chr11-119356918-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004205.5(USP2):āc.1735A>Gā(p.Thr579Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000356 in 1,406,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 31)
Exomes š: 0.0000036 ( 0 hom. )
Consequence
USP2
NM_004205.5 missense
NM_004205.5 missense
Scores
4
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.82
Genes affected
USP2 (HGNC:12618): (ubiquitin specific peptidase 2) This gene encodes a member of the family of de-ubiquitinating enzymes, which belongs to the peptidase C19 superfamily. The encoded protein is a ubiquitin-specific protease which is required for TNF-alpha (tumor necrosis factor alpha) -induced NF-kB (nuclear factor kB) signaling. This protein deubiquitinates polyubiquitinated target proteins such as fatty acid synthase, murine double minute 2 (MDM2), MDM4/MDMX and cyclin D1. MDM2 and MDM4 are negative regulators of the p53 tumor suppressor and cyclin D1 is required for cell cycle G1/S transition. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]
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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=0.21371448).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP2 | NM_004205.5 | c.1735A>G | p.Thr579Ala | missense_variant | 13/13 | ENST00000260187.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP2 | ENST00000260187.7 | c.1735A>G | p.Thr579Ala | missense_variant | 13/13 | 1 | NM_004205.5 | ||
USP2 | ENST00000525735.1 | c.1108A>G | p.Thr370Ala | missense_variant | 12/12 | 1 | P1 | ||
USP2 | ENST00000455332.6 | c.1006A>G | p.Thr336Ala | missense_variant | 12/12 | 1 | |||
USP2-AS1 | ENST00000706409.1 | n.251+201T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000356 AC: 5AN: 1406420Hom.: 0 Cov.: 32 AF XY: 0.00000288 AC XY: 2AN XY: 694288
GnomAD4 exome
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5
AN:
1406420
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Cov.:
32
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AC XY:
2
AN XY:
694288
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
0.0030, 0.046
.;B;B
Vest4
MutPred
0.40
.;Loss of glycosylation at T579 (P = 0.0222);.;
MVP
MPC
0.31
ClinPred
D
GERP RS
Varity_R
gMVP
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.