chr13-95877294-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020121.4(UGGT2):c.3458T>C(p.Ile1153Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000415 in 1,445,900 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000041 ( 1 hom. )
Consequence
UGGT2
NM_020121.4 missense
NM_020121.4 missense
Scores
8
6
5
Clinical Significance
Conservation
PhyloP100: 8.54
Genes affected
UGGT2 (HGNC:15664): (UDP-glucose glycoprotein glucosyltransferase 2) UDP-glucose:glycoprotein glucosyltransferase (UGT) is a soluble protein of the endoplasmic reticulum (ER) that selectively reglucosylates unfolded glycoproteins, thus providing quality control for protein transport out of the ER.[supplied by OMIM, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.863
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGGT2 | NM_020121.4 | c.3458T>C | p.Ile1153Thr | missense_variant | 29/39 | ENST00000376747.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGGT2 | ENST00000376747.8 | c.3458T>C | p.Ile1153Thr | missense_variant | 29/39 | 1 | NM_020121.4 | P1 | |
UGGT2 | ENST00000463054.1 | n.1101T>C | non_coding_transcript_exon_variant | 6/6 | 2 | ||||
UGGT2 | ENST00000476866.5 | n.47T>C | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
UGGT2 | ENST00000491509.5 | n.733T>C | non_coding_transcript_exon_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 238692Hom.: 0 AF XY: 0.0000233 AC XY: 3AN XY: 128870
GnomAD3 exomes
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3
AN:
238692
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3
AN XY:
128870
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GnomAD4 exome AF: 0.00000415 AC: 6AN: 1445900Hom.: 1 Cov.: 30 AF XY: 0.00000835 AC XY: 6AN XY: 718208
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30
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GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ExAC
?
AF:
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1
Asia WGS
AF:
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1
AN:
3478
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 | Jun 06, 2023 | The c.3458T>C (p.I1153T) alteration is located in exon 29 (coding exon 29) of the UGGT2 gene. This alteration results from a T to C substitution at nucleotide position 3458, causing the isoleucine (I) at amino acid position 1153 to be replaced by a threonine (T). 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
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of stability (P = 0.0075);
MVP
MPC
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