NM_003482.3(KMT2D):c.11047C>T (p.Gln3683Ter) AND Kabuki syndrome

Clinical significance:Pathogenic (Last evaluated: Mar 5, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001382674.1

Allele description [Variation Report for NM_003482.3(KMT2D):c.11047C>T (p.Gln3683Ter)]

NM_003482.3(KMT2D):c.11047C>T (p.Gln3683Ter)

Gene:
KMT2D:lysine methyltransferase 2D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.12
Genomic location:
Preferred name:
NM_003482.3(KMT2D):c.11047C>T (p.Gln3683Ter)
HGVS:
  • NC_000012.12:g.49033658G>A
  • NG_027827.1:g.26667C>T
  • NM_003482.3:c.11047C>T
  • NP_003473.3:p.Gln3683Ter
  • NC_000012.11:g.49427441G>A
Protein change:
Q3683*
Links:
dbSNP: rs1565779530
NCBI 1000 Genomes Browser:
rs1565779530
Molecular consequence:
  • NM_003482.3:c.11047C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Kabuki syndrome
Synonyms:
Kabuki make-up syndrome; Niikawa-Kuroki syndrome
Identifiers:
MONDO: MONDO:0016512; MedGen: C0796004; OMIM: PS147920

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001581570Invitaecriteria provided, single submitter
Pathogenic
(Mar 5, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome.

Hannibal MC, Buckingham KJ, Ng SB, Ming JE, Beck AE, McMillin MJ, Gildersleeve HI, Bigham AW, Tabor HK, Mefford HC, Cook J, Yoshiura K, Matsumoto T, Matsumoto N, Miyake N, Tonoki H, Naritomi K, Kaname T, Nagai T, Ohashi H, Kurosawa K, Hou JW, et al.

Am J Med Genet A. 2011 Jul;155A(7):1511-6. doi: 10.1002/ajmg.a.34074. Epub 2011 Jun 10.

PubMed [citation]
PMID:
21671394
PMCID:
PMC3121928

How genetically heterogeneous is Kabuki syndrome?: MLL2 testing in 116 patients, review and analyses of mutation and phenotypic spectrum.

Banka S, Veeramachaneni R, Reardon W, Howard E, Bunstone S, Ragge N, Parker MJ, Crow YJ, Kerr B, Kingston H, Metcalfe K, Chandler K, Magee A, Stewart F, McConnell VP, Donnelly DE, Berland S, Houge G, Morton JE, Oley C, Revencu N, Park SM, et al.

Eur J Hum Genet. 2012 Apr;20(4):381-8. doi: 10.1038/ejhg.2011.220. Epub 2011 Nov 30.

PubMed [citation]
PMID:
22126750
PMCID:
PMC3306863
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001581570.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln3683*) in the KMT2D gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with Kabuki syndrome (PMID: 21671394). ClinVar contains an entry for this variant (Variation ID: 635179). Loss-of-function variants in KMT2D are known to be pathogenic (PMID: 22126750). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 7, 2021

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