NM_014159.7(SETD2):c.1321C>T (p.Arg441Ter) AND Acute megakaryoblastic leukemia without down syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 1, 2020
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:: RCV001293749.1

Allele description [Variation Report for NM_014159.7(SETD2):c.1321C>T (p.Arg441Ter)]

NM_014159.7(SETD2):c.1321C>T (p.Arg441Ter)

Gene:

SETD2:SET domain containing 2, histone lysine methyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_014159.7(SETD2):c.1321C>T (p.Arg441Ter)

HGVS:

NC_000003.12:g.47123315G>A
NG_032091.1:g.45663C>T
NM_001349370.3:c.1189C>T
NM_014159.7:c.1321C>TMANE SELECT
NP_001336299.1:p.Arg397Ter
NP_054878.5:p.Arg441Ter
LRG_775t1:c.1321C>T
LRG_775:g.45663C>T
NC_000003.11:g.47164805G>A
NM_014159.6:c.1321C>T
NR_146158.3:n.1510C>T

Protein change:

R397*

Links:

dbSNP: rs1293916143

NCBI 1000 Genomes Browser:

rs1293916143

Molecular consequence:

NR_146158.3:n.1510C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001349370.3:c.1189C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_014159.7:c.1321C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Acute megakaryoblastic leukemia without down syndrome
Identifiers:: MONDO: MONDO:0018004; MedGen: C5679860

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001480502	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	criteria provided, single submitter (AMP Guidelines, 2017)	Likely pathogenic (Sep 1, 2020)	somatic	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

SCV001480502

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

criteria provided, single submitter

(AMP Guidelines, 2017)

Likely pathogenic
(Sep 1, 2020)

somatic

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	somatic	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN.

J Mol Diagn. 2017 Jan;19(1):4-23. doi: 10.1016/j.jmoldx.2016.10.002. Review.

PubMed [citation]

PMID:: 27993330
PMCID:: PMC5707196

Details of each submission

From Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV001480502.1

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

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

Last Updated: Dec 24, 2023

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