FUCA2

protein-coding

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

Gene summary

This gene encodes a plasma alpha-L-fucosidase, which represents 10-20% of the total cellular fucosidase activity. The protein is a member of the glycosyl hydrolase 29 family, and catalyzes the hydrolysis of the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. This enzyme is essential for Helicobacter pylori adhesion to human gastric cancer cells. [provided by RefSeq, Aug 2010]

MANE transcript

NM_032020.5

Inheritance

—

ClinVar variants

U:64B:5

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr6:143,494,812-143,511,720

External References & Databases

Ensembl (ENSG00000001036)

Transcript & Mutation Effects

hg38 • Region Span ~16.9 kb

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GenCC 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 FUCA2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 5

High myopiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032020.5. 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	1 clinvar	2
missense			64 clinvar	3 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	4	1	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032020.5	RefSeq	NP_114409.2	7	MANE Select
ENST00000002165.11	Ensembl	ENSP00000002165.5	7	MANE Select
ENST00000451668.1	Ensembl	ENSP00000398119.1	2	Standard
ENST00000871527.1	Ensembl	ENSP00000541586.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Other glycan degradation - Homo sapiens (human)
Neutrophil degranulation
Post-translational protein phosphorylation
Post-translational protein modification
Metabolism of proteins

Biological Process

fucose metabolic process
response to bacterium
glycoside catabolic process
neutrophil degranulation
post-translational protein modification

Molecular Function

alpha-L-fucosidase activity
protein binding

Cellular Component

extracellular region
extracellular space
lysosome
endoplasmic reticulum lumen
azurophil granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000002165
Coding exons: 7
Length: 16880
Individuals with no LoFs: 125644
Homozygous LoFs: 1
Heterozygous LoFs: 103
Defined: 125748
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.824	214	251	0.854	0.0000123	3044
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00036	0.00032	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00028	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.0013	0.0012	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.414

Intolerance Scores

LoFtool: 0.860
RVIS EVS: 0.6
RVIS percentile EVS: 82.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.217

Gene Damage Prediction

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