PFKFB3

6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3, the group of 6-phosphofructo-2-kinases/fructose-2,6-biphosphatases|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:6144933-6254644

Links

ENSG00000170525 ∙ NCBI:5209 ∙ OMIM:605319 ∙ HGNC:8874 ∙ Uniprot:Q16875 ∙ 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 PFKFB3 gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PFKFB3 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in PFKFB3

This is a list of pathogenic ClinVar variants found in the PFKFB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-6203321-C-T		not specified	Uncertain significance (Jul 19, 2023)
10-6215228-C-A		not specified	Uncertain significance (Dec 16, 2022)
10-6215265-A-G		not specified	Uncertain significance (Feb 27, 2024)
10-6216142-C-A		not specified	Uncertain significance (Apr 12, 2022)
10-6216157-A-G		not specified	Uncertain significance (Feb 06, 2023)
10-6217151-C-T		not specified	Uncertain significance (Feb 07, 2023)
10-6219573-T-C		not specified	Uncertain significance (Sep 14, 2022)
10-6219659-A-G		not specified	Uncertain significance (Sep 23, 2023)
10-6219674-G-A		not specified	Uncertain significance (Jan 10, 2022)
10-6220797-G-A		not specified	Uncertain significance (Dec 06, 2022)
10-6220854-C-T		not specified	Uncertain significance (Aug 30, 2022)
10-6221405-G-A		not specified	Uncertain significance (Jul 13, 2021)
10-6221484-G-A		not specified	Uncertain significance (Jul 05, 2023)
10-6221494-C-T			Benign (Jul 16, 2018)
10-6221516-G-A		not specified	Uncertain significance (Aug 02, 2023)
10-6221644-G-A		not specified	Uncertain significance (Nov 17, 2022)
10-6222973-A-T		not specified	Uncertain significance (Oct 22, 2021)
10-6223966-C-A		not specified	Uncertain significance (Jan 04, 2024)
10-6223992-C-T			Likely benign (Jul 30, 2018)
10-6223993-G-A		not specified	Uncertain significance (Apr 07, 2022)
10-6224155-G-A		not specified	Uncertain significance (Apr 07, 2022)
10-6224166-A-G		not specified	Uncertain significance (Jul 13, 2021)
10-6224170-A-G		not specified	Uncertain significance (Apr 12, 2022)
10-6226251-C-A		not specified	Uncertain significance (Jul 09, 2021)
10-6226273-C-T		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PFKFB3	protein_coding	protein_coding	ENST00000379775	15	90615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.246	0.754	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	262	349	0.750	0.0000241	3402
Missense in Polyphen		77	149.45	0.51522		1492
Synonymous	-0.801	160	148	1.08	0.0000109	996
Loss of Function	3.83	7	29.4	0.238	0.00000125	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000478	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Synthesis and degradation of fructose 2,6-bisphosphate.
• Pathway: Fructose and mannose metabolism - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Aminosugars metabolism;Metabolism of carbohydrates;Fructose Mannose metabolism;Glycolysis Gluconeogenesis;Metabolism;fructose 2,6-bisphosphate synthesis;Glycolysis;Glucose metabolism;HIF-1-alpha transcription factor network (Consensus)

Recessive Scores

• pRec: 0.348

Intolerance Scores

• loftool: 0.125
• rvis_EVS: -1.4
• rvis_percentile_EVS: 4.19

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.756
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pfkfb3
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; cellular phenotype

Gene ontology

• Biological process: fructose metabolic process;fructose 2,6-bisphosphate metabolic process;brain development;dephosphorylation;positive regulation of glycolytic process;carbohydrate phosphorylation
• Cellular component: nucleoplasm;cytosol
• Molecular function: 6-phosphofructo-2-kinase activity;fructose-2,6-bisphosphate 2-phosphatase activity;ATP binding