10-129840949-CTG-C
Position:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001375380.1(EBF3):c.1454_1455del(p.Thr485SerfsTer4) 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 Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
EBF3
NM_001375380.1 frameshift
NM_001375380.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 10.0
Genes affected
EBF3 (HGNC:19087): (EBF transcription factor 3) This gene encodes a member of the early B-cell factor (EBF) family of DNA binding transcription factors. EBF proteins are involved in B-cell differentiation, bone development and neurogenesis, and may also function as tumor suppressors. The encoded protein inhibits cell survival through the regulation of genes involved in cell cycle arrest and apoptosis, and aberrant methylation or deletion of this gene may play a role in multiple malignancies including glioblastoma multiforme and gastric carcinoma. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 10-129840949-CTG-C is Pathogenic according to our data. Variant chr10-129840949-CTG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2674611.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EBF3 | NM_001375380.1 | c.1454_1455del | p.Thr485SerfsTer4 | frameshift_variant | 14/17 | ENST00000440978.2 | NP_001362309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBF3 | ENST00000440978.2 | c.1454_1455del | p.Thr485SerfsTer4 | frameshift_variant | 14/17 | 3 | NM_001375380.1 | ENSP00000387543 | ||
EBF3 | ENST00000368648.8 | c.1427_1428del | p.Thr476SerfsTer4 | frameshift_variant | 15/17 | 1 | ENSP00000357637 | A1 | ||
EBF3 | ENST00000355311.10 | c.1454_1455del | p.Thr485SerfsTer4 | frameshift_variant | 14/16 | 5 | ENSP00000347463 | P4 | ||
EBF3 | ENST00000675373.1 | n.1099_1100del | non_coding_transcript_exon_variant | 11/14 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypotonia, ataxia, and delayed development syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center | Apr 09, 2020 | The c.1427_1428delCA (p.Thr476SerfsTer4) variant in the EBF3 gene is a heterozygous frameshift variant, resulting in a premature stop codon downstream. This variant localizes to coding exon 14 of the gene (16 coding exons in total; NM_001005463.3). This variant is absent in the Genome Aggregation Database (gnomAD), indicating it is not a common benign variant in the populations represented in this database. To the best of our knowledge, this specific variant has not been described in the literature to be associated with disease. However, loss-of-function variants in EBF3 have been established to be disease causing (PMID: 29162653). A nearby variant (p.Thr464Profs*10) has been reported in an affected individual (PMID: 29162653). No loss-of-function variants downstream to this one have been reported in affected individuals. - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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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
Publications
No publications associated with this variant yet.