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NM_001039876.3(SYNE4):c.828_829del (p.Cys276fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 27, 2023
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:
RCV003677077.1

Allele description [Variation Report for NM_001039876.3(SYNE4):c.828_829del (p.Cys276fs)]

NM_001039876.3(SYNE4):c.828_829del (p.Cys276fs)

Gene:
SYNE4:spectrin repeat containing nuclear envelope family member 4 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
19q13.12
Genomic location:
Preferred name:
NM_001039876.3(SYNE4):c.828_829del (p.Cys276fs)
HGVS:
  • NC_000019.10:g.36006461CA[2]
  • NG_042831.1:g.7328TG[2]
  • NM_001039876.3:c.828_829delMANE SELECT
  • NM_001297735.3:c.489_490del
  • NP_001034965.1:p.Cys276fs
  • NP_001284664.1:p.Cys163fs
  • LRG_1385t1:c.828_829del
  • LRG_1385:g.7328TG[2]
  • LRG_1385p1:p.Cys276fs
  • NC_000019.9:g.36497363CA[2]
  • NC_000019.9:g.36497363_36497364del
Protein change:
C163fs
Molecular consequence:
  • NM_001039876.3:c.828_829del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001297735.3:c.489_490del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004406033Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 27, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

The LINC complex is essential for hearing.

Horn HF, Brownstein Z, Lenz DR, Shivatzki S, Dror AA, Dagan-Rosenfeld O, Friedman LM, Roux KJ, Kozlov S, Jeang KT, Frydman M, Burke B, Stewart CL, Avraham KB.

J Clin Invest. 2013 Feb;123(2):740-50. doi: 10.1172/JCI66911. Epub 2013 Jan 25.

PubMed [citation]
PMID:
23348741
PMCID:
PMC3561815

A Novel Variant in SYNE4 Confirms its Causative Role in Sensorineural Hearing Loss.

Masterson J, Yıldırım B, Gökkaya E, Tokgöz Yılmaz S, Tekin M.

Balkan Med J. 2018 Mar 15;35(2):196-198. doi: 10.4274/balkanmedj.2017.0946. Epub 2017 Sep 29.

PubMed [citation]
PMID:
28958982
PMCID:
PMC5863260
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004406033.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with SYNE4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys276Trpfs*13) in the SYNE4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SYNE4 are known to be pathogenic (PMID: 23348741, 28958982).

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

Last Updated: Feb 28, 2024