NM_001197104.2(KMT2A):c.7349del (p.Leu2450fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 6, 2018
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:: RCV001008918.1

Allele description [Variation Report for NM_001197104.2(KMT2A):c.7349del (p.Leu2450fs)]

NM_001197104.2(KMT2A):c.7349del (p.Leu2450fs)

Gene:

KMT2A:lysine methyltransferase 2A [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001197104.2(KMT2A):c.7349del (p.Leu2450fs)

HGVS:

NC_000011.10:g.118503241del
NG_027813.1:g.71752del
NM_001197104.2:c.7349delMANE SELECT
NM_005933.4:c.7340del
NP_001184033.1:p.Leu2450fs
NP_005924.2:p.Leu2447fs
LRG_613t1:c.7349del
LRG_613:g.71752del
NC_000011.9:g.118373956del
NM_001197104.1:c.7349delT

Protein change:

L2447fs

Links:

dbSNP: rs1591281736

NCBI 1000 Genomes Browser:

rs1591281736

Molecular consequence:

NM_001197104.2:c.7349del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005933.4:c.7340del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Staphylococcus aureus F54494, whole genome shotgun sequencing project
Staphylococcus aureus F54494, whole genome shotgun sequencing project
gi|582228359|gb|JDIH00000000.1|JDIH 000

Nucleotide
Mus musculus cDNA clone IMAGE:9054096, containing frame-shift errors
Mus musculus cDNA clone IMAGE:9054096, containing frame-shift errors
gi|219519424|gb|BC145533.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168724	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 6, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168724

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 6, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV001168724.1

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

Description

The c.7349delT variant in the KMT2A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.7349delT variant causes a frameshift starting with codon Leucine 2450, changes this amino acid to a Tryptophan residue, and creates a premature Stop codon at position 6 of the new reading frame, denoted p.Leu2450TrpfsX6. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.7349delT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.7349delT as a pathogenic variant.

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

Last Updated: Apr 23, 2022

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