9-129868212-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001110303.4(USP20):​c.898C>T​(p.Arg300Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000372 in 1,613,902 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00040 ( 1 hom. )

Consequence

USP20
NM_001110303.4 missense

Scores

9
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.83
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.39323625).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
USP20NM_001110303.4 linkc.898C>T p.Arg300Cys missense_variant Exon 11 of 26 ENST00000372429.8 NP_001103773.2 Q9Y2K6
USP20NM_001008563.5 linkc.898C>T p.Arg300Cys missense_variant Exon 11 of 26 NP_001008563.2 Q9Y2K6
USP20NM_006676.8 linkc.898C>T p.Arg300Cys missense_variant Exon 11 of 25 NP_006667.3 Q9Y2K6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
USP20ENST00000372429.8 linkc.898C>T p.Arg300Cys missense_variant Exon 11 of 26 1 NM_001110303.4 ENSP00000361506.3 Q9Y2K6

Frequencies

GnomAD3 genomes
AF:
0.000112
AC:
17
AN:
152114
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000189
AC:
47
AN:
248932
Hom.:
0
AF XY:
0.000222
AC XY:
30
AN XY:
135096
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000290
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000164
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000354
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.000400
AC:
584
AN:
1461670
Hom.:
1
Cov.:
91
AF XY:
0.000407
AC XY:
296
AN XY:
727138
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.0000562
Gnomad4 NFE exome
AF:
0.000492
Gnomad4 OTH exome
AF:
0.000199
GnomAD4 genome
AF:
0.000112
AC:
17
AN:
152232
Hom.:
0
Cov.:
33
AF XY:
0.000121
AC XY:
9
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000345
Hom.:
0
Bravo
AF:
0.000106
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.00130
AC:
5
ESP6500AA
AF:
0.000240
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000231
AC:
28
EpiCase
AF:
0.000218
EpiControl
AF:
0.000296

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
May 06, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.898C>T (p.R300C) alteration is located in exon 11 (coding exon 9) of the USP20 gene. This alteration results from a C to T substitution at nucleotide position 898, causing the arginine (R) at amino acid position 300 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.34
CADD
Pathogenic
32
DANN
Uncertain
1.0
DEOGEN2
Benign
0.027
T;T;T
Eigen
Uncertain
0.40
Eigen_PC
Uncertain
0.35
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Uncertain
0.91
.;.;D
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.39
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.5
M;M;M
PrimateAI
Uncertain
0.55
T
PROVEAN
Benign
0.26
N;N;N
REVEL
Benign
0.20
Sift
Uncertain
0.0030
D;D;D
Sift4G
Uncertain
0.047
D;D;D
Polyphen
1.0
D;D;D
Vest4
0.65
MVP
0.58
MPC
1.1
ClinPred
0.22
T
GERP RS
4.2
RBP_binding_hub_radar
1.1
RBP_regulation_power_radar
2.8
Varity_R
0.097
gMVP
0.12

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200929938; hg19: chr9-132630491; API