NM_001127222.2(CACNA1A):c.6378C>T (p.Ser2126=) AND not specified

Clinical significance:Benign (Last evaluated: Jan 28, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000116530.7

Allele description [Variation Report for NM_001127222.2(CACNA1A):c.6378C>T (p.Ser2126=)]

NM_001127222.2(CACNA1A):c.6378C>T (p.Ser2126=)

Gene:
CACNA1A:calcium voltage-gated channel subunit alpha1 A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_001127222.2(CACNA1A):c.6378C>T (p.Ser2126=)
HGVS:
  • NC_000019.10:g.13209460G>A
  • NG_011569.1:g.302001C>T
  • NM_000068.4:c.6396C>T
  • NM_001127221.1:c.6381C>T
  • NM_001127221.2:c.6381C>T
  • NM_001127222.2:c.6378C>TMANE SELECT
  • NM_001174080.2:c.6387C>T
  • NM_023035.3:c.6396C>T
  • NP_000059.3:p.Ser2132=
  • NP_001120693.1:p.Ser2127=
  • NP_001120693.1:p.Ser2127=
  • NP_001120694.1:p.Ser2126=
  • NP_001167551.1:p.Ser2129=
  • NP_075461.2:p.Ser2132=
  • LRG_7t1:c.6381C>T
  • LRG_7:g.302001C>T
  • LRG_7p1:p.Ser2127=
  • NC_000019.9:g.13320274G>A
  • NM_000068.2:c.6381C>T
Links:
dbSNP: rs16050
NCBI 1000 Genomes Browser:
rs16050
Molecular consequence:
  • NM_000068.4:c.6396C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127221.1:c.6381C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127221.2:c.6381C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127222.2:c.6378C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001174080.2:c.6387C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_023035.3:c.6396C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

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
SCV000150481Genetic Services Laboratory,University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000230675EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Jul 4, 2014)
germlineclinical testing

Citation Link,

SCV000519801GeneDxcriteria provided, single submitter
Benign
(Jan 28, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From Genetic Services Laboratory,University of Chicago, SCV000150481.2

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000230675.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000519801.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

Last Updated: Nov 27, 2021

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