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NM_024757.5(EHMT1):c.21+1_21+5del AND Kleefstra syndrome 1

Germline classification:
Likely pathogenic (1 submission)
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:
RCV001251096.1

Allele description [Variation Report for NM_024757.5(EHMT1):c.21+1_21+5del]

NM_024757.5(EHMT1):c.21+1_21+5del

Genes:
LOC130003135:ATAC-STARR-seq lymphoblastoid silent region 20636 [Gene]
EHMT1:euchromatic histone lysine methyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_024757.5(EHMT1):c.21+1_21+5del
HGVS:
  • NC_000009.12:g.137619050_137619054del
  • NG_011776.1:g.5059_5063del
  • NM_001145527.2:c.21+1_21+5del
  • NM_001354259.2:c.-9+1_-9+5del
  • NM_001354263.2:c.21+1_21+5del
  • NM_001354611.2:c.21+1_21+5del
  • NM_001354612.2:c.-9+1_-9+5del
  • NM_024757.5:c.21+1_21+5delMANE SELECT
  • NC_000009.11:g.140513502_140513506del
  • NM_024757.4:c.21+1_21+5del
Links:
dbSNP: rs1842769868
NCBI 1000 Genomes Browser:
rs1842769868
Molecular consequence:
  • NM_001145527.2:c.21+1_21+5del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354259.2:c.-9+1_-9+5del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354263.2:c.21+1_21+5del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354611.2:c.21+1_21+5del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354612.2:c.-9+1_-9+5del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_024757.5:c.21+1_21+5del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Kleefstra syndrome 1
Identifiers:
MONDO: MONDO:0027407; MedGen: C0795833; Orphanet: 261494; OMIM: 610253

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001426470Centogene AG - the Rare Disease Company
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicde novoclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyesnot providednot providednot providednot providednot 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

Successful application of genome sequencing in a diagnostic setting: 1007 index cases from a clinically heterogeneous cohort.

Bertoli-Avella AM, Beetz C, Ameziane N, Rocha ME, Guatibonza P, Pereira C, Calvo M, Herrera-Ordonez N, Segura-Castel M, Diego-Alvarez D, Zawada M, Kandaswamy KK, Werber M, Paknia O, Zielske S, Ugrinovski D, Warnack G, Kampe K, Iurașcu MI, Cozma C, Vogel F, Alhashem A, et al.

Eur J Hum Genet. 2021 Jan;29(1):141-153. doi: 10.1038/s41431-020-00713-9. Epub 2020 Aug 28.

PubMed [citation]
PMID:
32860008
PMCID:
PMC7852664

Details of each submission

From Centogene AG - the Rare Disease Company, SCV001426470.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 14, 2023