NM_001127222.2(CACNA1A):c.5393C>T (p.Ser1798Leu) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jul 27, 2022
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:: RCV000485872.7

Allele description [Variation Report for NM_001127222.2(CACNA1A):c.5393C>T (p.Ser1798Leu)]

NM_001127222.2(CACNA1A):c.5393C>T (p.Ser1798Leu)

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.5393C>T (p.Ser1798Leu)

HGVS:

NC_000019.10:g.13231717G>A
NG_011569.1:g.279744C>T
NM_000068.4:c.5411C>T
NM_001127221.2:c.5396C>T
NM_001127222.2:c.5393C>TMANE SELECT
NM_001174080.2:c.5402C>T
NM_023035.3:c.5411C>T
NP_000059.3:p.Ser1804Leu
NP_001120693.1:p.Ser1799Leu
NP_001120693.1:p.Ser1799Leu
NP_001120694.1:p.Ser1798Leu
NP_001167551.1:p.Ser1801Leu
NP_075461.2:p.Ser1804Leu
LRG_7t1:c.5396C>T
LRG_7:g.279744C>T
LRG_7p1:p.Ser1799Leu
NC_000019.9:g.13342531G>A
NM_001127221.1:c.5396C>T
NM_001127222.1:c.5393C>T

Protein change:

S1798L

Links:

dbSNP: rs1064794261

NCBI 1000 Genomes Browser:

rs1064794261

Molecular consequence:

NM_000068.4:c.5411C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127221.2:c.5396C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127222.2:c.5393C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001174080.2:c.5402C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_023035.3:c.5411C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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glutaredoxin [Synechococcus phage ACG-2014f]
glutaredoxin [Synechococcus phage ACG-2014f]
gi|723025623|gb|AIX29554.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000568529	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jul 27, 2022)	germline	clinical testing	Citation Link,
SCV001446865	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 23, 2020)	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

SCV000568529

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jul 27, 2022)

germline

clinical testing

Citation Link,

SCV001446865

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 23, 2020)

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	yes	not provided	not provided	not provided	1	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 GeneDx, SCV000568529.8

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 32899500, 32458086, 24091540, 32116539, 35219921, Kubota2021[Case Report])

#	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		not provided	not provided	not provided	not provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001446865.1

#	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	yes	1	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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