NM_001754.5(RUNX1):c.209A>C (p.Lys70Thr) AND Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 10, 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:: RCV001936461.5

Allele description [Variation Report for NM_001754.5(RUNX1):c.209A>C (p.Lys70Thr)]

NM_001754.5(RUNX1):c.209A>C (p.Lys70Thr)

Gene:

RUNX1:RUNX family transcription factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.12

Genomic location:

Preferred name:

NM_001754.5(RUNX1):c.209A>C (p.Lys70Thr)

HGVS:

NC_000021.9:g.34886985T>G
NG_011402.2:g.1102727A>C
NM_001001890.3:c.128A>C
NM_001122607.2:c.128A>C
NM_001754.5:c.209A>CMANE SELECT
NP_001001890.1:p.Lys43Thr
NP_001116079.1:p.Lys43Thr
NP_001745.2:p.Lys70Thr
LRG_482:g.1102727A>C
NC_000021.8:g.36259282T>G

Protein change:

K43T

Links:

dbSNP: rs1411791016

NCBI 1000 Genomes Browser:

rs1411791016

Molecular consequence:

NM_001001890.3:c.128A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001122607.2:c.128A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001754.5:c.209A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1
Synonyms:: Platelet disorder, Aspirin-like; Familial platelet disorder with associated myeloid malignancy; Familial Platelet Disorder with Propensity to Acute Myelogenous Leukemia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100083; MeSH: C563324; MedGen: C1832388; Orphanet: 71290; OMIM: 601399

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Fundicoccus fermenti strain:F-1
Fundicoccus fermenti strain:F-1
Novel indigo-reducing bacterial species

BioProject
LAMA2 laminin subunit alpha 2 [Homo sapiens]
LAMA2 laminin subunit alpha 2 [Homo sapiens]
Gene ID:3908

Gene
Gene Links for GEO Profiles (Select 95963931) (1)
Gene
C6orf58 chromosome 6 open reading frame 58 [Homo sapiens]
C6orf58 chromosome 6 open reading frame 58 [Homo sapiens]
Gene ID:352999

Gene
Gene Links for GEO Profiles (Select 95985433) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002197698	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 10, 2020)	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

SCV002197698

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 10, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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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 Invitae, SCV002197698.3

#	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 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"). This variant has not been reported in the literature in individuals with RUNX1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces lysine with threonine at codon 70 of the RUNX1 protein (p.Lys70Thr). The lysine residue is moderately conserved and there is a moderate physicochemical difference between lysine and threonine.

#	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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