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.

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.

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			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					10	10
Total	0	0	36	2	11

Variants in GFUS

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

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

Position	Type	Phenotype	Significance	ClinVar
8-143612720-G-C			Benign (May 15, 2021)
8-143612883-G-A			Benign (May 26, 2021)
8-143612918-G-C		not specified	Uncertain significance (Mar 07, 2023)
8-143612927-C-G		not specified	Uncertain significance (Nov 14, 2023)
8-143612965-G-A		not specified	Uncertain significance (Jun 06, 2023)
8-143613006-C-T			Benign (May 17, 2021)
8-143613148-G-A			Benign (May 23, 2021)
8-143613208-G-C		not specified	Uncertain significance (Oct 03, 2022)
8-143613216-C-T		not specified	Likely benign (Aug 16, 2022)
8-143613258-G-A		not specified	Uncertain significance (Jan 17, 2024)
8-143613288-G-A		not specified	Uncertain significance (Dec 06, 2023)
8-143613329-C-A			Benign (May 17, 2021)
8-143613396-C-T			Benign (May 15, 2021)
8-143613537-T-C		not specified	Uncertain significance (Oct 02, 2023)
8-143613538-G-A		not specified	Uncertain significance (Dec 26, 2023)
8-143613559-C-A			Uncertain significance (Jul 01, 2023)
8-143613561-G-A		not specified	Uncertain significance (Apr 04, 2023)
8-143613562-C-T		not specified	Uncertain significance (Feb 07, 2025)
8-143613565-C-T		not specified	Uncertain significance (Feb 28, 2023)
8-143613598-C-T		not specified	Uncertain significance (Feb 18, 2025)
8-143613600-C-T		not specified	Uncertain significance (Jun 11, 2021)
8-143613697-A-G			Benign (May 15, 2021)
8-143613787-G-A		not specified	Uncertain significance (Jul 31, 2023)
8-143614033-T-C			Benign (May 15, 2021)
8-143614168-G-A		not specified	Uncertain significance (Nov 23, 2024)

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