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

Recent activity

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Murina rongjiangensis voucher GZHU 15200 cytochrome oxidase subunit 1 (COI) gene...
Murina rongjiangensis voucher GZHU 15200 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
gi|1789824097|gb|MN549082.1|

Nucleotide
Tapinoma melanocephalum
Tapinoma melanocephalum
Tapinoma melanocephalum Raw sequence reads

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001426470	Centogene AG - the Rare Disease Company	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 32860008

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001426470

Centogene AG - the Rare Disease Company

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

de novo

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 14, 2023

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