PFKP

phosphofructokinase, platelet

Basic information

Region (hg38): 10:3066333-3137718

Links

ENSG00000067057 ∙ NCBI:5214 ∙ OMIM:171840 ∙ HGNC:8878 ∙ Uniprot:Q01813 ∙ 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 PFKP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PFKP 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				5	15	20
missense			52	2		54
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				1		1
Total	0	0	52	9	15

Variants in PFKP

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

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

Position	Type	Phenotype	Significance	ClinVar
10-3067617-G-C		not specified	Uncertain significance (Oct 26, 2021)
10-3067677-G-A		not specified	Uncertain significance (Dec 06, 2021)
10-3099295-C-T		not specified	Likely benign (Oct 10, 2023)
10-3099296-G-A		not specified	Uncertain significance (Apr 09, 2024)
10-3099299-G-A		not specified	Uncertain significance (May 31, 2023)
10-3099330-G-A		not specified	Uncertain significance (Oct 06, 2021)
10-3099350-G-A		not specified	Uncertain significance (Jan 04, 2024)
10-3101408-C-T		not specified	Uncertain significance (Feb 28, 2024)
10-3101411-G-A		not specified	Uncertain significance (Aug 02, 2022)
10-3101419-C-T		not specified	Uncertain significance (Oct 03, 2022)
10-3101437-A-C		not specified	Uncertain significance (Dec 03, 2021)
10-3101444-T-A		not specified	Uncertain significance (Oct 30, 2023)
10-3101452-G-A		not specified	Uncertain significance (Apr 07, 2023)
10-3101477-G-T		not specified	Uncertain significance (Jun 02, 2024)
10-3101488-A-G		not specified	Uncertain significance (Oct 12, 2022)
10-3101508-C-T			Likely benign (Jul 30, 2018)
10-3101513-G-A		not specified	Uncertain significance (May 17, 2023)
10-3103783-G-C		not specified	Uncertain significance (Jul 22, 2022)
10-3103786-C-T			Benign (Dec 18, 2018)
10-3103809-A-G		not specified	Uncertain significance (Apr 28, 2022)
10-3103811-G-A		not specified	Uncertain significance (May 09, 2024)
10-3103812-C-A		not specified	Uncertain significance (Dec 03, 2021)
10-3103846-C-T			Benign (Aug 16, 2018)
10-3103861-C-T			Benign (Jul 23, 2018)
10-3103896-T-C		not specified	Uncertain significance (Nov 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PFKP	protein_coding	protein_coding	ENST00000381125	22	71380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.83e-25	0.00324	125553	1	193	125747	0.000772

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00709	521	521	1.00	0.0000350	5109
Missense in Polyphen		177	215.27	0.82221		1944
Synonymous	-5.01	309	215	1.43	0.0000166	1516
Loss of Function	0.711	40	45.2	0.886	0.00000244	476

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00325	0.00311
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000766	0.000761
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000630	0.000624
Middle Eastern	0.000766	0.000761
South Asian	0.00115	0.00111
Other	0.00133	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis.
• Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Fructose and mannose metabolism - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);RNA degradation - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Galactose metabolism - Homo sapiens (human);Pentose phosphate pathway - Homo sapiens (human);Cori Cycle;Pathways in clear cell renal cell carcinoma;Glycolysis and Gluconeogenesis;phosphoinositides and their downstream targets;Metabolism of carbohydrates;Glycolysis Gluconeogenesis;Glycolysis and Gluconeogenesis;Metabolism;Pentose phosphate cycle;Glycolysis;Galactose metabolism;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.313

Intolerance Scores

• loftool: 0.567
• rvis_EVS: -2.63
• rvis_percentile_EVS: 0.79

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.498
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pfkp

Gene ontology

• Biological process: fructose 6-phosphate metabolic process;glucose catabolic process;fructose 1,6-bisphosphate metabolic process;canonical glycolysis;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;cytoplasm;cytosol;6-phosphofructokinase complex;membrane;extracellular exosome
• Molecular function: 6-phosphofructokinase activity;ATP binding;AMP binding;protein-containing complex binding;cadherin binding;metal ion binding;monosaccharide binding;fructose-6-phosphate binding