NM_014256.4:c.179C>G

Variant summary

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

The NM_014256.4(B3GNT3):ā€‹c.179C>Gā€‹(p.Pro60Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,278 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.000013 ( 0 hom., cov: 27)

Consequence

B3GNT3
NM_014256.4 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0450
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=0.072110355).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
B3GNT3NM_014256.4 linkc.179C>G p.Pro60Arg missense_variant Exon 2 of 3 ENST00000318683.7 NP_055071.2 Q9Y2A9
B3GNT3XM_011527626.3 linkc.179C>G p.Pro60Arg missense_variant Exon 2 of 3 XP_011525928.1 Q9Y2A9
B3GNT3XM_047438042.1 linkc.179C>G p.Pro60Arg 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.179C>G p.Pro60Arg missense_variant Exon 2 of 3 1 NM_014256.4 ENSP00000321874.5 Q9Y2A9
B3GNT3ENST00000595387.1 linkc.179C>G p.Pro60Arg missense_variant Exon 2 of 3 1 ENSP00000472638.1 Q9Y2A9
B3GNT3ENST00000599265.5 linkc.179C>G p.Pro60Arg missense_variant Exon 2 of 3 3 ENSP00000471733.1 M0R199
B3GNT3ENST00000600777.1 linkc.179C>G p.Pro60Arg missense_variant Exon 2 of 2 3 ENSP00000468914.1 M0QX58

Frequencies

GnomAD3 genomes
AF:
0.0000132
AC:
2
AN:
151278
Hom.:
0
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000295
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000409
AC:
1
AN:
244480
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
132810
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000914
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
69
GnomAD4 genome
AF:
0.0000132
AC:
2
AN:
151278
Hom.:
0
Cov.:
27
AF XY:
0.00
AC XY:
0
AN XY:
73878
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000295
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.070
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
0.46
DANN
Benign
0.76
DEOGEN2
Benign
0.013
T;T;T;T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.071
N
LIST_S2
Benign
0.34
T;.;T;T
M_CAP
Benign
0.040
D
MetaRNN
Benign
0.072
T;T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.2
.;L;.;L
PrimateAI
Benign
0.38
T
PROVEAN
Uncertain
-2.4
.;N;.;.
REVEL
Benign
0.016
Sift
Benign
0.53
.;T;.;.
Sift4G
Benign
0.30
T;T;T;T
Polyphen
0.0030
.;B;.;B
Vest4
0.12, 0.12
MutPred
0.24
Loss of glycosylation at P60 (P = 0.0372);Loss of glycosylation at P60 (P = 0.0372);Loss of glycosylation at P60 (P = 0.0372);Loss of glycosylation at P60 (P = 0.0372);
MVP
0.16
MPC
0.74
ClinPred
0.020
T
GERP RS
-2.0
Varity_R
0.039
gMVP
0.29

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: rs377004909; hg19: chr19-17918795; API