rs778590557
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PM4_SupportingBS1_Supporting
The NM_001211.6(BUB1B):c.1171_1173del(p.Glu391del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000594 in 1,613,974 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.00036 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00062 ( 2 hom. )
Consequence
BUB1B
NM_001211.6 inframe_deletion
NM_001211.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.43
Genes affected
BUB1B (HGNC:1149): (BUB1 mitotic checkpoint serine/threonine kinase B) This gene encodes a kinase involved in spindle checkpoint function. The protein has been localized to the kinetochore and plays a role in the inhibition of the anaphase-promoting complex/cyclosome (APC/C), delaying the onset of anaphase and ensuring proper chromosome segregation. Impaired spindle checkpoint function has been found in many forms of cancer. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_001211.6. Strenght limited to Supporting due to length of the change: 1aa.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000361 (55/152210) while in subpopulation NFE AF= 0.000647 (44/68012). AF 95% confidence interval is 0.000495. There are 0 homozygotes in gnomad4. There are 19 alleles in male gnomad4 subpopulation. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1B | NM_001211.6 | c.1171_1173del | p.Glu391del | inframe_deletion | 9/23 | ENST00000287598.11 | |
LOC107984763 | XR_001751506.2 | n.218-16455_218-16453del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1B | ENST00000287598.11 | c.1171_1173del | p.Glu391del | inframe_deletion | 9/23 | 1 | NM_001211.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000362 AC: 55AN: 152092Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000354 AC: 89AN: 251240Hom.: 0 AF XY: 0.000353 AC XY: 48AN XY: 135792
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GnomAD4 exome AF: 0.000618 AC: 903AN: 1461764Hom.: 2 AF XY: 0.000611 AC XY: 444AN XY: 727184
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 13, 2022 | In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Mosaic variegated aneuploidy syndrome 1 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 29, 2023 | This variant, c.1171_1173del, results in the deletion of 1 amino acid(s) of the BUB1B protein (p.Glu391del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs778590557, gnomAD 0.06%). This variant has been observed in individual(s) with colorectal cancer (PMID: 27239782). This variant is also known as p.Glu390del. ClinVar contains an entry for this variant (Variation ID: 403741). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | St. Jude Molecular Pathology, St. Jude Children's Research Hospital | Nov 13, 2023 | The BUB1B c.1171_1173del (p.Glu391del) change has a maximum subpopulation frequency of 0.065% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The change results in the deletion of a single glutamic acid residue in the BUB3-binding domain. Functional studies indicate that this variant does not affect binding to the spindle assembly checkpoint proteins BUB1 and BUB3 (PMID: 27239782). This variant has been reported in an individual with colorectal cancer (PMID: 27239782). This variant is also known as p.Glu390del in the literature. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2021 | The c.1171_1173delGAG (p.E391del) alteration is located in exon 9 (coding exon 9) of the BUB1B gene. This alteration consists of an in-frame deletion of 3 nucleotides between nucleotide positions c.1171 and c.1173, resulting in the deletion of 1 residue. This variant was detected in two siblings who had early-onset colorectal cancer and breast cancer (<50y); however, it was also detected in their unaffected brother, and in healthy control individuals (Hahn, 2016). Experimental studies showed no significant difference in the binding of BUB1 or BUB3 to BUBR1 between this alteration and wild type (Hahn, 2016). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Colorectal cancer;C1850343:Mosaic variegated aneuploidy syndrome 1;C1864389:Premature chromatid separation trait Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 24, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at