rs202018501

Variant summary

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

The NM_000149.4(FUT3):​c.911G>T​(p.Arg304Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 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: 𝑓 0.0000066 ( 0 hom., cov: 32)

Consequence

FUT3
NM_000149.4 missense

Scores

16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32
Variant links:
Genes affected
FUT3 (HGNC:4014): (fucosyltransferase 3 (Lewis blood group)) The Lewis histo-blood group system comprises a set of fucosylated glycosphingolipids that are synthesized by exocrine epithelial cells and circulate in body fluids. The glycosphingolipids function in embryogenesis, tissue differentiation, tumor metastasis, inflammation, and bacterial adhesion. They are secondarily absorbed to red blood cells giving rise to their Lewis phenotype. This gene is a member of the fucosyltransferase family, which catalyzes the addition of fucose to precursor polysaccharides in the last step of Lewis antigen biosynthesis. It encodes an enzyme with alpha(1,3)-fucosyltransferase and alpha(1,4)-fucosyltransferase activities. Mutations in this gene are responsible for the majority of Lewis antigen-negative phenotypes. Differences in the expression of this gene are associated with host susceptibility to viral infection. [provided by RefSeq, Aug 2020]

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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=0.112293065).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FUT3NM_000149.4 linkc.911G>T p.Arg304Leu missense_variant Exon 3 of 3 NP_000140.1 P21217A8K737
FUT3NM_001097639.3 linkc.911G>T p.Arg304Leu missense_variant Exon 3 of 3 NP_001091108.3 P21217A8K737
FUT3NM_001097640.3 linkc.911G>T p.Arg304Leu missense_variant Exon 3 of 3 NP_001091109.3 P21217A8K737

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FUT3ENST00000303225.12 linkc.911G>T p.Arg304Leu missense_variant Exon 3 of 3 1 ENSP00000305603.5 P21217
FUT3ENST00000458379.7 linkc.911G>T p.Arg304Leu missense_variant Exon 2 of 2 1 ENSP00000416443.1 P21217
FUT3ENST00000589620.6 linkc.911G>T p.Arg304Leu missense_variant Exon 3 of 3 1 ENSP00000465804.1 P21217
FUT3ENST00000589918.5 linkc.911G>T p.Arg304Leu missense_variant Exon 3 of 3 1 ENSP00000468123.1 P21217

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152098
Hom.:
0
Cov.:
32
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:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
34
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152098
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.085
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
0.95
DANN
Benign
0.85
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.033
N
M_CAP
Benign
0.0055
T
MetaRNN
Benign
0.11
T;T;T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-1.9
N;N;.;.
REVEL
Benign
0.013
Sift
Benign
0.17
T;T;.;.
Sift4G
Benign
0.33
T;T;T;T
Vest4
0.17
MutPred
0.46
Loss of methylation at K300 (P = 0.0479);Loss of methylation at K300 (P = 0.0479);Loss of methylation at K300 (P = 0.0479);Loss of methylation at K300 (P = 0.0479);
MVP
0.16
MPC
0.72
ClinPred
0.085
T
GERP RS
-0.36
gMVP
0.34

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: rs202018501; hg19: chr19-5843940; API