525.1:c.2634T>G
NM_001406526.1:c.2634T>G
NM_001406527.1:c.2400T>G
NM_001406528.1:c.2400T>G
NM_001406530.1:c.2394T>G
NM_001406531.1:c.2382T>G
NM_001406532.1:c.2382T>G
NM_001406534.1:c.2400T>G
NM_001406535.1:c.2634T>G
NM_001406536.1:c.2304T>G
NM_001406537.1:c.2490T>G
NM_001406538.1:c.2400T>G
NM_001406539.1:c.2205T>G
NM_001406540.1:c.2382T>G
NM_001406541.1:c.2148T>G
NM_001406542.1:c.2148T>G
NM_001406543.1:c.2286T>G
NM_001406544.1:c.2052T>G
NM_001406545.1:c.1986T>G
NM_001406546.1:c.2148T>G
NM_001406547.1:c.1986T>G
NM_001406548.1:c.1344T>G
NP_000044.2:p.Asn878Lys
NP_001005918.1:p.Asn716Lys
NP_001230111.1:p.Asn767Lys
NP_001317507.1:p.Asn800Lys
NP_001317508.1:p.Asn794Lys
NP_001393440.1:p.Asn878Lys
NP_001393441.1:p.Asn878Lys
NP_001393442.1:p.Asn878Lys
NP_001393443.1:p.Asn867Lys
NP_001393444.1:p.Asn878Lys
NP_001393445.1:p.Asn878Lys
NP_001393446.1:p.Asn846Lys
NP_001393447.1:p.Asn846Lys
NP_001393448.1:p.Asn878Lys
NP_001393449.1:p.Asn830Lys
NP_001393450.1:p.Asn830Lys
NP_001393451.1:p.Asn830Lys
NP_001393452.1:p.Asn878Lys
NP_001393453.1:p.Asn819Lys
NP_001393454.1:p.Asn878Lys
NP_001393455.1:p.Asn878Lys
NP_001393456.1:p.Asn800Lys
NP_001393457.1:p.Asn800Lys
NP_001393459.1:p.Asn798Lys
NP_001393460.1:p.Asn794Lys
NP_001393461.1:p.Asn794Lys
NP_001393463.1:p.Asn800Lys
NP_001393464.1:p.Asn878Lys
NP_001393465.1:p.Asn768Lys
NP_001393466.1:p.Asn830Lys
NP_001393467.1:p.Asn800Lys
NP_001393468.1:p.Asn735Lys
NP_001393469.1:p.Asn794Lys
NP_001393470.1:p.Asn716Lys
NP_001393471.1:p.Asn716Lys
NP_001393472.1:p.Asn762Lys
NP_001393473.1:p.Asn684Lys
NP_001393474.1:p.Asn662Lys
NP_001393475.1:p.Asn716Lys
NP_001393476.1:p.Asn662Lys
NP_001393477.1:p.Asn448Lys
NC_000013.10:g.52524239A>C

Protein change:

N448K

Molecular consequence:

NM_000053.4:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.2148T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2301T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2400T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2382T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406511.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406512.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406513.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406514.1:c.2601T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406515.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406516.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406517.1:c.2538T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406518.1:c.2538T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406519.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406520.1:c.2490T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406521.1:c.2490T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406522.1:c.2490T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406523.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406524.1:c.2457T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406525.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406526.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406527.1:c.2400T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406528.1:c.2400T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406530.1:c.2394T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406531.1:c.2382T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406532.1:c.2382T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406534.1:c.2400T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406535.1:c.2634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406536.1:c.2304T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406537.1:c.2490T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406538.1:c.2400T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406539.1:c.2205T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406540.1:c.2382T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406541.1:c.2148T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406542.1:c.2148T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406543.1:c.2286T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406544.1:c.2052T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406545.1:c.1986T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406546.1:c.2148T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406547.1:c.1986T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406548.1:c.1344T>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004013810	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 35385937, 18483695, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004013810

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

[Phenotypes and ATP7B gene variants in 316 children with Wilson disease].

Lu ZK, Cheng J, Li SM, Lin YT, Zhang W, Li XZ, Sheng HY, Mao XJ, Mei HF, Zheng RD, Liang CL, Jiang MY, Huang YL, Liu L, Zeng CH.

Zhonghua Er Ke Za Zhi. 2022 Apr 2;60(4):317-322. doi: 10.3760/cma.j.cn112140-20210827-00708. Chinese.

PubMed [citation]

PMID:: 35385937

Mutational analysis of ATP7B gene in Egyptian children with Wilson disease: 12 novel mutations.

Abdelghaffar TY, Elsayed SM, Elsobky E, Bochow B, Büttner J, Schmidt H.

J Hum Genet. 2008;53(8):681. doi: 10.1007/s10038-008-0298-7. Epub 2008 May 16.

PubMed [citation]

PMID:: 18483695

See all PubMed Citations (3)

Details of each submission

From 3billion, SCV004013810.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (3)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.67; 3Cnet: 0.80). Same nucleotide change resulting in same amino acid change has been previously reported to be associated with ATP7B related disorder (PMID: 18483695). A different missense change at the same codon (p.Asn878Thr) has been reported to be associated with ATP7B related disorder (PMID: 35385937). However the evidence of pathogenicity is insufficient at this time. Therefore, this variant is classified as Uncertain significance according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Jul 22, 2023

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