rs145475599

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2

The NM_000149.4(FUT3):​c.596A>T​(p.Asn199Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,704 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: 0.0000055 ( 0 hom. )

Consequence

FUT3
NM_000149.4 missense

Scores

4
5
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89
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.

PP3
MetaRNN computational evidence supports a deleterious effect, 0.965
BS2
High AC in GnomAdExome4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FUT3NM_000149.4 linkc.596A>T p.Asn199Ile missense_variant Exon 3 of 3 NP_000140.1 P21217A8K737
FUT3NM_001097639.3 linkc.596A>T p.Asn199Ile missense_variant Exon 3 of 3 NP_001091108.3 P21217A8K737
FUT3NM_001097640.3 linkc.596A>T p.Asn199Ile 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.596A>T p.Asn199Ile missense_variant Exon 3 of 3 1 ENSP00000305603.5 P21217
FUT3ENST00000458379.7 linkc.596A>T p.Asn199Ile missense_variant Exon 2 of 2 1 ENSP00000416443.1 P21217
FUT3ENST00000589620.6 linkc.596A>T p.Asn199Ile missense_variant Exon 3 of 3 1 ENSP00000465804.1 P21217
FUT3ENST00000589918.5 linkc.596A>T p.Asn199Ile missense_variant Exon 3 of 3 1 ENSP00000468123.1 P21217

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000796
AC:
2
AN:
251270
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135840
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:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000547
AC:
8
AN:
1461704
Hom.:
0
Cov.:
34
AF XY:
0.00000688
AC XY:
5
AN XY:
727158
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:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000756
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.47
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.26
CADD
Benign
15
DANN
Uncertain
0.99
Eigen
Uncertain
0.29
Eigen_PC
Benign
0.053
FATHMM_MKL
Uncertain
0.85
D
M_CAP
Benign
0.016
T
MetaRNN
Pathogenic
0.97
D;D;D;D
MetaSVM
Benign
-0.38
T
PrimateAI
Uncertain
0.52
T
PROVEAN
Pathogenic
-8.6
D;D;.;.
REVEL
Benign
0.20
Sift
Pathogenic
0.0
D;D;.;.
Sift4G
Pathogenic
0.0010
D;D;D;D
Vest4
0.62
MutPred
0.83
Loss of ubiquitination at K201 (P = 0.0435);Loss of ubiquitination at K201 (P = 0.0435);Loss of ubiquitination at K201 (P = 0.0435);Loss of ubiquitination at K201 (P = 0.0435);
MVP
0.73
MPC
1.6
ClinPred
1.0
D
GERP RS
2.2
gMVP
0.68

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: rs145475599; hg19: chr19-5844255; COSMIC: COSV54606235; COSMIC: COSV54606235; API