ClinVar Miner

Submissions for variant NM_181697.3(PRDX1):c.515-1G>T

gnomAD frequency: 0.00004  dbSNP: rs751828470
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV001815417 SCV002062807 pathogenic not provided 2021-11-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001815417 SCV003517898 pathogenic not provided 2022-05-21 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of PRDX1 exon 6 and aberrant antisense transcription that results in MMACHC promoter hypermethylation and MMACHC silencing (PMID: 29302025). ClinVar contains an entry for this variant (Variation ID: 495209). This variant has been observed in individual(s) with epi-cobalamin C deficiency (PMID: 29302025, 32099815, 34215320). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant in the MMACHC gene. This variant is present in population databases (rs751828470, gnomAD 0.009%). This sequence change falls in intron 5 of the PRDX1 gene. It does not directly change the encoded amino acid sequence of the PRDX1 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein.
Genome-Nilou Lab RCV003451324 SCV004178242 pathogenic Cobalamin C disease 2023-04-11 criteria provided, single submitter clinical testing
OMIM RCV000585802 SCV000693721 pathogenic METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblC TYPE, DIGENIC 2022-11-03 no assertion criteria provided literature only

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