NM_004448.4(ERBB2):c.3250G>T (p.Asp1084Tyr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 3, 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:: RCV001067270.8

Allele description [Variation Report for NM_004448.4(ERBB2):c.3250G>T (p.Asp1084Tyr)]

NM_004448.4(ERBB2):c.3250G>T (p.Asp1084Tyr)

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.3250G>T (p.Asp1084Tyr)

HGVS:

NC_000017.11:g.39727385G>T
NG_007503.1:g.44246G>T
NM_001005862.3:c.3160G>T
NM_001289936.2:c.3205G>T
NM_001289937.2:c.3160-304G>T
NM_001382782.1:c.3160G>T
NM_001382783.1:c.3160G>T
NM_001382784.1:c.3367G>T
NM_001382785.1:c.3352G>T
NM_001382786.1:c.3331G>T
NM_001382787.1:c.3325G>T
NM_001382788.1:c.3280G>T
NM_001382789.1:c.3271G>T
NM_001382790.1:c.3247G>T
NM_001382791.1:c.3241G>T
NM_001382792.1:c.3214G>T
NM_001382793.1:c.3208G>T
NM_001382794.1:c.3208G>T
NM_001382795.1:c.3202G>T
NM_001382796.1:c.3163G>T
NM_001382797.1:c.3151G>T
NM_001382798.1:c.3094G>T
NM_001382799.1:c.3070G>T
NM_001382800.1:c.3064G>T
NM_001382801.1:c.3046G>T
NM_001382802.1:c.2992G>T
NM_001382803.1:c.3118-304G>T
NM_001382804.1:c.2422G>T
NM_001382805.1:c.2299G>T
NM_001382806.1:c.2212G>T
NM_004448.4:c.3250G>TMANE SELECT
NP_001005862.1:p.Asp1054Tyr
NP_001276865.1:p.Asp1069Tyr
NP_001369711.1:p.Asp1054Tyr
NP_001369712.1:p.Asp1054Tyr
NP_001369713.1:p.Asp1123Tyr
NP_001369714.1:p.Asp1118Tyr
NP_001369715.1:p.Asp1111Tyr
NP_001369716.1:p.Asp1109Tyr
NP_001369717.1:p.Asp1094Tyr
NP_001369718.1:p.Asp1091Tyr
NP_001369719.1:p.Asp1083Tyr
NP_001369720.1:p.Asp1081Tyr
NP_001369721.1:p.Asp1072Tyr
NP_001369722.1:p.Asp1070Tyr
NP_001369723.1:p.Asp1070Tyr
NP_001369724.1:p.Asp1068Tyr
NP_001369725.1:p.Asp1055Tyr
NP_001369726.1:p.Asp1051Tyr
NP_001369727.1:p.Asp1032Tyr
NP_001369728.1:p.Asp1024Tyr
NP_001369729.1:p.Asp1022Tyr
NP_001369730.1:p.Asp1016Tyr
NP_001369731.1:p.Asp998Tyr
NP_001369733.1:p.Asp808Tyr
NP_001369734.1:p.Asp767Tyr
NP_001369735.1:p.Asp738Tyr
NP_004439.2:p.Asp1084Tyr
NP_004439.2:p.Asp1084Tyr
LRG_724t2:c.3250G>T
LRG_724:g.44246G>T
LRG_724p2:p.Asp1084Tyr
NC_000017.10:g.37883638G>T
NM_004448.3:c.3250G>T
NR_110535.2:n.3488G>T

Protein change:

D1016Y

Links:

dbSNP: rs200796676

NCBI 1000 Genomes Browser:

rs200796676

Molecular consequence:

NM_001289937.2:c.3160-304G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001382803.1:c.3118-304G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001005862.3:c.3160G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001289936.2:c.3205G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382782.1:c.3160G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382783.1:c.3160G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382784.1:c.3367G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382785.1:c.3352G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382786.1:c.3331G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382787.1:c.3325G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382788.1:c.3280G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382789.1:c.3271G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382790.1:c.3247G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382791.1:c.3241G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382792.1:c.3214G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382793.1:c.3208G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382794.1:c.3208G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382795.1:c.3202G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382796.1:c.3163G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382797.1:c.3151G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382798.1:c.3094G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382799.1:c.3070G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382800.1:c.3064G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382801.1:c.3046G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382802.1:c.2992G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382804.1:c.2422G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382805.1:c.2299G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001382806.1:c.2212G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004448.4:c.3250G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_110535.2:n.3488G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Pandoraea captiosa strain LMG 31118, whole genome shotgun sequence
Pandoraea captiosa strain LMG 31118, whole genome shotgun sequence
gi|1754548356|ref|NZ_CABPSQ01000003

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001232321	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 3, 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

SCV001232321

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 3, 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, SCV001232321.5

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

Description

This variant has not been reported in the literature in individuals affected with ERBB2-related conditions. 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 860880). This variant is present in population databases (rs200796676, gnomAD 0.01%). This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 1084 of the ERBB2 protein (p.Asp1084Tyr).

#	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

ClinVar

Relating variation to medicine