ClinVar Miner

Submissions for variant NM_025243.4(SLC19A3):c.980-14A>G

gnomAD frequency: 0.00008  dbSNP: rs200542114
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000514518 SCV000610996 pathogenic not provided 2017-06-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000697912 SCV000826546 pathogenic Biotin-responsive basal ganglia disease 2025-01-27 criteria provided, single submitter clinical testing This sequence change falls in intron 3 of the SLC19A3 gene. It does not directly change the encoded amino acid sequence of the SLC19A3 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs200542114, gnomAD 0.02%). This variant has been observed in individuals with thiamine metabolism dysfunction syndrome 2, also known as biotin-responsive basal ganglia disease (PMID: 20065143, 22777947, 24957181, 26657515). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 446038). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 20065143, 26657515). For these reasons, this variant has been classified as Pathogenic.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000514518 SCV001447110 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000697912 SCV002020636 pathogenic Biotin-responsive basal ganglia disease 2021-06-25 criteria provided, single submitter clinical testing
GeneDx RCV000514518 SCV002584253 pathogenic not provided 2024-12-29 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect (PMID: 20065143); This variant is associated with the following publications: (PMID: 27621386, 24957181, 20065143, 26657515, 31589614, 31440721, 31557427, 34352085, 31061755, 31095747, 34276785, 35094435, 34631424, 32600842, 22777947)
Fulgent Genetics, Fulgent Genetics RCV000697912 SCV002803833 pathogenic Biotin-responsive basal ganglia disease 2023-12-21 criteria provided, single submitter clinical testing
OMIM RCV000697912 SCV000025002 pathogenic Biotin-responsive basal ganglia disease 2010-01-01 no assertion criteria provided literature only

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