URI1 p.Asp232Val
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is . The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
Uncertain significance
The NM_003796.3(URI1):c.695A>T(p.Asp232Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,608,496 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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
URI1
NM_003796.3 missense
NM_003796.3 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 2.00
Publications
1 publications found
Genes affected
URI1 (HGNC:13236): (URI1 prefoldin like chaperone) This gene encodes member of the prefoldin family of molecular chaperones. The encoded protein functions as a scaffolding protein and plays roles in ubiquitination and transcription, in part though interactions with the RNA polymerase II subunit RPB5. This gene may play a role in multiple malignancies including ovarian cancer and hepatocellular carcinoma. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 22. [provided by RefSeq, Nov 2011]
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new If you want to explore the variant's impact on the transcript NM_003796.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
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 (REVEL=0.171).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003796.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| URI1 | TSL:1 MANE Select | c.695A>T | p.Asp232Val | missense | Exon 8 of 11 | ENSP00000376097.2 | O94763-1 | ||
| URI1 | TSL:1 | c.641A>T | p.Asp214Val | missense | Exon 8 of 11 | ENSP00000353817.4 | O94763-4 | ||
| URI1 | TSL:1 | n.*528A>T | 3_prime_UTR | Exon 7 of 10 | ENSP00000461003.1 | I3L467 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000405 AC: 1AN: 247096 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
247096
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456196Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 723588 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1456196
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
723588
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33386
American (AMR)
AF:
AC:
0
AN:
44566
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25900
East Asian (EAS)
AF:
AC:
0
AN:
39546
South Asian (SAS)
AF:
AC:
0
AN:
85512
European-Finnish (FIN)
AF:
AC:
0
AN:
52992
Middle Eastern (MID)
AF:
AC:
0
AN:
5740
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1108396
Other (OTH)
AF:
AC:
0
AN:
60158
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.725
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000657 AC: 1AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74478 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152300
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74478
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41570
American (AMR)
AF:
AC:
0
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10614
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68012
Other (OTH)
AF:
AC:
0
AN:
2114
Alfa
AF:
Hom.:
Bravo
AF:
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
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
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
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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Other links and lift over
dbSNP: rs548314725 ;
hg19: chr19-30499920;