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NM_003482.4(KMT2D):c.15921+1G>A AND Kabuki syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 31, 2017
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:
RCV000555530.5

Allele description [Variation Report for NM_003482.4(KMT2D):c.15921+1G>A]

NM_003482.4(KMT2D):c.15921+1G>A

Gene:
KMT2D:lysine methyltransferase 2D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.12
Genomic location:
Preferred name:
NM_003482.4(KMT2D):c.15921+1G>A
HGVS:
  • NC_000012.12:g.49024809C>T
  • NG_027827.1:g.35516G>A
  • NM_003482.4:c.15921+1G>AMANE SELECT
  • NC_000012.11:g.49418592C>T
  • NM_003482.3:c.15921+1G>A
Links:
dbSNP: rs1555185299
NCBI 1000 Genomes Browser:
rs1555185299
Molecular consequence:
  • NM_003482.4:c.15921+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000636648Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Mar 31, 2017) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Molecular analysis, pathogenic mechanisms, and readthrough therapy on a large cohort of Kabuki syndrome patients.

Micale L, Augello B, Maffeo C, Selicorni A, Zucchetti F, Fusco C, De Nittis P, Pellico MT, Mandriani B, Fischetto R, Boccone L, Silengo M, Biamino E, Perria C, Sotgiu S, Serra G, Lapi E, Neri M, Ferlini A, Cavaliere ML, Chiurazzi P, Monica MD, et al.

Hum Mutat. 2014 Jul;35(7):841-50. doi: 10.1002/humu.22547. Epub 2014 Apr 9.

PubMed [citation]
PMID:
24633898
PMCID:
PMC4234006
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000636648.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant has not been reported in the literature in individuals with a KMT2D-related disease. In summary, donor and acceptor splice site variants are typically loss-of-function (PMID: 16199547), and loss-of-function variants in KMT2D are known to be pathogenic (PMID: 24633898, 22126750). However, without additional functional and/or genetic data, this variant has been classified as Likely Pathogenic. This sequence change affects a donor splice site in intron 49 of the KMT2D gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

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

Last Updated: Sep 29, 2024