ClinVar Genomic variation as it relates to human health
NM_001127222.2(CACNA1A):c.4633C>T (p.Arg1545Ter)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001127222.2(CACNA1A):c.4633C>T (p.Arg1545Ter)
Variation ID: 8507 Accession: VCV000008507.13
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 19p13.13 19: 13255217 (GRCh38) [ NCBI UCSC ] 19: 13366031 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 15, 2018 Jul 23, 2024 Jun 7, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001127222.2:c.4633C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001120694.1:p.Arg1545Ter nonsense NM_000068.4:c.4645C>T NP_000059.3:p.Arg1549Ter nonsense NM_001127221.2:c.4636C>T NP_001120693.1:p.Arg1546Ter nonsense NM_001174080.2:c.4636C>T NP_001167551.1:p.Arg1546Ter nonsense NM_023035.3:c.4645C>T NP_075461.2:p.Arg1549Ter nonsense NC_000019.10:g.13255217G>A NC_000019.9:g.13366031G>A NG_011569.1:g.256244C>T LRG_7:g.256244C>T LRG_7t1:c.4636C>T LRG_7p1:p.Arg1546Ter - Protein change
- R1549*, R1546*, R1545*
- Other names
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- Canonical SPDI
- NC_000019.10:13255216:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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CACNA1A | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3521 | 3832 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Feb 2, 2022 | RCV000009032.8 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 11, 2016 | RCV000622947.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 5, 2021 | RCV000763032.3 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Dec 9, 2022 | RCV002466397.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Jun 7, 2023 | RCV002512927.3 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Oct 15, 2018)
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criteria provided, single submitter
Method: curation
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Episodic ataxia type 2
Affected status: unknown
Allele origin:
unknown
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SIB Swiss Institute of Bioinformatics
Accession: SCV000883282.1
First in ClinVar: May 09, 2018 Last updated: May 09, 2018 |
Comment:
This variant is interpreted as Likely Pathogenic, for Episodic ataxia 2, autosomal dominant. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or … (more)
This variant is interpreted as Likely Pathogenic, for Episodic ataxia 2, autosomal dominant. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PVS1-Strong => PVS1 downgraded in strength to Strong. PP1-Moderate => PP1 upgraded in strength to Moderate (https://www.ncbi.nlm.nih.gov/pubmed/10408533). (less)
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Pathogenic
(Apr 08, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV002770606.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
Comment:
This variant segregates with episodic ataxia in at least one family. This variant was not reported in large, multi-ethnic, general populations (http://gnomad.broadinstitute.org). In some published … (more)
This variant segregates with episodic ataxia in at least one family. This variant was not reported in large, multi-ethnic, general populations (http://gnomad.broadinstitute.org). In some published literature, this variant is referred to as p.R1549X. Assessment of experimental evidence suggests this variant results in abnormal protein function. This variant diminished calcium channel activity (PMID: 11723274, 16306128). (less)
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Pathogenic
(Sep 05, 2021)
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criteria provided, single submitter
Method: clinical testing
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Episodic ataxia type 2
Migraine, familial hemiplegic, 1 Spinocerebellar ataxia type 6 Developmental and epileptic encephalopathy, 42
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000893507.2
First in ClinVar: Mar 31, 2019 Last updated: Dec 31, 2022 |
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Pathogenic
(Jun 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Developmental and epileptic encephalopathy, 42
Episodic ataxia type 2
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003443180.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 28, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this premature translational stop signal affects CACNA1A function (PMID: 11723274). … (more)
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this premature translational stop signal affects CACNA1A function (PMID: 11723274). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 8507). This variant is also known as p.Arg1549*. This premature translational stop signal has been observed in individual(s) with CACNA1A-related conditions (PMID: 29062094, 29883219, 31302675). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg1546*) in the CACNA1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CACNA1A are known to be pathogenic (PMID: 10371528, 19486177, 25735478, 27250579). (less)
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Pathogenic
(Feb 02, 2022)
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criteria provided, single submitter
Method: clinical testing
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Episodic ataxia type 2
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002767074.2
First in ClinVar: Dec 24, 2022 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with CACNA1A-related disease. Episodic ataxia, type 2 (MIM#108500) is caused by variants with a loss of function mechanism (PMID: 28566750). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. Reduced penetrance has been reported for patients with episodic ataxia type 2 (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity. Two families with episodic ataxia, intellectual disability and/or epilepsy have been reported with intrafamilial variability (PMID: 32910250, PMID: 30142438). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other variants predicted to result in NMD comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER, ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been previously reported in patients with episodic ataxia type 2 (ClinVar, PMID: 10408533, PMID: 29883219). (SP) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Oct 25, 2019)
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criteria provided, single submitter
Method: research
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Episodic ataxia type 2
Affected status: yes
Allele origin:
paternal
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HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: CSER-SouthSeq
Accession: SCV001190491.1 First in ClinVar: May 09, 2018 Last updated: May 09, 2018 |
Comment:
ACMG codes: PVS1, PS3, PM2, PP5
Number of individuals with the variant: 1
Clinical Features:
