rs182226982

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014256.4(B3GNT3):​c.299C>A​(p.Pro100His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

B3GNT3
NM_014256.4 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.111
Variant links:
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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14026421).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
B3GNT3NM_014256.4 linkc.299C>A p.Pro100His missense_variant Exon 2 of 3 ENST00000318683.7 NP_055071.2 Q9Y2A9
B3GNT3XM_011527626.3 linkc.299C>A p.Pro100His missense_variant Exon 2 of 3 XP_011525928.1 Q9Y2A9
B3GNT3XM_047438042.1 linkc.299C>A p.Pro100His missense_variant Exon 2 of 3 XP_047293998.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
B3GNT3ENST00000318683.7 linkc.299C>A p.Pro100His missense_variant Exon 2 of 3 1 NM_014256.4 ENSP00000321874.5 Q9Y2A9
B3GNT3ENST00000595387.1 linkc.299C>A p.Pro100His missense_variant Exon 2 of 3 1 ENSP00000472638.1 Q9Y2A9
B3GNT3ENST00000599265.5 linkc.299C>A p.Pro100His missense_variant Exon 2 of 3 3 ENSP00000471733.1 M0R199
B3GNT3ENST00000600777.1 linkc.299C>A p.Pro100His missense_variant Exon 2 of 2 3 ENSP00000468914.1 M0QX58

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461654
Hom.:
0
Cov.:
37
AF XY:
0.00000138
AC XY:
1
AN XY:
727132
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.093
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
2.5
DANN
Benign
0.97
DEOGEN2
Benign
0.028
T;T;T;T
Eigen
Benign
-0.86
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.066
N
LIST_S2
Benign
0.46
T;.;T;T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.14
T;T;T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.34
.;N;.;N
PrimateAI
Benign
0.37
T
PROVEAN
Benign
-1.5
.;N;.;.
REVEL
Benign
0.059
Sift
Uncertain
0.014
.;D;.;.
Sift4G
Uncertain
0.012
D;D;D;D
Polyphen
0.51
.;P;.;P
Vest4
0.13, 0.13
MutPred
0.32
Loss of catalytic residue at P99 (P = 0.016);Loss of catalytic residue at P99 (P = 0.016);Loss of catalytic residue at P99 (P = 0.016);Loss of catalytic residue at P99 (P = 0.016);
MVP
0.38
MPC
1.7
ClinPred
0.20
T
GERP RS
-1.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.083
gMVP
0.39

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: rs182226982; hg19: chr19-17918915; COSMIC: COSV100592874; API