FUT2

fucosyltransferase 2, the group of Fucosyltransferases

Basic information

Region (hg38): 19:48695970-48705951

Previous symbols: [ "SE" ]

Links

ENSG00000176920 ∙ NCBI:2524 ∙ OMIM:182100 ∙ HGNC:4013 ∙ Uniprot:Q10981 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bombay phenotype	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	14918471; 13269394; 13767673; 5763629; 7246545; 7180848; 6177241; 6859043; 2118655; 7912436; 9299444
Digenic inheritance (with FUT1) has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FUT2 gene.

• Inborn genetic diseases (16 variants)
• not provided (6 variants)
• Familial Otitis Media (3 variants)
• Vitamin b12 plasma level quantitative trait locus 1 (2 variants)
• Vitamin b12 plasma level quantitative trait locus 1;Bombay phenotype (1 variants)
• SECRETOR/NONSECRETOR POLYMORPHISM (1 variants)
• Fucosyltransferase 6 deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FUT2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	2	4
missense			14	2	1	17
nonsense	1				2	3
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	14	4	6

Highest pathogenic variant AF is 0.000506

Variants in FUT2

This is a list of pathogenic ClinVar variants found in the FUT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-48702966-G-A		not specified	Likely benign (Dec 19, 2022)
19-48703021-T-C		not specified	Likely benign (Aug 28, 2023)
19-48703029-A-G		Fucosyltransferase 6 deficiency • Familial Otitis Media	Benign (-)
19-48703048-G-A		not specified	Uncertain significance (Jun 13, 2022)
19-48703168-G-A		not specified	Uncertain significance (Jun 22, 2021)
19-48703198-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-48703199-A-G		FUT2-related disorder	Likely benign (Mar 18, 2019)
19-48703203-T-C		not specified	Uncertain significance (Aug 30, 2022)
19-48703205-C-T		Familial Otitis Media	confers sensitivity (-)
19-48703253-G-A		not specified	Uncertain significance (Apr 07, 2022)
19-48703267-C-T		Familial Otitis Media	confers sensitivity (-)
19-48703291-C-T		Familial Otitis Media	confers sensitivity (-)
19-48703304-C-T		FUT2-related disorder	Benign (Apr 10, 2019)
19-48703309-C-T		not specified	Uncertain significance (Apr 25, 2022)
19-48703346-C-T		FUT2-related disorder	Benign (Oct 29, 2020)
19-48703364-A-G			Benign (Aug 17, 2018)
19-48703368-C-T		Familial Otitis Media	confers sensitivity (-)
19-48703369-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-48703374-A-T		SECRETOR/NONSECRETOR POLYMORPHISM, JAPANESE TYPE • Familial Otitis Media	Benign; confers sensitivity (Apr 19, 1996)
19-48703387-A-T		not specified	Uncertain significance (Aug 10, 2023)
19-48703400-C-G		FUT2-related disorder	Likely benign (Oct 28, 2019)
19-48703417-G-A		Vitamin b12 plasma level quantitative trait locus 1 • SECRETOR/NONSECRETOR POLYMORPHISM • Familial Otitis Media • Vitamin b12 plasma level quantitative trait locus 1;Bombay phenotype	Benign (Aug 12, 2021)
19-48703473-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-48703479-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-48703543-T-G		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FUT2	protein_coding	protein_coding	ENST00000425340	1	9980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.32e-14	0.00206	50593	21396	53651	125640	0.365

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.277	219	208	1.05	0.0000147	2228
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.789	0.781
Ashkenazi Jewish	0.451	0.450
East Asian	0.0222	0.0220
Finnish	0.375	0.372
European (Non-Finnish)	0.476	0.469
Middle Eastern	0.0222	0.0220
South Asian	0.316	0.296
Other	0.432	0.423

dbNSFP

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}.
• Pathway: 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;Glycosphingolipid biosynthesis - globoseries (Consensus)

Intolerance Scores

• loftool: 0.150
• rvis_EVS: 0.82
• rvis_percentile_EVS: 88.04

Haploinsufficiency Scores

• pHI: 0.0518
• hipred: N
• hipred_score: 0.146
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fut2
• Phenotype: immune system phenotype; digestive/alimentary phenotype; reproductive system phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;protein glycosylation;fucosylation;L-fucose catabolic process
• Cellular component: Golgi apparatus;integral component of membrane;Golgi cisterna membrane;extracellular exosome
• Molecular function: galactoside 2-alpha-L-fucosyltransferase activity;fucosyltransferase activity