ClinVar Miner

Submissions for variant NM_015909.4(NBAS):c.1501C>T (p.Arg501Ter)

gnomAD frequency: 0.00001  dbSNP: rs759960319
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetics and Molecular Pathology, SA Pathology RCV000755658 SCV002761519 likely pathogenic Infantile liver failure syndrome 2 2021-05-18 criteria provided, single submitter clinical testing The NBAS c.1501C>T variant is a single nucleotide change which is predicted to result in premature termination of the protein product at codon 501 (PVS1). This variant has been identified in a patient with short stature, hypogammaglobinaemia, ocular involvement, and elevated liver transaminases (PMID:30825388) (PS4_mod). This variant is in dbSNP (rs759960319) but is rare in population databases (gnomAD 4/251424, 0 homozygotes). This variant has been reported in ClinVar as pathogenic for Infantile liver failure syndrome 2 by another diagnostic laboratory (ClinVar Variation ID: 609275). The NBAS c.1501C>T variant is classified as LIKELY PATHOGENIC (PS4_mod, PVS1)
Labcorp Genetics (formerly Invitae), Labcorp RCV003117538 SCV003786370 pathogenic not provided 2023-12-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg501*) in the NBAS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NBAS are known to be pathogenic (PMID: 26073778, 26541327, 27789416, 28031453). This variant is present in population databases (rs759960319, gnomAD 0.009%). This premature translational stop signal has been observed in individual(s) with NBAS-related conditions (PMID: 30825388). ClinVar contains an entry for this variant (Variation ID: 617878). For these reasons, this variant has been classified as Pathogenic.
Laboratory of Medical Genetics, University of Torino RCV000755658 SCV000882687 pathogenic Infantile liver failure syndrome 2 2018-11-07 no assertion criteria provided clinical testing Found in compound heterozygosity with c.6840G>A

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