chr1-43360529-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001255.3(CDC20):c.784C>T(p.Arg262Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000235 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
CDC20
NM_001255.3 stop_gained
NM_001255.3 stop_gained
Scores
5
1
1
Clinical Significance
Conservation
PhyloP100: 4.88
Genes affected
CDC20 (HGNC:1723): (cell division cycle 20) CDC20 appears to act as a regulatory protein interacting with several other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes, nuclear movement prior to anaphase and chromosome separation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 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 1-43360529-C-T is Pathogenic according to our data. Variant chr1-43360529-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 2443922.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC20 | NM_001255.3 | c.784C>T | p.Arg262Ter | stop_gained | 7/11 | ENST00000310955.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC20 | ENST00000310955.11 | c.784C>T | p.Arg262Ter | stop_gained | 7/11 | 1 | NM_001255.3 | P1 | |
CDC20 | ENST00000372462.1 | c.784C>T | p.Arg262Ter | stop_gained | 6/10 | 1 | P1 | ||
CDC20 | ENST00000478882.1 | n.559C>T | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251442Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135888
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GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461830Hom.: 0 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 727220
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Oocyte maturation defect 14 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 10, 2023 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
A;A
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at