FUCA2

alpha-L-fucosidase 2, the group of Alpha-L-fucosidases

Basic information

Region (hg38): 6:143494812-143511720

Links

ENSG00000001036 ∙ NCBI:2519 ∙ OMIM:136820 ∙ HGNC:4008 ∙ Uniprot:Q9BTY2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FUCA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FUCA2 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				1	1	2
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	29	3	1

Variants in FUCA2

This is a list of pathogenic ClinVar variants found in the FUCA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-143495726-G-C		not specified	Uncertain significance (Nov 10, 2024)
6-143495733-C-T		not specified	Likely benign (Dec 09, 2024)
6-143495790-T-C		not specified	Uncertain significance (Dec 07, 2023)
6-143501937-A-G			Benign (Feb 26, 2018)
6-143501957-T-G		not specified	Uncertain significance (Dec 14, 2022)
6-143501960-G-C		not specified	Uncertain significance (Aug 04, 2024)
6-143502001-A-C		not specified	Uncertain significance (Jun 05, 2023)
6-143502005-T-C		not specified	Uncertain significance (Jun 22, 2023)
6-143502025-C-T		not specified	Uncertain significance (Mar 07, 2025)
6-143502119-G-T		not specified	Uncertain significance (Jan 26, 2023)
6-143502129-A-T			Benign (Mar 01, 2018)
6-143502398-T-A		not specified	Uncertain significance (Oct 03, 2022)
6-143502421-T-A		not specified	Uncertain significance (Feb 05, 2024)
6-143502480-G-A		not specified	Uncertain significance (Dec 14, 2021)
6-143502536-T-C		not specified	Uncertain significance (Mar 08, 2025)
6-143502557-C-T		not specified	Uncertain significance (Mar 10, 2025)
6-143503934-A-C		not specified	Uncertain significance (Feb 12, 2025)
6-143503938-A-G		not specified	Uncertain significance (Feb 08, 2025)
6-143503953-A-G		not specified	Uncertain significance (Feb 05, 2025)
6-143503964-G-A		not specified	Uncertain significance (Jul 20, 2021)
6-143504009-T-A		not specified	Uncertain significance (Aug 02, 2021)
6-143504061-G-A		not specified	Uncertain significance (Nov 30, 2021)
6-143504115-A-G		not specified	Uncertain significance (Oct 04, 2022)
6-143504154-T-C		not specified	Uncertain significance (Mar 30, 2024)
6-143504257-A-G			Benign (Mar 01, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FUCA2	protein_coding	protein_coding	ENST00000002165	7	16880

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.39e-7	0.956	125644	1	103	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.824	214	251	0.854	0.0000123	3044
Missense in Polyphen		69	85.673	0.80538		1032
Synonymous	-0.595	105	97.5	1.08	0.00000491	892
Loss of Function	1.93	14	24.3	0.577	0.00000120	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000793	0.000791
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000278	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000361	0.000352
Middle Eastern	0.000278	0.000272
South Asian	0.00135	0.00124
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Alpha-L-fucosidase is responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N- acetylglucosamine of the carbohydrate moieties of glycoproteins.
• Pathway: Other glycan degradation - Homo sapiens (human);Neutrophil degranulation;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.414

Intolerance Scores

• loftool: 0.860
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.291
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fuca2
• Phenotype: normal phenotype

Gene ontology

• Biological process: fucose metabolic process;response to bacterium;glycoside catabolic process;neutrophil degranulation;post-translational protein modification;cellular protein metabolic process;regulation of entry of bacterium into host cell
• Cellular component: extracellular region;extracellular space;lysosome;endoplasmic reticulum lumen;azurophil granule lumen;extracellular exosome
• Molecular function: alpha-L-fucosidase activity;protein binding