ClinVar Miner

Submissions for variant NM_001127222.2(CACNA1A):c.6125C>T (p.Thr2042Met)

gnomAD frequency: 0.00003  dbSNP: rs563345694
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000710970 SCV000528222 likely benign not provided 2021-06-18 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 30755392)
Invitae RCV000541910 SCV000656780 likely benign Episodic ataxia type 2; Developmental and epileptic encephalopathy, 42 2024-01-04 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000710970 SCV000841286 uncertain significance not provided 2018-08-27 criteria provided, single submitter clinical testing
Center for Personalized Medicine, Children's Hospital Los Angeles RCV000735340 SCV000854493 uncertain significance Muscle weakness; Spasticity; Hypertonia; Neurogenic bladder; Spastic gait; Abnormal cerebral white matter morphology; Cerebral venous thrombosis; Bone marrow hypocellularity; Myelitis; Abnormal thalamic MRI signal intensity; Abnormal brainstem MRI signal intensity; Combined immunodeficiency criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000710970 SCV000892545 uncertain significance not provided 2018-06-01 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000764178 SCV000895180 uncertain significance Episodic ataxia type 2; Spinocerebellar ataxia type 6; Migraine, familial hemiplegic, 1; Developmental and epileptic encephalopathy, 42 2018-10-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002356583 SCV002656996 likely benign Inborn genetic diseases 2019-01-17 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV003985342 SCV004107122 uncertain significance CACNA1A-related disorder 2022-12-28 criteria provided, single submitter clinical testing The CACNA1A c.6125C>T variant is predicted to result in the amino acid substitution p.Thr2042Met. This variant was reported in an individual with cerebral white matter abnormalities, cerebral venous thrombosis, myelitis, immunodeficiency, and spasticity (referred to as c.6128C>T, p.Thr2043Met in Supplemental Table 2, Ji et al. 2019. PubMed ID: 30755392). This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD ( At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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