FUT2

protein-coding

fucosyltransferase 2, the group of Fucosyltransferases

Gene summary

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]

Previous symbols:

MANE transcript

NM_000511.6

Inheritance

ClinVar variants

P:1U:53B:12

Top phenotype

Bombay phenotype

gnomAD constraint

pLI —, LoF o/e 1.5

Max pathogenic AF

—

Genomic locus

chr19:48,695,971-48,705,951

External References & Databases

Ensembl (ENSG00000176920)

Transcript & Mutation Effects

hg38 • Region Span ~10.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Bombay phenotypeBG

Manifestation: Hematologic

Intervention: Hematologic

Rationale: Variants associated with a blood group may be important in specific situations (eg, related to transfusion)

Comments: Digenic inheritance (with FUT1) has been described

Refs: 14918471; 13269394; 13767673; 5763629; 7246545; 7180848; 6177241; 6859043; 2118655; 7912436; 9299444

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FUT2 variants in ClinVar

9 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 9

Familial Otitis MediaTotal: 6

FUT2-related disorderTotal: 3

Bombay phenotypeTotal: 2

SECRETOR/NONSECRETOR POLYMORPHISM, JAPANESE TYPETotal: 1

Type 2 diabetes mellitusTotal: 1

Fucosyltransferase 6 deficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000511.6. 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			1 clinvar	3 clinvar	2 clinvar	6
missense			51 clinvar	3 clinvar	2 clinvar	56
nonsense		1 clinvar	1 clinvar		1 clinvar	3
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)						0
Total	0	1	53	6	6	66

Highest pathogenic variant AF is 0.0003601341

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000511.6	RefSeq	NP_000502.4	1	MANE Select
ENST00000425340.3	Ensembl	ENSP00000387498.2	1	MANE Select
NM_001097638.3	RefSeq	NP_001091107.1	1	Standard
ENST00000522966.2	Ensembl	ENSP00000430227.2	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
Globo Sphingolipid Metabolism
Glycosphingolipid biosynthesis - lactoseries
Glycosphingolipid biosynthesis - neolactoseries

Biological Process

carbohydrate metabolic process
protein glycosylation
fucosylation
L-fucose catabolic process

Molecular Function

galactoside 2-alpha-L-fucosyltransferase activity
fucosyltransferase activity

Cellular Component

Golgi apparatus
integral component of membrane
Golgi cisterna membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000425340
Coding exons: 1
Length: 9980
Individuals with no LoFs: 50593
Homozygous LoFs: 21396
Heterozygous LoFs: 53651
Defined: 125640
p: 0.365

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.277	219	208	1.05	0.0000147	2228
Missense (PolyPhen)		97	95.352	1.0173		1057
Synonymous	-0.994	103	90.9	1.13	0.00000701	714
Loss of Function	-1.56	17	11.3	1.50	7.72e-7	92

Population LoF Frequency

Population	CAF	p-value	Status
African	0.52	0.51	notable
Latino/Admixed American	0.27	0.26	notable
Ashkenazi Jewish	0.45	0.45	notable
East Asian	0.022	0.022	notable
Finnish	0.38	0.37	notable
European (Non-Finnish)	0.48	0.47	notable
South Asian	0.32	0.30	notable
Other	0.43	0.42	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates the transfer of fucose to the terminal galactose on glycan chains of cell surface glycoproteins and glycolipids (PubMed:7876235). The resulting epitope plays a role in cell-cell interaction including host-microbe interaction (PubMed:12692541, PubMed:8018146). Mediates interaction with intestinal microbiota influencing its composition (PubMed:21625510, PubMed:24733310, PubMed:22068912). Creates a soluble precursor oligosaccharide FuC-alpha ((1,2)Galbeta-) called the H antigen which is an essential substrate for the final step in the soluble ABO blood group antigen synthesis pathway (PubMed:7876235). {ECO:0000269|PubMed:21625510, ECO:0000269|PubMed:22068912, ECO:0000269|PubMed:24733310, ECO:0000269|PubMed:7876235, ECO:0000269|PubMed:8018146}.;

Intolerance Scores

LoFtool: 0.150
RVIS EVS: 0.82
RVIS percentile EVS: 88.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.126

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High