11-78196385-G-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020798.4(USP35):c.140G>A(p.Arg47His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
USP35
NM_020798.4 missense
NM_020798.4 missense
Scores
1
3
14
Clinical Significance
Conservation
PhyloP100: 3.56
Publications
0 publications found
Genes affected
USP35 (HGNC:20061): (ubiquitin specific peptidase 35) This gene encodes a member of the peptidase C19 family of ubiquitin-specific proteases. These deubiquitinating enzymes (DUBs) catalyze the removal of ubiquitin proteins from other proteins. The encoded protein associates with polarized mitochondria and has been shown to inhibit NF-kappa B activation and delay PARK2-mediated degradation of mitochondria. Expression of this gene is upregulated by the let-7a microRNA and reduced expression has been observed in human tumor tissues. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23874852).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020798.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| USP35 | TSL:5 MANE Select | c.140G>A | p.Arg47His | missense | Exon 2 of 11 | ENSP00000431876.1 | Q9P2H5-1 | ||
| USP35 | TSL:1 | c.-59-1551G>A | intron | N/A | ENSP00000436001.1 | E9PRM2 | |||
| USP35 | c.140G>A | p.Arg47His | missense | Exon 2 of 11 | ENSP00000539601.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1313500Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 650908
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1313500
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
650908
African (AFR)
AF:
AC:
0
AN:
25590
American (AMR)
AF:
AC:
0
AN:
21070
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19410
East Asian (EAS)
AF:
AC:
0
AN:
30584
South Asian (SAS)
AF:
AC:
0
AN:
70326
European-Finnish (FIN)
AF:
AC:
0
AN:
33772
Middle Eastern (MID)
AF:
AC:
0
AN:
4478
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1054636
Other (OTH)
AF:
AC:
0
AN:
53634
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of sheet (P = 0.0817)
MVP
MPC
ClinPred
T
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
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