X-120526771-T-TA
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001079872.2(CUL4B):c.2677_2678insT(p.Tyr893LeufsTer17) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 23)
Consequence
CUL4B
NM_001079872.2 frameshift
NM_001079872.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.94
Genes affected
CUL4B (HGNC:2555): (cullin 4B) This gene is a member of the cullin family. The encoded protein forms a complex that functions as an E3 ubiquitin ligase and catalyzes the polyubiquitination of specific protein substrates in the cell. The protein interacts with a ring finger protein, and is required for the proteolysis of several regulators of DNA replication including chromatin licensing and DNA replication factor 1 and cyclin E. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Frameshift in the end of transcript resulting in stoplost. Downstream stopcodon found after 902 codons.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.2677_2678insT | p.Tyr893LeufsTer17 | frameshift_variant | 20/20 | ENST00000371322.11 | |
CUL4B | NM_001330624.2 | c.2692_2693insT | p.Tyr898LeufsTer17 | frameshift_variant | 21/21 | ||
CUL4B | NM_001369145.1 | c.2143_2144insT | p.Tyr715LeufsTer17 | frameshift_variant | 20/20 | ||
CUL4B | NM_003588.4 | c.2731_2732insT | p.Tyr911LeufsTer17 | frameshift_variant | 22/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUL4B | ENST00000371322.11 | c.2677_2678insT | p.Tyr893LeufsTer17 | frameshift_variant | 20/20 | 1 | NM_001079872.2 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD4 exome Cov.: 23
GnomAD4 exome
Cov.:
23
GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
X-linked intellectual disability Cabezas type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 18, 2021 | 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has been observed in individual(s) with clinical features of Cabezas type X-linked syndromic intellectual disability (Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change results in a frameshift in the CUL4B gene (p.Tyr911Leufs*17). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 3 amino acid(s) of the CUL4B protein and extend the protein by 13 additional amino acid residues. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.