NM_001205293.3(CACNA1E):c.6248G>A (p.Arg2083Gln) AND Developmental and epileptic encephalopathy, 69

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 11, 2023
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:: RCV001837715.3

Allele description [Variation Report for NM_001205293.3(CACNA1E):c.6248G>A (p.Arg2083Gln)]

NM_001205293.3(CACNA1E):c.6248G>A (p.Arg2083Gln)

Gene:

CACNA1E:calcium voltage-gated channel subunit alpha1 E [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q25.3

Genomic location:

Preferred name:

NM_001205293.3(CACNA1E):c.6248G>A (p.Arg2083Gln)

Other names:

p.Arg2083Gln

HGVS:

NC_000001.11:g.181796707G>A
NG_050616.1:g.318397G>A
NM_000721.4:c.6119G>A
NM_001205293.3:c.6248G>AMANE SELECT
NM_001205294.2:c.6062G>A
NP_000712.2:p.Arg2040Gln
NP_001192222.1:p.Arg2083Gln
NP_001192223.1:p.Arg2021Gln
NC_000001.10:g.181765843G>A
NM_000721.4:c.6119G>A

Protein change:

R2021Q

Links:

dbSNP: rs758936777

NCBI 1000 Genomes Browser:

rs758936777

Molecular consequence:

NM_000721.4:c.6119G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001205293.3:c.6248G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001205294.2:c.6062G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

Unknown function

Observations:

Condition(s)

Name:: Developmental and epileptic encephalopathy, 69
Synonyms:: EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 69
Identifiers:: MONDO: MONDO:0032657; MedGen: C4748988; OMIM: 618285

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002098319	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 1, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002813392	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 19, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004179686	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002098319

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 1, 2021)

germline

clinical testing

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

SCV002813392

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 19, 2021)

unknown

clinical testing

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

SCV004179686

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 11, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
Hindu	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV002098319.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Hindu	1	not provided	not provided	clinical testing	PubMed (1)

Description

A heterozygous missense variation in exon 47 of the CACNA1E gene that results in the amino acid substitution of Glutamine for Arginine at codon 2083 was detected. The observed variant c.6248G>A(p.Arg2083Gln) has not been reported in the 1000 genomes and gnomAD databases. The in silico predictions of the variant are probably damaging by PolyPhen-2(HumDiv) and damaging by SIFT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a variant of uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002813392.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV004179686.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 30, 2023

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