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:: RCV003677077.2

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

Recent activity

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PRELI domain-containing protein 1, mitochondrial [Rattus norvegicus]
PRELI domain-containing protein 1, mitochondrial [Rattus norvegicus]
gi|57526905|ref|NP_001009636.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004406033	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 27, 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

SCV004406033

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 27, 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, SCV004406033.1

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

#	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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