FCSK

fucose kinase

Basic information

Region (hg38): 16:70454595-70480274

Previous symbols: [ "FUK" ]

Links

ENSG00000157353 ∙ NCBI:197258 ∙ OMIM:608675 ∙ HGNC:29500 ∙ Uniprot:Q8N0W3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital disorder of glycosylation with defective fucosylation 2 (Limited), mode of inheritance: AR
• congenital disorder of glycosylation with defective fucosylation 2 (Limited), mode of inheritance: Unknown
• congenital disorder of glycosylation with defective fucosylation 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation with defective fucosylation 2	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Neurologic; Ophthalmologic	30503518

ClinVar

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

• not_provided (451 variants)
• not_specified (229 variants)
• FCSK-related_disorder (52 variants)
• Congenital_disorder_of_glycosylation_with_defective_fucosylation_2 (26 variants)
• Neurodevelopmental_disorder (2 variants)
• Congenital_disorder_of_glycosylation_with_defective_fucosylation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCSK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145059.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	107	13	121
missense		1	332	29	10	372
nonsense		2	13			15
start loss						0
frameshift		3	8			11
splice donor/acceptor (+/-2bp)		3	6	1		10
Total	0	9	360	137	23

Highest pathogenic variant AF is 0.00020477244

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCSK	protein_coding	protein_coding	ENST00000288078	23	25854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-29	0.000768	124543	0	263	124806	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.396	634	663	0.957	0.0000427	6783
Missense in Polyphen		165	198.22	0.8324		2102
Synonymous	0.155	287	290	0.988	0.0000189	2346
Loss of Function	0.750	48	53.9	0.890	0.00000284	552

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00400	0.00397
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00146	0.00145
Finnish	0.0000999	0.0000928
European (Non-Finnish)	0.00103	0.000945
Middle Eastern	0.00146	0.00145
South Asian	0.000699	0.000686
Other	0.00137	0.00132

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Takes part in the salvage pathway for reutilization of fucose from the degradation of oligosaccharides.
• Pathway: Fructose and mannose metabolism - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Fructose intolerance, hereditary;Fructose and Mannose Degradation;Fructosuria;Fructose Mannose metabolism;Post-translational protein modification;Metabolism of proteins;GDP-fucose biosynthesis;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;GDP-L-fucose biosynthesis II (from L-fucose) (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.427
• rvis_EVS: -0.92
• rvis_percentile_EVS: 9.83

Haploinsufficiency Scores

• pHI: 0.193
• hipred: N
• hipred_score: 0.251
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fuk

Gene ontology

• Biological process: GDP-L-fucose salvage;carbohydrate phosphorylation;response to dopamine
• Cellular component: cytosol
• Molecular function: ATP binding;fucokinase activity