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NC_000007.14:g.152175569_152524553dup AND Kleefstra syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 26, 2020
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:
RCV001542428.1

Allele description [Variation Report for NC_000007.14:g.152175569_152524553dup]

NC_000007.14:g.152175569_152524553dup

Genes:
  • LOC129999676:ATAC-STARR-seq lymphoblastoid active region 26877 [Gene]
  • LOC129999677:ATAC-STARR-seq lymphoblastoid active region 26878 [Gene]
  • LOC129999678:ATAC-STARR-seq lymphoblastoid active region 26879 [Gene]
  • LOC129999679:ATAC-STARR-seq lymphoblastoid active region 26880 [Gene]
  • LOC129999680:ATAC-STARR-seq lymphoblastoid active region 26881 [Gene]
  • LOC129999681:ATAC-STARR-seq lymphoblastoid silent region 18830 [Gene]
  • LOC129999682:ATAC-STARR-seq lymphoblastoid silent region 18831 [Gene]
  • LOC129999683:ATAC-STARR-seq lymphoblastoid silent region 18832 [Gene]
  • LOC129999684:ATAC-STARR-seq lymphoblastoid silent region 18833 [Gene]
  • LOC129389938:MPRA-validated peak6855 silencer [Gene]
  • LOC123956272:Sharpr-MPRA regulatory region 15588 [Gene]
  • LOC123956273:Sharpr-MPRA regulatory region 5889 [Gene]
  • LINC01003:long intergenic non-protein coding RNA 1003 [Gene - HGNC]
  • KMT2C:lysine methyltransferase 2C [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
7q36.1
Genomic location:
Chr7: 152175569 - 152524553 (on Assembly GRCh38)
Preferred name:
NC_000007.14:g.152175569_152524553dup
HGVS:
NC_000007.14:g.152175569_152524553dup
Observations:
1

Condition(s)

Name:
Kleefstra syndrome 2 (KLEFS2)
Identifiers:
MONDO: MONDO:0054701; MedGen: C4540395; OMIM: 617768

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001761130New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Jun 26, 2020) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV001761130.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited 349 kb duplication results in duplication of the first 38 exons (of 59) of the KMT2C gene. The majority of pathogenic variants in KMT2C are nonsense or frameshift [3,4], suggesting loss-of-function is the likely mechanism of disease. Moreover, ClinGen Dosage Sensitivity curation [5] indicates that the KMT2C gene has haploinsufficiency score of 3 (i.e. sufficient evidence for haploinsufficiency) whereas triplosensitivity score is zero (i.e., no evidence for triplosensitivity). There are no additional protein coding genes located within this duplication. Based on the available evidence, the 349 kb duplication inherited from an asymptomatic parent is assessed as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Oct 14, 2023