NM_004364.5(CEBPA):c.22G>A (p.Glu8Lys) AND Acute myeloid leukemia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 13, 2023
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:: RCV000802599.6

Allele description [Variation Report for NM_004364.5(CEBPA):c.22G>A (p.Glu8Lys)]

NM_004364.5(CEBPA):c.22G>A (p.Glu8Lys)

Genes:

LOC130064183:ATAC-STARR-seq lymphoblastoid silent region 10495 [Gene]
CEBPA:CCAAT enhancer binding protein alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.11

Genomic location:

Preferred name:

NM_004364.5(CEBPA):c.22G>A (p.Glu8Lys)

HGVS:

NC_000019.10:g.33302393C>T
NG_012022.1:g.5132G>A
NM_001285829.2:c.-336G>A
NM_001287424.2:c.127G>A
NM_001287435.2:c.-21G>A
NM_004364.5:c.22G>AMANE SELECT
NP_001274353.1:p.Glu43Lys
NP_004355.2:p.Glu8Lys
NP_004355.2:p.Glu8Lys
LRG_456:g.5132G>A
NC_000019.9:g.33793299C>T
NM_004364.4:c.22G>A

Protein change:

E43K

Links:

dbSNP: rs1600024672

NCBI 1000 Genomes Browser:

rs1600024672

Molecular consequence:

NM_001285829.2:c.-336G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001287435.2:c.-21G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001287424.2:c.127G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004364.5:c.22G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Acute myeloid leukemia (AML)
Synonyms:: Acute myeloid leukemia, adult; AML adult; Acute myelogenous leukemia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018874; MeSH: D015470; MedGen: C0023467; Orphanet: 519; OMIM: 601626; Human Phenotype Ontology: HP:0004808

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000942436	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 2023)	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

SCV000942436

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 2023)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000942436.4

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

Description

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 8 of the CEBPA protein (p.Glu8Lys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CEBPA-related conditions. ClinVar contains an entry for this variant (Variation ID: 647973). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.

#	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: Mar 5, 2024

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