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NM_182914.3(SYNE2):c.7877A>G (p.Asp2626Gly) AND Emery-Dreifuss muscular dystrophy 5, autosomal dominant

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 14, 2022
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:
RCV001071570.7

Allele description [Variation Report for NM_182914.3(SYNE2):c.7877A>G (p.Asp2626Gly)]

NM_182914.3(SYNE2):c.7877A>G (p.Asp2626Gly)

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.7877A>G (p.Asp2626Gly)
HGVS:
  • NC_000014.9:g.64051790A>G
  • NG_011756.2:g.294892A>G
  • NM_015180.6:c.7877A>G
  • NM_182914.3:c.7877A>GMANE SELECT
  • NP_055995.4:p.Asp2626Gly
  • NP_878918.2:p.Asp2626Gly
  • LRG_872t1:c.7877A>G
  • LRG_872:g.294892A>G
  • LRG_872p1:p.Asp2626Gly
  • NC_000014.8:g.64518508A>G
  • NG_011756.1:g.203826A>G
  • NM_182914.2:c.7877A>G
Protein change:
D2626G
Links:
dbSNP: rs2097229314
NCBI 1000 Genomes Browser:
rs2097229314
Molecular consequence:
  • NM_015180.6:c.7877A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_182914.3:c.7877A>G - 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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001236879Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 14, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV001236879.5

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 2626 of the SYNE2 protein (p.Asp2626Gly). 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 sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 864393). This variant has not been reported in the literature in individuals affected with SYNE2-related conditions. This variant is not present in population databases (gnomAD no frequency).

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

Last Updated: Feb 14, 2024