NM_003919.3(SGCE):c.1157C>T (p.Thr386Met) AND Myoclonic dystonia 11

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 27, 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:: RCV003506682.2

Allele description [Variation Report for NM_003919.3(SGCE):c.1157C>T (p.Thr386Met)]

NM_003919.3(SGCE):c.1157C>T (p.Thr386Met)

Genes:

CASD1:CAS1 domain containing 1 [Gene - OMIM - HGNC]
SGCE:sarcoglycan epsilon [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.3

Genomic location:

Preferred name:

NM_003919.3(SGCE):c.1157C>T (p.Thr386Met)

HGVS:

NC_000007.14:g.94598871G>A
NG_008893.3:g.62702C>T
NM_001099400.2:c.1130C>T
NM_001099401.2:c.1157C>T
NM_001301139.2:c.1034C>T
NM_001346713.2:c.1265C>T
NM_001346715.2:c.1238C>T
NM_001346717.2:c.1130C>T
NM_001346719.2:c.1070C>T
NM_001346720.2:c.884C>T
NM_001362807.2:c.1043C>T
NM_001362808.2:c.857C>T
NM_001362809.2:c.1007C>T
NM_003919.3:c.1157C>TMANE SELECT
NP_001092870.1:p.Thr377Met
NP_001092871.1:p.Thr386Met
NP_001288068.1:p.Thr345Met
NP_001333642.1:p.Thr422Met
NP_001333644.1:p.Thr413Met
NP_001333646.1:p.Thr377Met
NP_001333648.1:p.Thr357Met
NP_001333649.1:p.Thr295Met
NP_001349736.1:p.Thr348Met
NP_001349737.1:p.Thr286Met
NP_001349738.1:p.Thr336Met
NP_003910.1:p.Thr386Met
LRG_206t1:c.1157C>T
LRG_206:g.62702C>T
LRG_206p1:p.Thr386Met
NC_000007.13:g.94228183G>A

Protein change:

T286M

Molecular consequence:

NM_001099400.2:c.1130C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099401.2:c.1157C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001301139.2:c.1034C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346713.2:c.1265C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346715.2:c.1238C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346717.2:c.1130C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346719.2:c.1070C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346720.2:c.884C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001362807.2:c.1043C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001362808.2:c.857C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001362809.2:c.1007C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003919.3:c.1157C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Myoclonic dystonia 11 (DYT11)
Synonyms:: Myoclonic dystonia; Dystonia 11; Dystonia, alcohol responsive; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008044; MedGen: C1834570; Orphanet: 36899; OMIM: 159900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004369473	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 27, 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

SCV004369473

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 27, 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, SCV004369473.1

#	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. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SGCE protein function. This variant has not been reported in the literature in individuals affected with SGCE-related conditions. This variant is present in population databases (rs370800943, gnomAD 0.01%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 386 of the SGCE protein (p.Thr386Met).

#	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

ClinVar

Relating variation to medicine