NM_024757.5(EHMT1):c.1922C>T (p.Thr641Met) AND Kleefstra syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 30, 2023
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:: RCV001956954.6

Allele description [Variation Report for NM_024757.5(EHMT1):c.1922C>T (p.Thr641Met)]

NM_024757.5(EHMT1):c.1922C>T (p.Thr641Met)

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.1922C>T (p.Thr641Met)

HGVS:

NC_000009.12:g.137776748C>T
NG_011776.1:g.162757C>T
NM_001145527.2:c.1922C>T
NM_001354259.2:c.1829C>T
NM_001354263.2:c.1901C>T
NM_024757.5:c.1922C>TMANE SELECT
NP_001138999.1:p.Thr641Met
NP_001341188.1:p.Thr610Met
NP_001341192.1:p.Thr634Met
NP_079033.4:p.Thr641Met
NC_000009.11:g.140671200C>T

Protein change:

T610M

Links:

dbSNP: rs1588649675

NCBI 1000 Genomes Browser:

rs1588649675

Molecular consequence:

NM_001145527.2:c.1922C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354259.2:c.1829C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354263.2:c.1901C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024757.5:c.1922C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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PREDICTED: Cucurbita pepo subsp. pepo ERBB-3 BINDING PROTEIN 1-like (LOC11178213...
PREDICTED: Cucurbita pepo subsp. pepo ERBB-3 BINDING PROTEIN 1-like (LOC111782137), mRNA
gi|1333175311|ref|XM_023662937.1|

Nucleotide
nonstructural protein 1 [Influenza A virus]
nonstructural protein 1 [Influenza A virus]
gi|2097121907|gb|UBB57910.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002251184	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 30, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002251184

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 30, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002251184.3

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

Description

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 641 of the EHMT1 protein (p.Thr641Met). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EHMT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1464695). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt EHMT1 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024

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Relating variation to medicine