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NM_001754.5(RUNX1):c.637_638del (p.Gln213fs) AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 26, 2024
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV004595742.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.637_638del (p.Gln213fs)]

NM_001754.5(RUNX1):c.637_638del (p.Gln213fs)

Gene:
RUNX1:RUNX family transcription factor 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
21q22.12
Genomic location:
Preferred name:
NM_001754.5(RUNX1):c.637_638del (p.Gln213fs)
Other names:
NM_001754.5:c.637_638del
HGVS:
  • NC_000021.9:g.34834577_34834578del
  • NG_011402.2:g.1155134_1155135del
  • NM_001001890.3:c.556_557del
  • NM_001122607.2:c.556_557del
  • NM_001754.5:c.637_638delMANE SELECT
  • NP_001001890.1:p.Gln186fs
  • NP_001116079.1:p.Gln186fs
  • NP_001745.2:p.Gln213Aspfs
  • NP_001745.2:p.Gln213fs
  • LRG_482t1:c.637_638del
  • LRG_482:g.1155134_1155135del
  • LRG_482p1:p.Gln213Aspfs
  • NC_000021.8:g.36206874_36206875del
  • NM_001754.4:c.637_638delCA
Protein change:
Q186fs
Molecular consequence:
  • NM_001001890.3:c.556_557del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001122607.2:c.556_557del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001754.5:c.637_638del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Identifiers:
MONDO: MONDO:0011071; MedGen: CN281654

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005088348ClinGen Myeloid Malignancy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)		Pathogenic
(Mar 26, 2024) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Myeloid Malignancy Variant Curation Expert Panel, SCV005088348.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_001754.5(RUNX1):c.637_638del (p.Gln213AspfsTer14) is a frameshift variant which is predicted to undergo nonsense mediated decay in a gene in which loss-of-function is an established mechanism (frameshift (-) c.98-c.758 as per VCEP specifications) (PVS1). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_Supporting). This variant is a nonsense/frameshift variants that is downstream of c.98 (PM5_Supporting). In summary, this variant meets criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PVS1, PM2_supporting, PM5_supporting.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 29, 2024