NM_182961.4(SYNE1):c.9715C>G (p.Gln3239Glu) AND not specified

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(2);Uncertain significance(1) (Last evaluated: Apr 14, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000370965.6

Allele description [Variation Report for NM_182961.4(SYNE1):c.9715C>G (p.Gln3239Glu)]

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

Gene:
SYNE1:spectrin repeat containing nuclear envelope protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q25.2
Genomic location:
Preferred name:
NM_182961.4(SYNE1):c.9715C>G (p.Gln3239Glu)
HGVS:
  • NC_000006.12:g.152369064G>C
  • NG_012855.2:g.273336C>G
  • NM_033071.3:c.9736C>G
  • NM_033071.5:c.9736C>G
  • NM_182961.4:c.9715C>GMANE SELECT
  • NP_149062.1:p.Gln3246Glu
  • NP_149062.2:p.Gln3246Glu
  • NP_892006.3:p.Gln3239Glu
  • LRG_427t1:c.9715C>G
  • LRG_427t2:c.9736C>G
  • LRG_427:g.273336C>G
  • LRG_427p1:p.Gln3239Glu
  • LRG_427p2:p.Gln3246Glu
  • NC_000006.11:g.152690199G>C
  • NM_182961.2:c.9715C>G
Protein change:
Q3239E
Links:
dbSNP: rs149901087
NCBI 1000 Genomes Browser:
rs149901087
Molecular consequence:
  • NM_033071.3:c.9736C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033071.5:c.9736C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_182961.4:c.9715C>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
7

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000334407EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Likely benign
(Apr 4, 2017)
germlineclinical testing

Citation Link,

SCV000615697Athena Diagnostics Inccriteria provided, single submitter
Likely benign
(Apr 14, 2021)
unknownclinical testing

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

SCV001159650ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratoriescriteria provided, single submitter
Uncertain significance
(Oct 5, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown7not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000334407.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided7not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided7not providednot providednot provided

From Athena Diagnostics Inc, SCV000615697.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001159650.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 laboratory. This variant is listed in the Genome Aggregation Database (gnomAD) with a population frequency of 0.6 percent in the Ashkenazi Jewish population (identified on 62 out of 10,152 chromosomes) and has been reported to the ClinVar database (Variation ID: 282775). The glutamine at position 3246 is moderately conserved and computational analyses of the p.Gln3246Glu variant on protein structure and function provide conflicting results (SIFT: tolerated, PolyPhen-2: possibly damaging). Altogether, there is not enough evidence to classify the p.Gln3246Glu variant with certainty.

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

Last Updated: Nov 11, 2021

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