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NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=) AND not specified

Germline classification:
Benign (10 submissions)
Last evaluated:
Jul 15, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000116523.38

Allele description [Variation Report for NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=)]

NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=)

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.3057G>A (p.Arg1019=)
HGVS:
  • NC_000019.10:g.13298576C>T
  • NG_011569.1:g.212885G>A
  • NM_000068.4:c.3069G>A
  • NM_001127221.2:c.3060G>A
  • NM_001127222.2:c.3057G>AMANE SELECT
  • NM_001174080.2:c.3060G>A
  • NM_023035.3:c.3069G>A
  • NP_000059.3:p.Arg1023=
  • NP_001120693.1:p.Arg1020=
  • NP_001120693.1:p.Arg1020=
  • NP_001120694.1:p.Arg1019=
  • NP_001167551.1:p.Arg1020=
  • NP_075461.2:p.Arg1023=
  • LRG_7t1:c.3060G>A
  • LRG_7:g.212885G>A
  • LRG_7p1:p.Arg1020=
  • NC_000019.9:g.13409390C>T
  • NM_000068.2:c.3060G>A
  • NM_001127221.1:c.3060G>A
  • NM_001127222.1:c.3057G>A
  • NP_001120693.1:p.(=)
  • p.Arg1020Arg
Links:
dbSNP: rs16025
NCBI 1000 Genomes Browser:
rs16025
Molecular consequence:
  • NM_000068.4:c.3069G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127221.2:c.3060G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127222.2:c.3057G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001174080.2:c.3060G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_023035.3:c.3069G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
34

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
SCV000150472Genetic Services Laboratory, University of Chicago
no assertion criteria provided
Likely benigngermlineclinical testing

SCV000202321Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Benign
(Mar 18, 2014)
germlineclinical testing

Citation Link,

SCV000306695PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benigngermlineclinical testing

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

SCV000518852GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Jan 8, 2016)
germlineclinical testing

Citation Link,

SCV000841259Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics criteria)
Benign
(May 3, 2021)
unknownclinical testing

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

SCV001744040Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Benigngermlineclinical testing

SCV001927163Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV001958697Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV001969241Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV005087884Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Jul 15, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown6not providednot providednot providednot providedclinical testing
not providedgermlineno28not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000150472.2

#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 Eurofins Ntd Llc (ga), SCV000202321.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided6not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided6not providednot providednot provided

From PreventionGenetics, part of Exact Sciences, SCV000306695.1

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

From GeneDx, SCV000518852.4

#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

From Athena Diagnostics, SCV000841259.3

#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 Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001744040.3

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001927163.1

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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001958697.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001969241.1

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

From Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan, SCV005087884.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided28not providednot providedclinical testing PubMed (1)

Description

This variant is classified as Benign based on local population frequency. This variant was detected in 30% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 28. Only high quality variants are reported.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot provided28not providednot providednot provided

Last Updated: May 16, 2025