FPGT

fucose-1-phosphate guanylyltransferase

Basic information

Region (hg38): 1:74198238-74234086

Links

ENSG00000254685 ∙ NCBI:8790 ∙ OMIM:603609 ∙ HGNC:3825 ∙ Uniprot:O14772 ∙ 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 FPGT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FPGT 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						0
missense			48	3		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	49	3	0

Variants in FPGT

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

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

Position	Type	Phenotype	Significance	ClinVar
1-74198247-C-A		not specified	Uncertain significance (Sep 26, 2022)
1-74198286-C-A		not specified	Uncertain significance (Sep 26, 2022)
1-74198294-G-T		not specified	Uncertain significance (Jun 05, 2024)
1-74198351-G-A		not specified	Uncertain significance (Jun 30, 2023)
1-74199678-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-74199699-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-74199727-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-74199766-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-74199816-G-C		not specified	Uncertain significance (Nov 08, 2022)
1-74199819-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-74201361-G-C		not specified	Uncertain significance (Sep 14, 2023)
1-74201392-A-G		not specified	Uncertain significance (Mar 11, 2022)
1-74201408-C-G		not specified	Uncertain significance (Sep 22, 2023)
1-74204397-A-G		not specified	Uncertain significance (Aug 12, 2021)
1-74204487-A-G		not specified	Uncertain significance (Nov 18, 2022)
1-74204522-A-C		not specified	Uncertain significance (Sep 12, 2023)
1-74204565-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-74204611-T-G		not specified	Uncertain significance (Sep 01, 2021)
1-74204633-A-G		not specified	Uncertain significance (May 27, 2022)
1-74204672-G-T		not specified	Uncertain significance (Aug 02, 2023)
1-74204681-G-C		not specified	Uncertain significance (Dec 05, 2022)
1-74204695-T-A		not specified	Uncertain significance (Mar 29, 2024)
1-74204705-G-C		not specified	Uncertain significance (Mar 15, 2024)
1-74204723-C-T		not specified	Uncertain significance (Nov 10, 2023)
1-74204738-C-T		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FPGT	protein_coding	protein_coding	ENST00000609362	4	35875

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-10	0.171	125622	1	125	125748	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.900	348	304	1.15	0.0000142	3880
Missense in Polyphen		105	92.678	1.133		1214
Synonymous	-1.12	128	113	1.13	0.00000544	1143
Loss of Function	0.604	17	19.9	0.854	9.18e-7	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00130	0.00130
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00125	0.00125
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000443	0.000431
Middle Eastern	0.00125	0.00125
South Asian	0.000394	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the formation of GDP-L-fucose from GTP and L- fucose-1-phosphate. Functions as a salvage pathway to reutilize L- fucose arising from the turnover of glycoproteins and glycolipids.
• 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: 0.108

Intolerance Scores

• loftool: 0.913
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.36

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.813

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fpgt

Gene ontology

• Biological process: fucose metabolic process
• Cellular component: cytoplasm;cytosol
• Molecular function: catalytic activity;GTP binding;fucose-1-phosphate guanylyltransferase activity