NM_182961.4(SYNE1):c.26345G>A (p.Arg8782Gln) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 26, 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:: RCV001860177.12

Allele description

NM_182961.4(SYNE1):c.26345G>A (p.Arg8782Gln)

Genes:

ESR1:estrogen receptor 1 [Gene - OMIM - HGNC]
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.26345G>A (p.Arg8782Gln)

HGVS:

NC_000006.12:g.152122485C>T
NG_008493.2:g.470795C>T
NG_012855.2:g.519915G>A
NM_001328100.2:c.851-2781C>T
NM_001347701.2:c.*156G>A
NM_001347702.2:c.2879G>A
NM_033071.5:c.26201G>A
NM_182961.4:c.26345G>AMANE SELECT
NP_001334631.1:p.Arg960Gln
NP_149062.1:p.Arg8734Gln
NP_149062.2:p.Arg8734Gln
NP_892006.3:p.Arg8782Gln
LRG_427t1:c.26345G>A
LRG_427t2:c.26201G>A
LRG_427:g.519915G>A
LRG_427p1:p.Arg8782Gln
LRG_427p2:p.Arg8734Gln
LRG_992:g.470795C>T
NC_000006.11:g.152443620C>T
NM_033071.3:c.26201G>A

Protein change:

R8734Q

Links:

dbSNP: rs550697327

NCBI 1000 Genomes Browser:

rs550697327

Molecular consequence:

NM_001347701.2:c.*156G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001328100.2:c.851-2781C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001347702.2:c.2879G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_033071.5:c.26201G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_182961.4:c.26345G>A - 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
SCV002218237	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 26, 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

SCV002218237

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 26, 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 Invitae, SCV002218237.2

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

Description

This sequence change replaces arginine with glutamine at codon 8734 of the SYNE1 protein (p.Arg8734Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs550697327, ExAC 0.02%). This variant has not been reported in the literature in individuals affected with SYNE1-related conditions. ClinVar contains an entry for this variant (Variation ID: 499024). 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: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.

#	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 16, 2024

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