NM_024757.5(EHMT1):c.1997G>C (p.Arg666Thr) AND Kleefstra syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 25, 2021
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:: RCV002024581.6

Allele description [Variation Report for NM_024757.5(EHMT1):c.1997G>C (p.Arg666Thr)]

NM_024757.5(EHMT1):c.1997G>C (p.Arg666Thr)

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.1997G>C (p.Arg666Thr)

HGVS:

NC_000009.12:g.137776823G>C
NG_011776.1:g.162832G>C
NM_001145527.2:c.1997G>C
NM_001354259.2:c.1904G>C
NM_001354263.2:c.1976G>C
NM_024757.5:c.1997G>CMANE SELECT
NP_001138999.1:p.Arg666Thr
NP_001341188.1:p.Arg635Thr
NP_001341192.1:p.Arg659Thr
NP_079033.4:p.Arg666Thr
NC_000009.11:g.140671275G>C

Protein change:

R635T

Links:

dbSNP: rs1588650026

NCBI 1000 Genomes Browser:

rs1588650026

Molecular consequence:

NM_001145527.2:c.1997G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354259.2:c.1904G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354263.2:c.1976G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024757.5:c.1997G>C - 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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GPN-loop GTPase 2 isoform 1 [Mus musculus]
GPN-loop GTPase 2 isoform 1 [Mus musculus]
gi|227499701|ref|NP_598645.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002316083	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 25, 2021)	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

SCV002316083

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 25, 2021)

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, SCV002316083.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with EHMT1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with threonine at codon 666 of the EHMT1 protein (p.Arg666Thr). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and threonine.

#	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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