NM_004448.4(ERBB2):c.3190G>A (p.Glu1064Lys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 11, 2022
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:: RCV003090457.3

Allele description [Variation Report for NM_004448.4(ERBB2):c.3190G>A (p.Glu1064Lys)]

NM_004448.4(ERBB2):c.3190G>A (p.Glu1064Lys)

Gene:

ERBB2:erb-b2 receptor tyrosine kinase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_004448.4(ERBB2):c.3190G>A (p.Glu1064Lys)

HGVS:

NC_000017.11:g.39727325G>A
NG_007503.1:g.44186G>A
NG_136453.1:g.1123G>A
NM_001005862.3:c.3100G>A
NM_001289936.2:c.3145G>A
NM_001289937.2:c.3159+322G>A
NM_001382782.1:c.3100G>A
NM_001382783.1:c.3100G>A
NM_001382784.1:c.3307G>A
NM_001382785.1:c.3292G>A
NM_001382786.1:c.3271G>A
NM_001382787.1:c.3265G>A
NM_001382788.1:c.3220G>A
NM_001382789.1:c.3211G>A
NM_001382790.1:c.3187G>A
NM_001382791.1:c.3181G>A
NM_001382792.1:c.3154G>A
NM_001382793.1:c.3148G>A
NM_001382794.1:c.3148G>A
NM_001382795.1:c.3142G>A
NM_001382796.1:c.3103G>A
NM_001382797.1:c.3091G>A
NM_001382798.1:c.3034G>A
NM_001382799.1:c.3010G>A
NM_001382800.1:c.3004G>A
NM_001382801.1:c.2986G>A
NM_001382802.1:c.2932G>A
NM_001382803.1:c.3117+322G>A
NM_001382804.1:c.2362G>A
NM_001382805.1:c.2239G>A
NM_001382806.1:c.2152G>A
NM_004448.4:c.3190G>AMANE SELECT
NP_001005862.1:p.Glu1034Lys
NP_001005862.1:p.Glu1034Lys
NP_001276865.1:p.Glu1049Lys
NP_001276865.1:p.Glu1049Lys
NP_001369711.1:p.Glu1034Lys
NP_001369712.1:p.Glu1034Lys
NP_001369713.1:p.Glu1103Lys
NP_001369714.1:p.Glu1098Lys
NP_001369715.1:p.Glu1091Lys
NP_001369716.1:p.Glu1089Lys
NP_001369717.1:p.Glu1074Lys
NP_001369718.1:p.Glu1071Lys
NP_001369719.1:p.Glu1063Lys
NP_001369720.1:p.Glu1061Lys
NP_001369721.1:p.Glu1052Lys
NP_001369722.1:p.Glu1050Lys
NP_001369723.1:p.Glu1050Lys
NP_001369724.1:p.Glu1048Lys
NP_001369725.1:p.Glu1035Lys
NP_001369726.1:p.Glu1031Lys
NP_001369727.1:p.Glu1012Lys
NP_001369728.1:p.Glu1004Lys
NP_001369729.1:p.Glu1002Lys
NP_001369730.1:p.Glu996Lys
NP_001369731.1:p.Glu978Lys
NP_001369733.1:p.Glu788Lys
NP_001369734.1:p.Glu747Lys
NP_001369735.1:p.Glu718Lys
NP_004439.2:p.Glu1064Lys
NP_004439.2:p.Glu1064Lys
LRG_724t1:c.3100G>A
LRG_724t2:c.3190G>A
LRG_724t4:c.3145G>A
LRG_724:g.44186G>A
LRG_724p1:p.Glu1034Lys
LRG_724p2:p.Glu1064Lys
LRG_724p4:p.Glu1049Lys
NC_000017.10:g.37883578G>A
NM_001005862.2:c.3100G>A
NM_001289936.1:c.3145G>A
NM_004448.3:c.3190G>A
NR_110535.2:n.3428G>A

Protein change:

E1002K

Molecular consequence:

NM_001289937.2:c.3159+322G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382803.1:c.3117+322G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001005862.3:c.3100G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001289936.2:c.3145G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382782.1:c.3100G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382783.1:c.3100G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382784.1:c.3307G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382785.1:c.3292G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382786.1:c.3271G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382787.1:c.3265G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382788.1:c.3220G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382789.1:c.3211G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382790.1:c.3187G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382791.1:c.3181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382792.1:c.3154G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382793.1:c.3148G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382794.1:c.3148G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382795.1:c.3142G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382796.1:c.3103G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382797.1:c.3091G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382798.1:c.3034G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382799.1:c.3010G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382800.1:c.3004G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382801.1:c.2986G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382802.1:c.2932G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382804.1:c.2362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382805.1:c.2239G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382806.1:c.2152G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004448.4:c.3190G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_110535.2:n.3428G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Mus musculus proprotein convertase subtilisin/kexin type 4 (Pcsk4), t...
PREDICTED: Mus musculus proprotein convertase subtilisin/kexin type 4 (Pcsk4), transcript variant X3, mRNA
gi|1907073935|ref|XM_006513360.5|

Nucleotide
PREDICTED: Mus musculus proprotein convertase subtilisin/kexin type 4 (Pcsk4), t...
PREDICTED: Mus musculus proprotein convertase subtilisin/kexin type 4 (Pcsk4), transcript variant X6, mRNA
gi|1907073940|ref|XM_006513363.5|

Nucleotide
Meth_Clone_4T1-P_Round_1
Meth_Clone_4T1-P_Round_1

biosample
vitamin K-dependent protein Z isoform X4 [Homo sapiens]
vitamin K-dependent protein Z isoform X4 [Homo sapiens]
gi|2462538267|ref|XP_054231085.1|

Protein
53556[uid] (0)
Conserved Domains

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003487598	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 11, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003487598

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 11, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003487598.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with ERBB2-related conditions. This variant is present in population databases (rs376450229, gnomAD 0.0009%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1064 of the ERBB2 protein (p.Glu1064Lys).

#	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

Last Updated: Sep 29, 2024

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