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NM_001754.5(RUNX1):c.330G>T (p.Lys110Asn) AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 9, 2023
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:
RCV003448447.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.330G>T (p.Lys110Asn)]

NM_001754.5(RUNX1):c.330G>T (p.Lys110Asn)

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.330G>T (p.Lys110Asn)
Other names:
NM_001754.5(RUNX1):c.330G>T; p.Lys110Asn
HGVS:
  • NC_000021.9:g.34886864C>A
  • NG_011402.2:g.1102848G>T
  • NM_001001890.3:c.249G>T
  • NM_001122607.2:c.249G>T
  • NM_001754.5:c.330G>TMANE SELECT
  • NP_001001890.1:p.Lys83Asn
  • NP_001116079.1:p.Lys83Asn
  • NP_001745.2:p.Lys110Asn
  • LRG_482:g.1102848G>T
  • NC_000021.8:g.36259161C>A
Protein change:
K110N
Links:
dbSNP: rs1569084082
NCBI 1000 Genomes Browser:
rs1569084082
Molecular consequence:
  • NM_001001890.3:c.249G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001122607.2:c.249G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001754.5:c.330G>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004176250ClinGen Myeloid Malignancy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)		Likely pathogenic
(Dec 9, 2023) 		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, SCV004176250.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_001754.5(RUNX1):c.330G>T (p.Lys110Asn) is a missense variant. This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). REVEL score is greater than 0.88 (0.884) and SpliceAI is not greater than 0.38 (0.00) (PP3). This variant affects one of the hotspot (K110) residues established by the MM-VCEP for RUNX1 (PM1). The c.328A>G variant is the same amino acid change (p.K110E) as a previously established pathogenic variant (ClinVar ID 14465) curated using MM-VCEP rules for RUNX1 (PS1). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM2_supporting, PP3, PM1, PS1.

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

Last Updated: Sep 29, 2024