GFPT2

protein-coding

glutamine-fructose-6-phosphate transaminase 2

Gene summary

Enables L-glutamine:D-fructose-6-phosphate transaminase (isomerizing) activity. Involved in UDP-N-acetylglucosamine biosynthetic process and fructose 6-phosphate metabolic process. Predicted to be located in cytosol. Implicated in type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_005110.4

Inheritance

—

ClinVar variants

U:96B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr5:180,300,698-180,353,336

External References & Databases

Ensembl (ENSG00000131459)

Transcript & Mutation Effects

hg38 • Region Span ~52.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GFPT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005110.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	5 clinvar	1 clinvar	8
missense			87 clinvar	1 clinvar		88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	96	6	1	103

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005110.4	RefSeq	NP_005101.1	19	MANE Select
ENST00000253778.13	Ensembl	ENSP00000253778.8	19	MANE Select
ENST00000503228.1	Ensembl	ENSP00000422771.1	2	Standard
ENST00000518906.1	Ensembl	ENSP00000431125.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

glutamine-fructose-6-phosphate transaminase (isomerizing) activity
protein binding
carbohydrate derivative binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253778
Coding exons: 19
Length: 52698
Individuals with no LoFs: 124780
Homozygous LoFs: 0
Heterozygous LoFs: 114
Defined: 124894
p: 0.000456

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.55	336	426	0.789	0.0000270	4457
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00046	0.00045	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00021	0.00019	rare
European (Non-Finnish)	0.00063	0.00063	rare
South Asian	0.00049	0.00049	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.286

Intolerance Scores

LoFtool: 0.590
RVIS EVS: -0.82
RVIS percentile EVS: 11.94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.736

Gene Damage Prediction

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