U.S. flag

An official website of the United States government

NM_182914.3(SYNE2):c.18632C>T (p.Thr6211Met) AND Emery-Dreifuss muscular dystrophy 5, autosomal dominant

Germline classification:
Benign/Likely benign (5 submissions)
Last evaluated:
Jan 28, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000002414.29

Allele description [Variation Report for NM_182914.3(SYNE2):c.18632C>T (p.Thr6211Met)]

NM_182914.3(SYNE2):c.18632C>T (p.Thr6211Met)

Gene:
SYNE2:spectrin repeat containing nuclear envelope protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q23.2
Genomic location:
Preferred name:
NM_182914.3(SYNE2):c.18632C>T (p.Thr6211Met)
Other names:
T89M
HGVS:
  • NC_000014.9:g.64210033C>T
  • NG_011756.2:g.453135C>T
  • NM_015180.6:c.18632C>T
  • NM_182914.3:c.18632C>TMANE SELECT
  • NP_055995.4:p.Thr6211Met
  • NP_878918.2:p.Thr6211Met
  • NP_878918.2:p.Thr6211Met
  • LRG_872t1:c.18632C>T
  • LRG_872:g.453135C>T
  • LRG_872p1:p.Thr6211Met
  • NC_000014.8:g.64676751C>T
  • NG_011756.1:g.362069C>T
  • NM_182914.2:c.18632C>T
  • Q8WXH0:p.Thr6211Met
Protein change:
T6211M; THR89MET
Links:
UniProtKB: Q8WXH0#VAR_062977; OMIM: 608442.0001; dbSNP: rs36215895
NCBI 1000 Genomes Browser:
rs36215895
Molecular consequence:
  • NM_015180.6:c.18632C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_182914.3:c.18632C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Emery-Dreifuss muscular dystrophy 5, autosomal dominant (EDMD5)
Synonyms:
EMERY-DREIFUSS MUSCULAR DYSTROPHY 5
Identifiers:
MONDO: MONDO:0013072; MedGen: C2751805; Orphanet: 261; OMIM: 612999

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000022572OMIM
no assertion criteria provided
Pathogenic
(Dec 1, 2007)
germlineliterature only

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

SCV000387590Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Likely benign
(Apr 27, 2017)
germlineclinical testing

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

Citation Link,

SCV000648899Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 28, 2024)
germlineclinical testing

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

SCV001139472Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)
Benign
(Aug 22, 2023)
germlineclinical testing

Citation Link,

SCV001440044Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Jan 1, 2019)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Nesprin-1 and -2 are involved in the pathogenesis of Emery Dreifuss muscular dystrophy and are critical for nuclear envelope integrity.

Zhang Q, Bethmann C, Worth NF, Davies JD, Wasner C, Feuer A, Ragnauth CD, Yi Q, Mellad JA, Warren DT, Wheeler MA, Ellis JA, Skepper JN, Vorgerd M, Schlotter-Weigel B, Weissberg PL, Roberts RG, Wehnert M, Shanahan CM.

Hum Mol Genet. 2007 Dec 1;16(23):2816-33. Epub 2007 Aug 29.

PubMed [citation]
PMID:
17761684

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
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000022572.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a father and his 2 children with Emery-Dreifuss muscular dystrophy (EDMD5; 612999), Zhang et al. (2007) identified a heterozygous 466C-T transition in exon 3 of the SYNE2 gene, resulting in a thr89-to-met (T89M) substitution in the first spectrin repeat. The father had general weakness since age 37 years, ptosis, increased serum creatine kinase, and left ventricular hypertrophy. His daughter had transient cardiac arrhythmia at age 10 to 14 years, and his son had limb weakness and winged scapulae at age 8 years, minor respiratory insufficiency, but no cardiac involvement. In an unrelated family with EDMD5, an affected woman was heterozygous for the T89M mutation and her affected son was heterozygous for T89M and a variant in the SYNE1 gene (V572L; 608441.0009), which was also present in heterozygosity in the unaffected father, calling into question the pathogenicity of the SYNE1 V572L variant. The mother had a history of muscle weakness and died at 30 years of age from cardiomyopathy, and her son had muscular dystrophy combined with severe dilated cardiomyopathy requiring heart transplant at age 26. The T89M mutation was not found in 384 control alleles. In vitro functional expression assays showed no change in binding of the SYNE2 T89M protein to emerin (EMD; 300384), but patient fibroblasts and muscle cells showed decreased localization of EMD, LMNA (150330), and SYNE2 to the nuclear envelope, impaired binding interactions of these 3 proteins, and disruptions in the organization of intranuclear heterochromatin.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000387590.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000648899.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV001139472.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440044.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024