ClinVar Miner

Submissions for variant NM_001953.5(TYMP):c.1300+1G>A

gnomAD frequency: 0.00001  dbSNP: rs1064792878
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000208711 SCV000797147 likely pathogenic Mitochondrial DNA depletion syndrome 1 2018-01-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV001266751 SCV001444928 pathogenic Inborn genetic diseases 2018-03-28 criteria provided, single submitter clinical testing
Invitae RCV002515561 SCV003444350 pathogenic not provided 2023-08-16 criteria provided, single submitter clinical testing Disruption of this splice site has been observed in individual(s) with mitochondrial neurogastrointestinal encephalomyopathy (PMID: 19056268). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 9 of the TYMP gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is also known as g.4009G>A. ClinVar contains an entry for this variant (Variation ID: 223069). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that disruption of this splice site results in skipping of exon 9, but is expected to preserve the integrity of the reading-frame (PMID: 19056268). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000208711 SCV004207518 pathogenic Mitochondrial DNA depletion syndrome 1 2023-05-10 criteria provided, single submitter clinical testing
GeneReviews RCV000208711 SCV000264551 pathogenic Mitochondrial DNA depletion syndrome 1 2016-01-14 no assertion criteria provided literature only
Natera, Inc. RCV001828047 SCV002081614 pathogenic Mitochondrial neurogastrointestinal encephalomyopathy 2021-06-25 no assertion criteria provided clinical testing

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