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NM_001039876.3(SYNE4):c.625G>A (p.Glu209Lys) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Oct 24, 2018
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:
RCV000825246.4

Allele description [Variation Report for NM_001039876.3(SYNE4):c.625G>A (p.Glu209Lys)]

NM_001039876.3(SYNE4):c.625G>A (p.Glu209Lys)

Gene:
SYNE4:spectrin repeat containing nuclear envelope family member 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.12
Genomic location:
Preferred name:
NM_001039876.3(SYNE4):c.625G>A (p.Glu209Lys)
HGVS:
  • NC_000019.10:g.36006665C>T
  • NG_042831.1:g.7129G>A
  • NM_001039876.3:c.625G>AMANE SELECT
  • NM_001297735.3:c.286G>A
  • NP_001034965.1:p.Glu209Lys
  • NP_001284664.1:p.Glu96Lys
  • LRG_1385t1:c.625G>A
  • LRG_1385:g.7129G>A
  • LRG_1385p1:p.Glu209Lys
  • NC_000019.9:g.36497567C>T
  • NM_001039876.1:c.625G>A
  • NM_001039876.2:c.625G>A
  • p.Glu209Lys
Protein change:
E209K
Links:
dbSNP: rs149470089
NCBI 1000 Genomes Browser:
rs149470089
Molecular consequence:
  • NM_001039876.3:c.625G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001297735.3:c.286G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000966530Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Likely benign
(Oct 24, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided22not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000966530.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)

Description

The p.Glu209Lys variant in SYNE4 is classified as likely benign due to a lack of conservation across species. Five mammals (squirrel monkey, bushbaby, david's m yotis, microbat, big brown bat) have a lysine (Lys) at this position. It has bee n identified in 0.04% (11/23762) of African chromosomes by the Genome Aggregatio n Database (gnomAD, http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied : BP4_Strong, PM2_Supporting.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided2not provided2not provided

Last Updated: Sep 29, 2024