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NM_003482.4(KMT2D):c.16469_16470del (p.Lys5490fs) AND Kabuki syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 3, 2022
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:
RCV001810066.1

Allele description [Variation Report for NM_003482.4(KMT2D):c.16469_16470del (p.Lys5490fs)]

NM_003482.4(KMT2D):c.16469_16470del (p.Lys5490fs)

Gene:
KMT2D:lysine methyltransferase 2D [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q13.12
Genomic location:
Preferred name:
NM_003482.4(KMT2D):c.16469_16470del (p.Lys5490fs)
HGVS:
  • NC_000012.12:g.49022095_49022096del
  • NG_027827.1:g.38230_38231del
  • NM_003482.4:c.16469_16470delMANE SELECT
  • NP_003473.3:p.Lys5490fs
  • NC_000012.11:g.49415878_49415879del
  • NM_003482.3:c.16469_16470del
Protein change:
K5490fs
Links:
dbSNP: rs1555184624
NCBI 1000 Genomes Browser:
rs1555184624
Molecular consequence:
  • NM_003482.4:c.16469_16470del - 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
SCV0020587753billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 3, 2022) 		germlineclinical testing

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

PMID:21658225

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 3billion, SCV002058775.1

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

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region (PVS1_VS). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). The variant has been reported to be associated with KMT2D related disorder (ClinVar ID: VCV001172600, PMID:21658225). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Jun 23, 2024