NM_003482.4(KMT2D):c.15858_15859del (p.Tyr5287fs) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 10, 2023
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:: RCV003200493.2

Allele description [Variation Report for NM_003482.4(KMT2D):c.15858_15859del (p.Tyr5287fs)]

NM_003482.4(KMT2D):c.15858_15859del (p.Tyr5287fs)

Gene:

KMT2D:lysine methyltransferase 2D [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.12

Genomic location:

Preferred name:

NM_003482.4(KMT2D):c.15858_15859del (p.Tyr5287fs)

HGVS:

NC_000012.12:g.49024872_49024873del
NG_027827.1:g.35452_35453del
NM_003482.4:c.15858_15859delMANE SELECT
NP_003473.3:p.Tyr5287Serfs
NP_003473.3:p.Tyr5287fs
NC_000012.11:g.49418655_49418656del
NM_003482.3:c.15858_15859delGT

Protein change:

Y5287fs

Molecular consequence:

NM_003482.4:c.15858_15859del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

Recent activity

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Mus musculus tankyrase 1 binding protein 1 (Tnks1bp1), mRNA
Mus musculus tankyrase 1 binding protein 1 (Tnks1bp1), mRNA
gi|157817552|ref|NM_001081260.2|

Nucleotide
YcjD AND (alive[prop]) (40)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003902571	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Mar 10, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003902571

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Mar 10, 2023)

germline

clinical testing

Citation Link

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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

Details of each submission

From Ambry Genetics, SCV003902571.2

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

Description

The c.15858_15859delGT (p.Y5287Sfs*19) alteration, located in exon 49 (coding exon 49) of the KMT2D gene, consists of a deletion of 2 nucleotides from position 15858 to 15859, causing a translational frameshift with a predicted alternate stop codon after 19 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as pathogenic.

#	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: May 1, 2024

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