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NM_182961.4(SYNE1):c.9715C>G (p.Gln3239Glu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Apr 14, 2021
Accession:
VCV000282775.11
Variation ID:
282775
Description:
single nucleotide variant
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NM_182961.4(SYNE1):c.9715C>G (p.Gln3239Glu)

Allele ID
267012
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q25.2
Genomic location
6: 152369064 (GRCh38) GRCh38 UCSC
6: 152690199 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.152690199G>C
NM_033071.3:c.9736C>G NP_149062.1:p.Gln3246Glu missense
NC_000006.12:g.152369064G>C
... more HGVS
Protein change
Q3239E, Q3246E
Other names
-
Canonical SPDI
NC_000006.12:152369063:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00046
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00069
1000 Genomes Project 0.00020
Links
ClinGen: CA4057232
dbSNP: rs149901087
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000312113.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000391866.2
Likely benign 1 criteria provided, single submitter Nov 13, 2020 RCV001085001.2
Likely benign 1 criteria provided, single submitter Dec 14, 2020 RCV000766628.6
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Apr 14, 2021 RCV000370965.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SYNE1 - - GRCh38
GRCh37
3503 3642

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 04, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000334407.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Oct 05, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001159650.1
Submitted: (Aug 05, 2019)
Evidence details
Comment:
The SYNE1: p.Gln3246Glu variant (rs149901087) has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Spinocerebellar ataxia, autosomal recessive 8
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000461346.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Emery-Dreifuss muscular dystrophy 4, autosomal dominant
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000461345.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Likely benign
(Nov 13, 2020)
criteria provided, single submitter
Method: clinical testing
Emery-Dreifuss muscular dystrophy 4, autosomal dominant
Spinocerebellar ataxia, autosomal recessive 8
Allele origin: germline
Invitae
Accession: SCV001015736.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 14, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV000615697.3
Submitted: (Sep 13, 2021)
Evidence details
Likely benign
(Dec 14, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000581805.4
Submitted: (Sep 30, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SYNE1 - - - -

Text-mined citations for rs149901087...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021