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.

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.

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				4	1	5
missense			35	1		36
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	35	6	1

Variants in GFPT2

This is a list of pathogenic ClinVar variants found in the GFPT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-180301546-C-T		GFPT2-related disorder	Likely benign (Jun 18, 2021)
5-180302440-C-G		not specified	Uncertain significance (Oct 26, 2022)
5-180302476-C-T		not specified	Uncertain significance (Dec 06, 2022)
5-180302555-G-A			Likely benign (Apr 05, 2018)
5-180304777-G-A		not specified	Uncertain significance (Feb 06, 2023)
5-180304876-G-T		not specified	Uncertain significance (Dec 28, 2023)
5-180304879-C-T		not specified	Uncertain significance (Sep 06, 2022)
5-180304901-G-C		not specified	Uncertain significance (Oct 26, 2021)
5-180304926-A-C		not specified	Uncertain significance (Jun 18, 2024)
5-180304928-C-G		not specified	Uncertain significance (Aug 20, 2023)
5-180307241-T-G		not specified	Uncertain significance (Mar 28, 2023)
5-180312451-G-A		not specified	Uncertain significance (Jul 13, 2022)
5-180313818-C-T		not specified	Uncertain significance (May 09, 2023)
5-180313869-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-180313880-C-T		not specified	Uncertain significance (Nov 21, 2022)
5-180313899-C-T		not specified	Uncertain significance (Jul 26, 2021)
5-180313940-G-A		not specified	Uncertain significance (May 30, 2024)
5-180313949-G-A		not specified	Uncertain significance (Oct 05, 2021)
5-180316354-G-C		not specified	Uncertain significance (Jan 03, 2024)
5-180316365-C-T		not specified	Uncertain significance (Nov 03, 2023)
5-180316383-G-A		not specified	Uncertain significance (Sep 15, 2021)
5-180316457-C-T		not specified	Uncertain significance (Jun 29, 2023)
5-180316763-C-T			Uncertain significance (Feb 08, 2023)
5-180316810-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-180318854-G-A			Benign (Apr 05, 2018)

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