NM_001039876.3(SYNE4):c.832C>T (p.Gln278Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 9, 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:: RCV003739879.2

Allele description [Variation Report for NM_001039876.3(SYNE4):c.832C>T (p.Gln278Ter)]

NM_001039876.3(SYNE4):c.832C>T (p.Gln278Ter)

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.832C>T (p.Gln278Ter)

HGVS:

NC_000019.10:g.36006458G>A
NG_042831.1:g.7336C>T
NM_001039876.3:c.832C>TMANE SELECT
NM_001297735.3:c.493C>T
NP_001034965.1:p.Gln278Ter
NP_001284664.1:p.Gln165Ter
LRG_1385t1:c.832C>T
LRG_1385:g.7336C>T
LRG_1385p1:p.Gln278Ter
NC_000019.9:g.36497360G>A

Protein change:

Q165*

Molecular consequence:

NM_001039876.3:c.832C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001297735.3:c.493C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004558223	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 9, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23348741, 28958982, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004558223

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 9, 2023)

germline

clinical testing

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

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004558223.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is present in population databases (rs757248672, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Gln278*) 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). This variant has not been reported in the literature in individuals affected with SYNE4-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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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