GFPT2

glutamine-fructose-6-phosphate transaminase 2

Basic information

Region (hg38): 5:180300698-180353336

Links

ENSG00000131459

∙ NCBI:9945 ∙ OMIM:603865 ∙ HGNC:4242 ∙ Uniprot:O94808 ∙ 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 GFPT2 gene.

not_specified (77 variants)
not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GFPT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005110.4. 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				5 clinvar	1 clinvar	6
missense			75 clinvar	1 clinvar		76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	6	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GFPT2	protein_coding	protein_coding	ENST00000253778	19	52698

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.39e-9	0.999	124780	0	114	124894	0.000456

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	336	426	0.789	0.0000270	4457
Missense in Polyphen		97	144.89	0.66947		1452
Synonymous	-0.648	188	177	1.06	0.0000126	1308
Loss of Function	2.85	20	39.3	0.509	0.00000225	437

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000736	0.000721
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.000223	0.000222
Finnish	0.000210	0.000186
European (Non-Finnish)	0.000628	0.000627
Middle Eastern	0.000223	0.000222
South Asian	0.000490	0.000490
Other	0.000500	0.000494

dbNSFP

Source: dbNSFP

Function: FUNCTION: Controls the flux of glucose into the hexosamine pathway. Most likely involved in regulating the availability of precursors for N- and O-linked glycosylation of proteins.;
Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Aminosugars metabolism;Fructose Mannose metabolism;Post-translational protein modification;Metabolism of proteins;UDP-<i>N</i>-acetyl-D-glucosamine biosynthesis II;Synthesis of UDP-N-acetyl-glucosamine;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 (Consensus)

Recessive Scores

pRec: 0.286

Intolerance Scores

loftool: 0.590
rvis_EVS: -0.82
rvis_percentile_EVS: 11.94

Haploinsufficiency Scores

pHI: 0.729
hipred: Y
hipred_score: 0.680
ghis: 0.556

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.736

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gfpt2
Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; vision/eye phenotype; skeleton phenotype; hearing/vestibular/ear phenotype;

Gene ontology

Biological process: fructose 6-phosphate metabolic process;UDP-N-acetylglucosamine metabolic process;UDP-N-acetylglucosamine biosynthetic process;energy reserve metabolic process;protein N-linked glycosylation;glutamine metabolic process;cellular response to leukemia inhibitory factor
Cellular component: cytosol
Molecular function: glutamine-fructose-6-phosphate transaminase (isomerizing) activity;protein binding;carbohydrate derivative binding