Imperforate anus (present) , Abnormal vertebral morphology (present) , Ebstein anomaly of the tricuspid valve (present) , Imperforate anus (present) , Patent foramen ovale (present) … (more)
Imperforate anus (present) , Abnormal vertebral morphology (present) , Ebstein anomaly of the tricuspid valve (present) , Imperforate anus (present) , Patent foramen ovale (present) , Hemivertebrae (present) (less)
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Pathogenic
(Dec 09, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV002762252.1
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022 |
Comment:
Described as R1549X and R1547X using alternate nomenclature, published functional studies demonstrate markedly decreased current densities compared to wild type (Jen et al., 2001; Jeng … (more)
Described as R1549X and R1547X using alternate nomenclature, published functional studies demonstrate markedly decreased current densities compared to wild type (Jen et al., 2001; Jeng et al., 2006); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 10408533, 29062094, 29482223, 16306128, 25525159, 29883219, 11723274) (less)
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Pathogenic
(Oct 11, 2016)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV000741874.3
First in ClinVar: Apr 15, 2018 Last updated: Jan 07, 2023 |
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Delayed speech and language development (present) , Encephalopathy (present) , Meningitis (present) , Strabismus (present) , Falls (present)
Sex: male
Ethnicity/Population group: Caucasian/Moroccan/Irish
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Median cleft lip and palate (present) , Coarctation of aorta (present) , Neurodevelopmental delay (present) , Microcephaly (present) , Positional foot deformity (present) , Strabismus … (more)
Median cleft lip and palate (present) , Coarctation of aorta (present) , Neurodevelopmental delay (present) , Microcephaly (present) , Positional foot deformity (present) , Strabismus (present) , Hypertelorism (present) , Wide nasal base (present) , Long palpebral fissure (present) , Long eyelashes (present) , Eversion of lateral third of lower eyelids (present) , Long philtrum (present) , Short columella (present) , Thin upper lip vermilion (present) , Preauricular pit (present) , Nevus flammeus of the forehead (present) , Cupped ear (present) , Prominent fingertip pads (present) , Single transverse palmar crease (present) , Broad thumb (present) , 2-3 toe syndactyly (present) , Brachydactyly (present) , Sleep apnea (present) , Asthma (present) , Torticollis (present) , Ventricular septal defect (present) , Prolonged neonatal jaundice (present) , Feeding difficulties in infancy (present) , Pes planus (present) , Constipation (present) , Robin sequence (present) , Gastrointestinal obstruction (present) , Branchial anomaly (present) , Protruding ear (present) (less)
Sex: female
Ethnicity/Population group: Hispanic
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Pathogenic
(Jul 13, 1999)
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no assertion criteria provided
Method: literature only
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EPISODIC ATAXIA, TYPE 2
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000029249.5
First in ClinVar: Apr 04, 2013 Last updated: Aug 29, 2020 |
Comment on evidence:
Jen et al. (1999) reported affected members of a family with episodic ataxia type 2 (EA2; 108500) who carried a 4914C-T substitution in exon 29 … (more)
Jen et al. (1999) reported affected members of a family with episodic ataxia type 2 (EA2; 108500) who carried a 4914C-T substitution in exon 29 of the CACNA1A gene. The substitution resulted in an arg1549-to-ter (R1549X) mutation (reported in the article as ARG1547TER) that predicts a truncated product containing the first 3 domains of the protein. The patients experienced attacks of vertigo, truncal and limb ataxia, nystagmus, and diffuse weakness during ataxic spells. See also 601011.0020. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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A novel pathogenic CACNA1A variant causing episodic ataxia type 2 (EA2) spectrum phenotype in four family members and a novel combined therapy. | Penkava J | Journal of neurology | 2020 | PMID: 32910250 |
Incidence and phenotypes of childhood-onset genetic epilepsies: a prospective population-based national cohort. | Symonds JD | Brain : a journal of neurology | 2019 | PMID: 31302675 |
Major intra-familial phenotypic heterogeneity and incomplete penetrance due to a CACNA1A pathogenic variant. | Angelini C | European journal of medical genetics | 2019 | PMID: 30142438 |
Episodic ataxia type 2 characterised by recurrent dizziness/vertigo: a report of four cases. | Ling X | The International journal of neuroscience | 2019 | PMID: 29883219 |
Genetic Variants Associated with Episodic Ataxia in Korea. | Choi KD | Scientific reports | 2017 | PMID: 29062094 |
Mutation Spectrum in the CACNA1A Gene in 49 Patients with Episodic Ataxia. | Sintas C | Scientific reports | 2017 | PMID: 28566750 |
Biallelic CACNA1A mutations cause early onset epileptic encephalopathy with progressive cerebral, cerebellar, and optic nerve atrophy. | Reinson K | American journal of medical genetics. Part A | 2016 | PMID: 27250579 |
CACNA1A haploinsufficiency causes cognitive impairment, autism and epileptic encephalopathy with mild cerebellar symptoms. | Damaj L | European journal of human genetics : EJHG | 2015 | PMID: 25735478 |
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. | Xiong HY | Science (New York, N.Y.) | 2015 | PMID: 25525159 |
CACNA1A nonsense mutation is associated with basilar-type migraine and episodic ataxia type 2. | Robbins MS | Headache | 2009 | PMID: 19486177 |
Dominant-negative effects of human P/Q-type Ca2+ channel mutations associated with episodic ataxia type 2. | Jeng CJ | American journal of physiology. Cell physiology | 2006 | PMID: 16306128 |
Clinical spectrum of episodic ataxia type 2. | Jen J | Neurology | 2004 | PMID: 14718690 |
Presynaptic failure of neuromuscular transmission and synaptic remodeling in EA2. | Maselli RA | Neurology | 2003 | PMID: 14694040 |
Effect of inherited abnormalities of calcium regulation on human neuromuscular transmission. | Maselli RA | Annals of the New York Academy of Sciences | 2003 | PMID: 14592859 |
Loss-of-function EA2 mutations are associated with impaired neuromuscular transmission. | Jen J | Neurology | 2001 | PMID: 11723274 |
A novel nonsense mutation in CACNA1A causes episodic ataxia and hemiplegia. | Jen J | Neurology | 1999 | PMID: 10408533 |
High prevalence of CACNA1A truncations and broader clinical spectrum in episodic ataxia type 2. | Denier C | Neurology | 1999 | PMID: 10371528 |
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Text-mined citations for rs121909324 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.