chr2-128113103-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020120.4(UGGT1):āc.541A>Gā(p.Lys181Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 1,593,954 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: š 0.000020 ( 0 hom., cov: 29)
Exomes š: 0.000017 ( 0 hom. )
Consequence
UGGT1
NM_020120.4 missense
NM_020120.4 missense
Scores
1
2
16
Clinical Significance
Conservation
PhyloP100: 8.15
Genes affected
UGGT1 (HGNC:15663): (UDP-glucose glycoprotein glucosyltransferase 1) 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=0.23523244).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGGT1 | NM_020120.4 | c.541A>G | p.Lys181Glu | missense_variant | 6/41 | ENST00000259253.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGGT1 | ENST00000259253.11 | c.541A>G | p.Lys181Glu | missense_variant | 6/41 | 1 | NM_020120.4 | P1 | |
UGGT1 | ENST00000376723.7 | c.*581A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/41 | 1 | ||||
UGGT1 | ENST00000438277.5 | c.*129A>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/26 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.0000458 AC: 11AN: 239916Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 129790
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GnomAD4 exome AF: 0.0000166 AC: 24AN: 1441770Hom.: 0 Cov.: 29 AF XY: 0.0000126 AC XY: 9AN XY: 716084
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 29 AF XY: 0.0000269 AC XY: 2AN XY: 74338
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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 | Jun 29, 2022 | The c.541A>G (p.K181E) alteration is located in exon 6 (coding exon 6) of the UGGT1 gene. This alteration results from a A to G substitution at nucleotide position 541, causing the lysine (K) at amino acid position 181 to be replaced by a glutamic acid (E). 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
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Loss of methylation at K181 (P = 0.0021);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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