9-129858474-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001110303.4(USP20):āc.206A>Gā(p.Lys69Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000291 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 33)
Exomes š: 0.000031 ( 0 hom. )
Consequence
USP20
NM_001110303.4 missense
NM_001110303.4 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 4.26
Genes affected
USP20 (HGNC:12619): (ubiquitin specific peptidase 20) This gene encodes a ubiquitin specific processing protease that was first identified as a substrate of the VHL (von Hippel-Lindau disease) protein E3 ubiquitin ligase complex. In addition to being ubiquitinated by the VHL-E3 ligase complex, this enzyme deubiquitinates hypoxia-inducible factor (HIF)-1 alpha and thereby causes increased expression of HIF-1alpha targeted genes which play a role in angiogenesis, glucose metabolism, cell proliferation and metastasis. The enzyme encoded by this gene also regulates G-protein coupled receptor signaling by mediating the deubiquitination of beta-2 adrenergic receptor (ADRB2). This enzyme is a ubiquitously expressed thiolester hydrolase. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22125357).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP20 | NM_001110303.4 | c.206A>G | p.Lys69Arg | missense_variant | 6/26 | ENST00000372429.8 | |
USP20 | NM_001008563.5 | c.206A>G | p.Lys69Arg | missense_variant | 6/26 | ||
USP20 | NM_006676.8 | c.206A>G | p.Lys69Arg | missense_variant | 6/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP20 | ENST00000372429.8 | c.206A>G | p.Lys69Arg | missense_variant | 6/26 | 1 | NM_001110303.4 | P1 | |
USP20 | ENST00000315480.9 | c.206A>G | p.Lys69Arg | missense_variant | 6/25 | 1 | P1 | ||
USP20 | ENST00000358355.5 | c.206A>G | p.Lys69Arg | missense_variant | 6/26 | 1 | P1 | ||
USP20 | ENST00000494971.2 | n.430A>G | non_coding_transcript_exon_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249538Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135382
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GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461856Hom.: 0 Cov.: 35 AF XY: 0.0000275 AC XY: 20AN XY: 727232
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74350
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2022 | The c.206A>G (p.K69R) alteration is located in exon 6 (coding exon 4) of the USP20 gene. This alteration results from a A to G substitution at nucleotide position 206, causing the lysine (K) at amino acid position 69 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MutPred
Loss of methylation at K69 (P = 0.0176);Loss of methylation at K69 (P = 0.0176);Loss of methylation at K69 (P = 0.0176);
MVP
MPC
0.25
ClinPred
T
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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