NM_182961.4(SYNE1):c.16831C>T (p.Arg5611Trp) AND Emery-Dreifuss muscular dystrophy 4, autosomal dominant

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Jan 1, 2019
Review status:: criteria provided, conflicting classifications

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:: RCV000785032.11

Allele description [Variation Report for NM_182961.4(SYNE1):c.16831C>T (p.Arg5611Trp)]

NM_182961.4(SYNE1):c.16831C>T (p.Arg5611Trp)

Genes:

LOC126859837:BRD4-independent group 4 enhancer GRCh37_chr6:152630775-152631974 [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.16831C>T (p.Arg5611Trp)

HGVS:

NC_000006.12:g.152310753G>A
NG_012855.2:g.331647C>T
NM_033071.5:c.16618C>T
NM_182961.4:c.16831C>TMANE SELECT
NP_149062.1:p.Arg5540Trp
NP_149062.2:p.Arg5540Trp
NP_892006.3:p.Arg5611Trp
LRG_427t1:c.16831C>T
LRG_427t2:c.16618C>T
LRG_427:g.331647C>T
LRG_427p1:p.Arg5611Trp
LRG_427p2:p.Arg5540Trp
NC_000006.11:g.152631888G>A
NM_033071.3:c.16618C>T
NM_182961.2:c.16831C>T
NM_182961.3:c.16831C>T

Protein change:

R5540W

Links:

dbSNP: rs369292604

NCBI 1000 Genomes Browser:

rs369292604

Molecular consequence:

NM_033071.5:c.16618C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_182961.4:c.16831C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

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

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
SCV000461109	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 12, 2018)	germline	clinical testing	Citation Link,
SCV000923585	Genomic Research Center, Shahid Beheshti University of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 1, 2019)	unknown	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

SCV000461109

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 12, 2018)

germline

clinical testing

Citation Link,

SCV000923585

Genomic Research Center, Shahid Beheshti University of Medical Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 1, 2019)

unknown

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	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000461109.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000923585.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 16, 2025

ClinVar

Relating variation to medicine