Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	27010
Gene name Gene Name - the full gene name approved by the HGNC.	Thiamin pyrophosphokinase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TPK1
Synonyms (NCBI Gene) Gene synonyms aliases	HTPK1, PP20, THMD5
Chromosome Chromosome number	7
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	7q35
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene functions as a homodimer and catalyzes the conversion of thiamine to thiamine pyrophosphate, a cofactor for some enzymes of the glycolytic and energy production pathways. Defects in this gene are a cause of thiamine metabo

Show/Hide all(14)

SNP ID	Visualize variation	Clinical significance	Consequence
rs113536847	G>A	Benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, 3 prime UTR variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs368458768	C>G,T	Pathogenic, uncertain-significance	Missense variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant, 3 prime UTR variant
rs371271054	T>C	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant, 3 prime UTR variant
rs375169579	T>A	Pathogenic-likely-pathogenic, pathogenic	Genic downstream transcript variant, intron variant
rs387906935	T>G	Pathogenic	Missense variant, intron variant, 5 prime UTR variant, coding sequence variant, synonymous variant, genic upstream transcript variant, non coding transcript variant
rs387906936	A>G	Pathogenic, uncertain-significance	Missense variant, intron variant, 5 prime UTR variant, coding sequence variant, genic upstream transcript variant, non coding transcript variant
rs747753388	C>T	Pathogenic-likely-pathogenic	Splice donor variant, intron variant, genic upstream transcript variant
rs769525399	C>G	Uncertain-significance, likely-pathogenic	Coding sequence variant, intron variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs776874412	C>T	Pathogenic	Splice acceptor variant, genic downstream transcript variant
rs863224237	T>C	Pathogenic, uncertain-significance	Genic upstream transcript variant, splice acceptor variant, upstream transcript variant
rs863224238	C>-	Pathogenic	Coding sequence variant, non coding transcript variant, 5 prime UTR variant, frameshift variant
rs1417315589	A>G	Pathogenic	Missense variant, intron variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs1554523224	A>C	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs1588141902	->T	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant, non coding transcript variant

Show/Hide all(62)

miRTarBase ID	miRNA	Experiments	Reference
MIRT525493	hsa-miR-548az-5p	PAR-CLIP	22012620
MIRT525492	hsa-miR-548t-5p	PAR-CLIP	22012620
MIRT525491	hsa-miR-106a-5p	PAR-CLIP	22012620
MIRT525490	hsa-miR-106b-5p	PAR-CLIP	22012620
MIRT525489	hsa-miR-17-5p	PAR-CLIP	22012620
MIRT525488	hsa-miR-20a-5p	PAR-CLIP	22012620
MIRT525487	hsa-miR-20b-5p	PAR-CLIP	22012620
MIRT525486	hsa-miR-519d-3p	PAR-CLIP	22012620
MIRT525485	hsa-miR-526b-3p	PAR-CLIP	22012620
MIRT525484	hsa-miR-93-5p	PAR-CLIP	22012620
MIRT525483	hsa-miR-371a-3p	PAR-CLIP	22012620
MIRT525482	hsa-miR-4717-3p	PAR-CLIP	22012620
MIRT525481	hsa-miR-4704-3p	PAR-CLIP	22012620
MIRT525480	hsa-miR-3064-3p	PAR-CLIP	22012620
MIRT525493	hsa-miR-548az-5p	PAR-CLIP	22012620
MIRT525492	hsa-miR-548t-5p	PAR-CLIP	22012620
MIRT525491	hsa-miR-106a-5p	PAR-CLIP	22012620
MIRT525490	hsa-miR-106b-5p	PAR-CLIP	22012620
MIRT525489	hsa-miR-17-5p	PAR-CLIP	22012620
MIRT525488	hsa-miR-20a-5p	PAR-CLIP	22012620
MIRT525487	hsa-miR-20b-5p	PAR-CLIP	22012620
MIRT525486	hsa-miR-519d-3p	PAR-CLIP	22012620
MIRT525485	hsa-miR-526b-3p	PAR-CLIP	22012620
MIRT525484	hsa-miR-93-5p	PAR-CLIP	22012620
MIRT525483	hsa-miR-371a-3p	PAR-CLIP	22012620
MIRT525482	hsa-miR-4717-3p	PAR-CLIP	22012620
MIRT525481	hsa-miR-4704-3p	PAR-CLIP	22012620
MIRT525480	hsa-miR-3064-3p	PAR-CLIP	22012620
MIRT1449375	hsa-miR-325	CLIP-seq
MIRT1449376	hsa-miR-4766-5p	CLIP-seq
MIRT1449377	hsa-miR-488	CLIP-seq
MIRT1449378	hsa-miR-628-3p	CLIP-seq
MIRT1449379	hsa-miR-141	CLIP-seq
MIRT1449380	hsa-miR-200a	CLIP-seq
MIRT1449381	hsa-miR-3127-5p	CLIP-seq
MIRT1449382	hsa-miR-3143	CLIP-seq
MIRT1449383	hsa-miR-3186-3p	CLIP-seq
MIRT1449384	hsa-miR-3918	CLIP-seq
MIRT1449385	hsa-miR-4268	CLIP-seq
MIRT1449386	hsa-miR-4448	CLIP-seq
MIRT1449387	hsa-miR-4477a	CLIP-seq
MIRT1449388	hsa-miR-4490	CLIP-seq
MIRT1449389	hsa-miR-4705	CLIP-seq
MIRT1449390	hsa-miR-4729	CLIP-seq
MIRT1449391	hsa-miR-543	CLIP-seq
MIRT2355672	hsa-miR-1267	CLIP-seq
MIRT2355673	hsa-miR-3545-3p	CLIP-seq
MIRT2355674	hsa-miR-3908	CLIP-seq
MIRT2355675	hsa-miR-4709-5p	CLIP-seq
MIRT1449390	hsa-miR-4729	CLIP-seq
MIRT2355676	hsa-miR-4753-3p	CLIP-seq
MIRT2355677	hsa-miR-539	CLIP-seq
MIRT2355678	hsa-miR-580	CLIP-seq
MIRT2462204	hsa-miR-4733-3p	CLIP-seq
MIRT2462205	hsa-miR-501-3p	CLIP-seq
MIRT2462206	hsa-miR-502-3p	CLIP-seq
MIRT2462207	hsa-miR-767-5p	CLIP-seq
MIRT2649232	hsa-miR-1255a	CLIP-seq
MIRT2649233	hsa-miR-1255b	CLIP-seq
MIRT2649234	hsa-miR-4328	CLIP-seq
MIRT2355675	hsa-miR-4709-5p	CLIP-seq
MIRT2649235	hsa-miR-4782-5p	CLIP-seq

