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NM_003482.4(KMT2D):c.3968dup (p.Gly1323_Arg1324insTer) AND Kabuki syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 16, 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:
RCV000853345.1

Allele description [Variation Report for NM_003482.4(KMT2D):c.3968dup (p.Gly1323_Arg1324insTer)]

NM_003482.4(KMT2D):c.3968dup (p.Gly1323_Arg1324insTer)

Genes:
LOC126861520:CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:49442744-49443943 [Gene]
KMT2D:lysine methyltransferase 2D [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
12q13.12
Genomic location:
Preferred name:
NM_003482.4(KMT2D):c.3968dup (p.Gly1323_Arg1324insTer)
HGVS:
  • NC_000012.12:g.49049158dup
  • NG_027827.1:g.11168dup
  • NM_003482.4:c.3968dupMANE SELECT
  • NP_003473.3:p.Gly1323_Arg1324insTer
  • NC_000012.11:g.49442941dup
  • NM_003482.3:c.3968dupG
Links:
dbSNP: rs1592150075
NCBI 1000 Genomes Browser:
rs1592150075
Molecular consequence:
  • NM_003482.4:c.3968dup - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000996207Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 16, 2018) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV000996207.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

This frameshifting variant in exon 12 of 54 introduces a premature stop codon and is therefore predicted to result in loss of normal protein function. This variant has not been previously reported or functionally characterized in the literature to our knowledge, but loss of function variants are an established mechanism of disease for KMT2D. The variant is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.3968dupG, p.Arg1324Ter variant is classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Mar 26, 2023