NM_003482.4(KMT2D):c.15108_15110del (p.His5036_Glu5037delinsGln) AND Kabuki syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 13, 2022
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV002466280.1

Allele description [Variation Report for NM_003482.4(KMT2D):c.15108_15110del (p.His5036_Glu5037delinsGln)]

NM_003482.4(KMT2D):c.15108_15110del (p.His5036_Glu5037delinsGln)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

12q13.12

Genomic location:

Preferred name:

NM_003482.4(KMT2D):c.15108_15110del (p.His5036_Glu5037delinsGln)

HGVS:

NC_000012.12:g.49026857_49026859del
NG_027827.1:g.33467_33469del
NM_003482.4:c.15108_15110delMANE SELECT
NP_003473.3:p.His5036_Glu5037delinsGln
NC_000012.11:g.49420640_49420642del
NM_003482.4:c.15108_15110delTGAMANE SELECT

Molecular consequence:

NM_003482.4:c.15108_15110del - inframe_indel - [Sequence Ontology: SO:0001820]

Observations:

Condition(s)

Name:: Kabuki syndrome 1 (KABUK1)
Identifiers:: MONDO: MONDO:0007843; MedGen: CN030661; Orphanet: 2322; OMIM: 147920

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002525858	Department of Medical Genetics, National Institute of Health	no assertion criteria provided	Pathogenic (Jun 13, 2022)	de novo	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002525858

Department of Medical Genetics, National Institute of Health

no assertion criteria provided

Pathogenic
(Jun 13, 2022)

de novo

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
Moroccan	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Department of Medical Genetics, National Institute of Health, SCV002525858.1

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

Description

We report the case of a 13- year-old Moroccan girl presenting with typic facial dysmorphy of Kabuki syndrome and psychomotor delay with mental retardation. Clinical exome sequencing identified a novel heterozygous variant: NM_003482.4(KMT2D):c.15108_15110delTGA (p.His5036_Glu5037delinsGln) in exon 49 of the KMT2D gene. This variant has not been previously reported and was not found in 138 Moroccan Clinical exomes (in-house database). It is classified as pathogenic on American College of Medical Genetics and Genomics (ACMG) according to these criteria: PM1,PM2,PM4, and PP3.

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

Last Updated: Dec 17, 2022

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