chr19-17808232-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_014256.4(B3GNT3):c.425G>T(p.Arg142Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,218 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
B3GNT3
NM_014256.4 missense
NM_014256.4 missense
Scores
4
9
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.26
Genes affected
B3GNT3 (HGNC:13528): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein and contains a signal anchor that is not cleaved. It prefers the substrates of lacto-N-tetraose and lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains and the biosynthesis of the backbone structure of dimeric sialyl Lewis a. It plays dominant roles in L-selectin ligand biosynthesis, lymphocyte homing and lymphocyte trafficking. [provided by RefSeq, Jul 2008]
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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, 0.835
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT3 | NM_014256.4 | c.425G>T | p.Arg142Leu | missense_variant | Exon 2 of 3 | ENST00000318683.7 | NP_055071.2 | |
B3GNT3 | XM_011527626.3 | c.425G>T | p.Arg142Leu | missense_variant | Exon 2 of 3 | XP_011525928.1 | ||
B3GNT3 | XM_047438042.1 | c.425G>T | p.Arg142Leu | missense_variant | Exon 2 of 3 | XP_047293998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GNT3 | ENST00000318683.7 | c.425G>T | p.Arg142Leu | missense_variant | Exon 2 of 3 | 1 | NM_014256.4 | ENSP00000321874.5 | ||
B3GNT3 | ENST00000595387.1 | c.425G>T | p.Arg142Leu | missense_variant | Exon 2 of 3 | 1 | ENSP00000472638.1 | |||
B3GNT3 | ENST00000599265.5 | c.425G>T | p.Arg142Leu | missense_variant | Exon 2 of 3 | 3 | ENSP00000471733.1 | |||
B3GNT3 | ENST00000600777.1 | c.*43G>T | downstream_gene_variant | 3 | ENSP00000468914.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461218Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 726866
GnomAD4 exome
AF:
AC:
1
AN:
1461218
Hom.:
Cov.:
36
AF XY:
AC XY:
1
AN XY:
726866
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;.;T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;M
PrimateAI
Pathogenic
T
PROVEAN
Pathogenic
.;D;.
REVEL
Uncertain
Sift
Uncertain
.;D;.
Sift4G
Uncertain
D;D;D
Polyphen
0.97
.;D;D
Vest4
0.68, 0.68
MutPred
Loss of MoRF binding (P = 0.0117);Loss of MoRF binding (P = 0.0117);Loss of MoRF binding (P = 0.0117);
MVP
MPC
1.9
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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