rs113993994
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_016038.4(SBDS):c.297_300del(p.Glu99AspfsTer21) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000112 in 1,613,940 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
SBDS
NM_016038.4 frameshift
NM_016038.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.00
Genes affected
SBDS (HGNC:19440): (SBDS ribosome maturation factor) This gene encodes a highly conserved protein that plays an essential role in ribosome biogenesis. The encoded protein interacts with elongation factor-like GTPase 1 to disassociate eukaryotic initiation factor 6 from the late cytoplasmic pre-60S ribosomal subunit allowing assembly of the 80S subunit. Mutations within this gene are associated with the autosomal recessive disorder Shwachman-Bodian-Diamond syndrome. This gene has a closely linked pseudogene that is distally located. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 7-66993375-GTCTT-G is Pathogenic according to our data. Variant chr7-66993375-GTCTT-G is described in ClinVar as [Pathogenic]. Clinvar id is 21539.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-66993375-GTCTT-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBDS | NM_016038.4 | c.297_300del | p.Glu99AspfsTer21 | frameshift_variant | 3/5 | ENST00000246868.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBDS | ENST00000246868.7 | c.297_300del | p.Glu99AspfsTer21 | frameshift_variant | 3/5 | 1 | NM_016038.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461806Hom.: 0 AF XY: 0.00000825 AC XY: 6AN XY: 727198
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:6Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 20, 2019 | Observed with a second SBDS variant in two other unrelated families in published literature (Shammas et al., 2005); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 15942154, 15701631) - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Aplastic anemia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 07, 2022 | - - |
SBDS-related condition Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 24, 2024 | The SBDS c.297_300delAAGA variant is predicted to result in a frameshift and premature protein termination (p.Glu99Aspfs*21). This variant has been reported to be causative for Shwachman-Diamond Syndrome (Shammas et al. 2005. PubMed ID: 15701631, reported as 292_295delAAAG). This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD. Frameshift variants in SBDS are expected to be pathogenic. This variant is interpreted as pathogenic. - |
Aplastic anemia;C4692625:Shwachman-Diamond syndrome 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 22, 2022 | - - |
Shwachman-Diamond syndrome 1 Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at