ClinVar Miner

Submissions for variant NM_000067.3(CA2):c.232+1G>A

dbSNP: rs573750741
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726247 SCV000343155 pathogenic not provided 2016-07-15 criteria provided, single submitter clinical testing
GeneDx RCV000726247 SCV001769535 pathogenic not provided 2022-01-10 criteria provided, single submitter clinical testing Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 16382316, 31130284, 25525159, 1301935, 25099932, 25674028, 28509178, 27717089, 15300855, 7959703, 29302074, 29620724, 30510438, 30109220, 32552793)
3billion RCV000373455 SCV002058668 pathogenic Osteopetrosis with renal tubular acidosis 2022-01-03 criteria provided, single submitter clinical testing Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region (PVS1_VS).The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000288909). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000004, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
OMIM RCV000373455 SCV000021116 pathogenic Osteopetrosis with renal tubular acidosis 1992-01-01 no assertion criteria provided literature only
Baylor Genetics RCV000373455 SCV000328860 pathogenic Osteopetrosis with renal tubular acidosis 2015-06-08 no assertion criteria provided clinical testing Our laboratory reported three molecular diagnoses in CA2 (NM_000067.2, c.232+1G>A), MCCC2 (NM_022132.4, c.1015G>A), and SPG11 (NM_025137.3, c.6100C>T) in one individual with clinical features of global developmental delay, developmental regression, autistic features, intellectual disability, hypotonia, ataxia, dysmorphic features, short stature, microcephaly, hyperextensibility, failure to thrive, structural brain abnormalities, skeletal abnormalities, and limb malformation. The CA2 variant has been previously reported as disease-causing [PMID 1301935]. Heterozygotes would be expected to be asymptomatic carriers.
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare RCV000373455 SCV000746078 pathogenic Osteopetrosis with renal tubular acidosis 2017-09-18 no assertion criteria provided clinical testing
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000373455 SCV001132952 pathogenic Osteopetrosis with renal tubular acidosis 2019-08-25 no assertion criteria provided clinical testing

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