chr19-5844638-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001382749.2(FUT3):c.202C>G(p.Arg68Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 11/19 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 0.0 ( 0 hom., cov: 21)
Failed GnomAD Quality Control
Consequence
FUT3
NM_001382749.2 missense
NM_001382749.2 missense
Scores
4
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.04
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 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT3 | NM_001097639.3 | c.202C>G | p.Trp68Gly | missense_variant | 3/3 | ENST00000709635.1 | |
FUT3 | NM_001382749.2 | c.202C>G | p.Arg68Gly | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT3 | ENST00000303225.12 | c.202C>G | p.Arg68Gly | missense_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 148072Hom.: 0 Cov.: 21 FAILED QC
GnomAD3 genomes
?
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21
FAILED QC
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GnomAD4 exome Cov.: 52
GnomAD4 exome
Cov.:
52
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 148072Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 71962
GnomAD4 genome
?
Data not reliable, filtered out with message: AC0
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21
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71962
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;.;.;.
REVEL
Benign
Sift
Uncertain
D;D;.;.;.;.
Sift4G
Uncertain
D;D;D;D;D;D
Vest4
MutPred
Loss of helix (P = 0.0376);Loss of helix (P = 0.0376);Loss of helix (P = 0.0376);Loss of helix (P = 0.0376);Loss of helix (P = 0.0376);Loss of helix (P = 0.0376);
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at