NM_024757.5(EHMT1):c.2868-1G>A AND Kleefstra syndrome 1

Germline classification:: Pathogenic (2 submissions)
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:: RCV000055963.4

Allele description [Variation Report for NM_024757.5(EHMT1):c.2868-1G>A]

NM_024757.5(EHMT1):c.2868-1G>A

Gene:

EHMT1:euchromatic histone lysine methyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_024757.5(EHMT1):c.2868-1G>A

HGVS:

NC_000009.12:g.137813005G>A
NG_011776.1:g.199014G>A
NM_001354263.2:c.2847-1G>A
NM_024757.5:c.2868-1G>AMANE SELECT
NC_000009.11:g.140707457G>A
NM_024757.4:c.2868-1G>A

Links:

dbSNP: rs137852722

NCBI 1000 Genomes Browser:

rs137852722

Molecular consequence:

NM_001354263.2:c.2847-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_024757.5:c.2868-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000087003	GeneReviews	no classification provided	not provided	germline	literature only
SCV005045870	Laboratory of Genetics, Children's Clinical University Hospital Latvia	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	curation	PubMed (2) [See all records that cite these PMIDs] 25741868, 39013458

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000087003

GeneReviews

no classification provided

not provided

germline

literature only

SCV005045870

Laboratory of Genetics, Children's Clinical University Hospital Latvia

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

germline

curation

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	germline	yes	not provided	not provided	not provided	not provided	not provided	literature only, curation

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

Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome.

Rots D, Bouman A, Yamada A, Levy M, Dingemans AJM, de Vries BBA, Ruiterkamp-Versteeg M, de Leeuw N, Ockeloen CW, Pfundt R, de Boer E, Kummeling J, van Bon B, van Bokhoven H, Kasri NN, Venselaar H, Alders M, Kerkhof J, McConkey H, Kuechler A, Elffers B, van Beeck Calkoen R, et al.

Am J Hum Genet. 2024 Aug 8;111(8):1605-1625. doi: 10.1016/j.ajhg.2024.06.008. Epub 2024 Jul 15.

PubMed [citation]

PMID:: 39013458
PMCID:: PMC11339614

Details of each submission

From GeneReviews, SCV000087003.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	not provided

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

From Laboratory of Genetics, Children's Clinical University Hospital Latvia, SCV005045870.1

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

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

Last Updated: Oct 8, 2024

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