ClinVar Miner

Submissions for variant NM_001079866.2(BCS1L):c.598C>T (p.Arg200Ter)

gnomAD frequency: 0.00004  dbSNP: rs776838028
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000497971 SCV000590222 pathogenic not provided 2017-06-02 criteria provided, single submitter clinical testing The R200X variant in the BCS1L gene has been reported previously, as identified by whole exome sequencing, in the compound heterozygous state, opposite of a BSC1L missense variant, in a teenage male who also harbored a hemizygous NLGN4X variant, although no phenotypic details were available (Posey et al., 2017). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R200X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret R200X as a pathogenic variant.
Invitae RCV000497971 SCV001583205 pathogenic not provided 2021-08-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg200*) in the BCS1L gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BCS1L are known to be pathogenic (PMID: 12215968, 17314340, 19162478, 19508421, 22277166, 25895478). This variant is present in population databases (rs776838028, ExAC 0.002%). This premature translational stop signal has been observed in individual(s) with BCS1L-related conditions (PMID: 27959697). ClinVar contains an entry for this variant (Variation ID: 374395). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000415338 SCV000328851 pathogenic Mitochondrial complex III deficiency nuclear type 1 2016-05-01 no assertion criteria provided clinical testing Our laboratory reported dual molecular diagnoses in BCS1L (NM_004328.4:c.598C>T; NM_004328.4:c.205C>T ; in trans) and NLGN4X (NM_181332.1:c.301C>T) in an individual with short stature, failure to thrive, rickets, Fanconi syndrome, delayed motor milestones, absent speech, developmental regression, intellectual disability, hypotonia, seizure disorder, gait ataxia, abnormal movements (laughing behavior and tongue protrusion), dysmorphic features, microcephaly, history of seizure disorder.
Counsyl RCV000415338 SCV000796961 likely pathogenic Mitochondrial complex III deficiency nuclear type 1 2018-01-05 no assertion criteria provided clinical testing

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