GFUS

GDP-L-fucose synthase, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 8:143612618-143618048

Previous symbols: [ "TSTA3" ]

Links

ENSG00000104522

∙ NCBI:7264 ∙ OMIM:137020 ∙ HGNC:12390 ∙ Uniprot:Q13630 ∙ 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 GFUS gene.

not_specified (58 variants)
not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GFUS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003313.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			57 clinvar	2 clinvar		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GFUS	protein_coding	protein_coding	ENST00000425753	10	5431

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-7	0.654	125686	0	56	125742	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.198	197	205	0.961	0.0000128	2116
Missense in Polyphen		55	62.807	0.8757		680
Synonymous	-1.98	113	89.2	1.27	0.00000658	615
Loss of Function	1.15	13	18.3	0.710	9.52e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00142	0.00139
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000295	0.000294
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the two-step NADP-dependent conversion of GDP- 4-dehydro-6-deoxy-D-mannose to GDP-fucose, involving an epimerase and a reductase reaction. {ECO:0000269|PubMed:8910301}.;
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 I (from GDP-D-mannose) (Consensus)

Recessive Scores

pRec: 0.159

Intolerance Scores

loftool: 0.247
rvis_EVS: -1.09
rvis_percentile_EVS: 7.05

Haploinsufficiency Scores

pHI: 0.108
hipred: N
hipred_score: 0.322
ghis: 0.525

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.151

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tsta3
Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; digestive/alimentary phenotype;

Gene ontology

Biological process: T cell mediated cytotoxicity;leukocyte cell-cell adhesion;GDP-mannose metabolic process;electron transport chain;'de novo' GDP-L-fucose biosynthetic process
Cellular component: cytosol;extracellular exosome
Molecular function: electron transfer activity;isomerase activity;GDP-4-dehydro-D-rhamnose reductase activity;identical protein binding;GDP-mannose 3,5-epimerase activity;GDP-L-fucose synthase activity;coenzyme binding