rs281377
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000511.6(FUT2):c.390C>G(p.Asn130Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. N130N) has been classified as Benign.
Frequency
Genomes: not found (cov: 32)
Consequence
FUT2
NM_000511.6 missense
NM_000511.6 missense
Scores
10
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0310
Genes affected
FUT2 (HGNC:4013): (fucosyltransferase 2 (H blood group)) This gene is one of two encoding the galactoside 2-L-fucosyltransferase enzyme. The encoded protein is important for the final step in the soluble ABO blood group antigen synthesis pathway. It is also involved in cell-cell interaction, cell surface expression, and cell proliferation. Mutations in this gene are a cause of the H-Bombay blood group where red blood cells lack the H antigen. [provided by RefSeq, May 2022]
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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 |
---|---|---|---|---|---|---|---|
FUT2 | NM_000511.6 | c.390C>G | p.Asn130Lys | missense_variant | 2/2 | ENST00000425340.3 | |
LOC105447645 | NR_131188.1 | n.503G>C | non_coding_transcript_exon_variant | 1/1 | |||
FUT2 | NM_001097638.3 | c.390C>G | p.Asn130Lys | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT2 | ENST00000425340.3 | c.390C>G | p.Asn130Lys | missense_variant | 2/2 | 1 | NM_000511.6 | P1 | |
FUT2 | ENST00000522966.2 | c.390C>G | p.Asn130Lys | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 86
GnomAD4 exome
Cov.:
86
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Uncertain
D;T;T
Sift4G
Benign
T;T;T
Polyphen
0.89
.;P;P
Vest4
0.29, 0.43
MutPred
Gain of ubiquitination at N130 (P = 0.0219);Gain of ubiquitination at N130 (P = 0.0219);Gain of ubiquitination at N130 (P = 0.0219);
MVP
MPC
0.75
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at