chr13-95877312-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020121.4(UGGT2):c.3440A>G(p.Gln1147Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000125 in 1,603,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
UGGT2
NM_020121.4 missense
NM_020121.4 missense
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 4.54
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 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.17600378).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGGT2 | NM_020121.4 | c.3440A>G | p.Gln1147Arg | missense_variant | 29/39 | ENST00000376747.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGGT2 | ENST00000376747.8 | c.3440A>G | p.Gln1147Arg | missense_variant | 29/39 | 1 | NM_020121.4 | P1 | |
UGGT2 | ENST00000463054.1 | n.1083A>G | non_coding_transcript_exon_variant | 6/6 | 2 | ||||
UGGT2 | ENST00000476866.5 | n.29A>G | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
UGGT2 | ENST00000491509.5 | n.715A>G | non_coding_transcript_exon_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1451304Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 721138
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74372
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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 | Nov 09, 2022 | The c.3440A>G (p.Q1147R) alteration is located in exon 29 (coding exon 29) of the UGGT2 gene. This alteration results from a A to G substitution at nucleotide position 3440, causing the glutamine (Q) at amino acid position 1147 to be replaced by an arginine (R). 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
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of catalytic residue at R1144 (P = 0);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at