NM_182961.4(SYNE1):c.17464G>C (p.Glu5822Gln) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 30, 2020
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:: RCV001308082.7

Allele description [Variation Report for NM_182961.4(SYNE1):c.17464G>C (p.Glu5822Gln)]

NM_182961.4(SYNE1):c.17464G>C (p.Glu5822Gln)

Genes:

LOC129997480:ATAC-STARR-seq lymphoblastoid active region 25287 [Gene]
SYNE1:spectrin repeat containing nuclear envelope protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q25.2

Genomic location:

Preferred name:

NM_182961.4(SYNE1):c.17464G>C (p.Glu5822Gln)

HGVS:

NC_000006.12:g.152301946C>G
NG_012855.2:g.340454G>C
NM_033071.5:c.17251G>C
NM_182961.4:c.17464G>CMANE SELECT
NP_149062.2:p.Glu5751Gln
NP_892006.3:p.Glu5822Gln
LRG_427t1:c.17464G>C
LRG_427t2:c.17251G>C
LRG_427:g.340454G>C
LRG_427p1:p.Glu5822Gln
NC_000006.11:g.152623081C>G
NM_033071.3:c.17251G>C

Protein change:

E5751Q

Links:

dbSNP: rs2095193468

NCBI 1000 Genomes Browser:

rs2095193468

Molecular consequence:

NM_033071.5:c.17251G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_182961.4:c.17464G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Autosomal recessive ataxia, Beauce type
Synonyms:: ATAXIA, RECESSIVE, OF BEAUCE; Spinocerebellar ataxia, autosomal recessive 8; SYNE1-Related Autosomal Recessive Cerebellar Ataxia
Identifiers:: MONDO: MONDO:0012549; MedGen: C1853116; Orphanet: 88644; OMIM: 610743

Name:: Emery-Dreifuss muscular dystrophy 4, autosomal dominant (EDMD4)
Synonyms:: EMERY-DREIFUSS MUSCULAR DYSTROPHY 4 WITH VARIABLE FEATURES
Identifiers:: MONDO: MONDO:0013071; MedGen: C2751807; Orphanet: 261; OMIM: 612998

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001497517	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 30, 2020)	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

SCV001497517

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 30, 2020)

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, SCV001497517.4

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

Description

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 C25"). 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. This variant has not been reported in the literature in individuals with SYNE1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with glutamine at codon 5751 of the SYNE1 protein (p.Glu5751Gln). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and glutamine.

#	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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