FUT9
protein-codingfucosyltransferase 9, the group of Fucosyltransferases
Gene summary
The protein encoded by this gene belongs to the glycosyltransferase family. It is localized to the golgi, and catalyzes the last step in the biosynthesis of Lewis X (LeX) antigen, the addition of a fucose to precursor polysaccharides. This protein is one of the few fucosyltransferases that synthesizes the LeX oligosaccharide (CD15) expressed in the organ buds progressing in mesenchyma during embryogenesis. It is also responsible for the expression of CD15 in mature granulocytes. A common haplotype of this gene has also been associated with susceptibility to placental malaria infection. [provided by RefSeq, Nov 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~199.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FUT9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006581.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 22 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 0 | 0 | 22 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006572.2 | 1 | MANE Select | |
| Ensembl | ENSP00000302599.4 | 1 | MANE Select | |
| Ensembl | ENSP00000557240.1 | 1 | Standard | |
| Ensembl | ENSP00000557240.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mannose type O-glycan biosynthesis - Homo sapiens (human)
- Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
- Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
- Globo Sphingolipid Metabolism
- Glycosphingolipid biosynthesis - neolactoseries
Biological Process
- carbohydrate metabolic process
- protein glycosylation
- nervous system development
- fucosylation
- L-fucose catabolic process
Molecular Function
- fucosyltransferase activity
- alpha-(1->3)-fucosyltransferase activity
Cellular Component
- Golgi apparatus
- integral component of membrane
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000302103
- Coding exons
- 1
- Length
- 199629
- Individuals with no LoFs
- 125612
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125616
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.02 | 111 | 189 | 0.586 | 0.00000947 | 2385 |
| Missense (PolyPhen) | 31 | 74.409 | 0.41662 | 905 | ||
| Synonymous | -0.397 | 75 | 70.8 | 1.06 | 0.00000363 | 659 |
| Loss of Function | 2.28 | 4 | 12.8 | 0.313 | 7.18e-7 | 151 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transfers a fucose to lacto-N-neotetraose but not to either alpha2,3-sialyl lacto-N-neotetraose or lacto-N-tetraose. Can catalyze the last step in the biosynthesis of Lewis antigen, the addition of a fucose to precursor polysaccharides. {ECO:0000269|PubMed:10386598}.;
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- LoFtool
- 0.337
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |