NM_005228.5(EGFR):c.3061C>T (p.Gln1021Ter) AND EGFR-related lung cancer

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 27, 2021
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:: RCV001950696.3

Allele description [Variation Report for NM_005228.5(EGFR):c.3061C>T (p.Gln1021Ter)]

NM_005228.5(EGFR):c.3061C>T (p.Gln1021Ter)

Gene:

EGFR:epidermal growth factor receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p11.2

Genomic location:

Preferred name:

NM_005228.5(EGFR):c.3061C>T (p.Gln1021Ter)

HGVS:

NC_000007.14:g.55201302C>T
NG_007726.3:g.187271C>T
NM_001346897.2:c.2926C>T
NM_001346898.2:c.3061C>T
NM_001346899.2:c.2926C>T
NM_001346900.2:c.2902C>T
NM_001346941.2:c.2260C>T
NM_005228.5:c.3061C>TMANE SELECT
NP_001333826.1:p.Gln976Ter
NP_001333827.1:p.Gln1021Ter
NP_001333828.1:p.Gln976Ter
NP_001333829.1:p.Gln968Ter
NP_001333870.1:p.Gln754Ter
NP_005219.2:p.Gln1021Ter
LRG_304:g.187271C>T
NC_000007.13:g.55268995C>T

Protein change:

Q1021*

Links:

dbSNP: rs2128971690

NCBI 1000 Genomes Browser:

rs2128971690

Molecular consequence:

NM_001346897.2:c.2926C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001346898.2:c.3061C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001346899.2:c.2926C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001346900.2:c.2902C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001346941.2:c.2260C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_005228.5:c.3061C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: EGFR-related lung cancer (EGFR)
Identifiers:: MedGen: CN130014

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002219065	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 27, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 7630400, 28726809, 29899996, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002219065

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 27, 2021)

germline

clinical testing

PubMed (4)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Epithelial immaturity and multiorgan failure in mice lacking epidermal growth factor receptor.

Miettinen PJ, Berger JE, Meneses J, Phung Y, Pedersen RA, Werb Z, Derynck R.

Nature. 1995 Jul 27;376(6538):337-41.

PubMed [citation]

PMID:: 7630400

Genomic diagnostics within a medically underserved population: efficacy and implications.

Strauss KA, Gonzaga-Jauregui C, Brigatti KW, Williams KB, King AK, Van Hout C, Robinson DL, Young M, Praveen K, Heaps AD, Kuebler M, Baras A, Reid JG, Overton JD, Dewey FE, Jinks RN, Finnegan I, Mellis SJ, Shuldiner AR, Puffenberger EG.

Genet Med. 2018 Jan;20(1):31-41. doi: 10.1038/gim.2017.76. Epub 2017 Jul 20.

PubMed [citation]

PMID:: 28726809

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV002219065.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with EGFR-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gln1021*) in the EGFR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EGFR are known to be pathogenic (PMID: 7630400, 28726809, 29899996).

#	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: Feb 28, 2024

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