Show/Hide all(21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004788	Function	Thiamine diphosphokinase activity	IBA
GO:0004788	Function	Thiamine diphosphokinase activity	IDA	11342111, 38547260
GO:0004788	Function	Thiamine diphosphokinase activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005524	Function	ATP binding	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006772	Process	Thiamine metabolic process	IEA
GO:0006772	Process	Thiamine metabolic process	IEA
GO:0009229	Process	Thiamine diphosphate biosynthetic process	IBA
GO:0009229	Process	Thiamine diphosphate biosynthetic process	IDA	11342111, 38547260
GO:0009229	Process	Thiamine diphosphate biosynthetic process	IEA
GO:0010510	Process	Regulation of pyruvate decarboxylation to acetyl-CoA	IMP	38547260
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030975	Function	Thiamine binding	IEA
GO:0042802	Function	Identical protein binding	IPI	25502805, 29892012, 31515488, 32296183
GO:0141200	Function	UTP thiamine diphosphokinase activity	IDA	38547260
GO:0141200	Function	UTP thiamine diphosphokinase activity	IEA

MIM	HGNC	e!Ensembl
606370	17358	ENSG00000196511

Protein

UniProt ID

Q9H3S4

Protein name

Thiamine pyrophosphokinase 1 (hTPK1) (EC 2.7.6.-) (Placental protein 20) (PP20) (Thiamin pyrophosphokinase 1)

Protein function

Catalyzes the phosphorylation of thiamine to thiamine pyrophosphate (TPP) utilizing UTP and therefore links the biosynthesis of TPP to pyrimidines metabolism (PubMed:38547260). By producing thiamine pyrophosphate, a cofactor of the mitochondrial

PDB

3S4Y , 9HJC

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04263	TPK_catalytic	32 → 154	Thiamin pyrophosphokinase, catalytic domain	Domain
PF04265	TPK_B1_binding	169 → 236	Thiamin pyrophosphokinase, vitamin B1 binding domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Detected in heart, kidney, testis, small intestine and peripheral blood leukocytes, and at very low levels in a variety of tissues. {ECO:0000269|PubMed:11342111, ECO:0000269|PubMed:11342117}.

Sequence

MEHAFTPLEPLLSTGNLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGER
ESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVD
VIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHVDTGMEG
DWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMA
IKS

Sequence length

243

Interactions

View interactions

	KEGG		Reactome
	Thiamine metabolism Metabolic pathways Biosynthesis of cofactors		Vitamin B1 (thiamin) metabolism

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Encephalopathy	childhood encephalopathy due to thiamine pyrophosphokinase deficiency	rs387906935, rs760398697, rs1563989427, rs375169579, rs747753388, rs863224237, rs769525399, rs368458768, rs776874412, rs1417315589, rs1554523224	N/A
leigh syndrome	Leigh syndrome	rs375169579	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Breast Cancer	Breast cancer	N/A	N/A	GWAS
Lymphocytic Leukemia	Chronic lymphocytic leukemia	N/A	N/A	GWAS

Show/Hide Text Mining Associations (6)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Breast Neoplasms	Associate	37551622
Lymphoma Primary Effusion	Associate	21685375
Muscle Hypotonia	Associate	36175994
Neoplasms	Associate	21685375, 25788274
Neoplasms	Inhibit	37551622
Pyruvate Dehydrogenase Complex Deficiency Disease	Associate	40225937

TPK1 (thiamin pyrophosphokinase 1)