rs762893326

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001077.4(UGT2B17):​c.806G>T​(p.Arg269Leu) 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 pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 20)

Consequence

UGT2B17
NM_001077.4 missense

Scores

3
3
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.225
Variant links:
Genes affected
UGT2B17 (HGNC:12547): (UDP glucuronosyltransferase family 2 member B17) This gene encodes a member of the uridine diphosphoglucuronosyltransferase protein family. The encoded enzyme catalyzes the transfer of glucuronic acid from uridine diphosphoglucuronic acid to a diverse array of substrates including steroid hormones and lipid-soluble drugs. This process, known as glucuronidation, is an intermediate step in the metabolism of steroids. Copy number variation in this gene is associated with susceptibility to osteoporosis.[provided by RefSeq, Apr 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.824

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UGT2B17NM_001077.4 linkc.806G>T p.Arg269Leu missense_variant Exon 3 of 7 ENST00000317746.3 NP_001068.1 O75795

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UGT2B17ENST00000317746.3 linkc.806G>T p.Arg269Leu missense_variant Exon 3 of 7 1 NM_001077.4 ENSP00000320401.2 O75795
UGT2B17ENST00000684088.1 linkc.56G>T p.Arg19Leu missense_variant Exon 2 of 5 ENSP00000507374.1 A0A804HJ67

Frequencies

GnomAD3 genomes
Cov.:
20
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
20
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.52
BayesDel_addAF
Benign
-0.060
T
BayesDel_noAF
Benign
-0.32
CADD
Benign
7.5
DANN
Uncertain
0.99
DEOGEN2
Benign
0.28
T
Eigen
Benign
-0.29
Eigen_PC
Benign
-0.50
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.75
T
M_CAP
Benign
0.0029
T
MetaRNN
Pathogenic
0.82
D
MetaSVM
Benign
-0.67
T
MutationAssessor
Pathogenic
3.9
H
PrimateAI
Benign
0.26
T
PROVEAN
Pathogenic
-4.9
D
REVEL
Benign
0.21
Sift
Benign
0.031
D
Sift4G
Uncertain
0.023
D
Vest4
0.44
MutPred
0.80
Gain of catalytic residue at N274 (P = 0.2174);
MVP
0.26
MPC
1.2
ClinPred
0.94
D
GERP RS
0.092
Varity_R
0.22
gMVP
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs762893326; hg19: chr4-69431357; API