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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	27010
Gene name	Thiamin pyrophosphokinase 1
Gene symbol	TPK1
Synonyms (NCBI Gene)	HTPK1PP20THMD5
Chromosome	7
Chromosome location	7q35
Summary	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

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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Childhood encephalopathy due to thiamine pyrophosphokinase deficiency	Likely pathogenic; Pathogenic	rs2151035560, rs2150697552, rs2150829457, rs2150827249, rs375169579, rs747753388, rs863224237, rs769525399, rs2548303507, rs1203658633, rs2548303949, rs2547520486, rs387906935, rs1563989427, rs368458768 View all (7 more)	RCV001379847 RCV001389581 RCV004765416 RCV001971347 RCV000578364 View all (17 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leigh syndrome	Pathogenic	rs375169579	RCV005361121	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
BREAST CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC LYMPHOCYTIC LEUKEMIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THIAMINE METABOLISM DYSFUNCTION SYNDROME 5	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TPK1-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (17)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Basal ganglia disease, biotin-responsive	Basal Ganglia Diseases	BEFREE	31404531		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	28182136		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	GWASCAT_DG	29059683		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	37551622	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood encephalopathy due to thiamine pyrophosphokinase deficiency	Encephalopathy	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Encephalopathies	Epileptic encephalopathy	BEFREE	25458521, 30483896		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh Syndrome	BEFREE	28706281		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	28182136		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30459934		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	28706281		★★★★★ ★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	28706281		★★★★★ ★☆☆☆☆ Found in Text Mining only
THIAMINE METABOLISM DYSFUNCTION SYNDROME 5 (EPISODIC ENCEPHALOPATHY TYPE)	THIAMINE METABOLISM DYSFUNCTION SYNDROME	ORPHANET_DG	22152682		★★★★★ ★☆☆☆☆ Found in Text Mining only
THIAMINE METABOLISM DYSFUNCTION SYNDROME 5 (EPISODIC ENCEPHALOPATHY TYPE)	THIAMINE METABOLISM DYSFUNCTION SYNDROME	UNIPROT_DG	22152682		★★★★★ ★☆☆☆☆ Found in Text Mining only
THIAMINE METABOLISM DYSFUNCTION SYNDROME 5 (EPISODIC ENCEPHALOPATHY TYPE)	THIAMINE METABOLISM DYSFUNCTION SYNDROME	CLINVAR_DG	22152682		★★★★★ ★☆☆☆☆ Found in Text Mining only
THIAMINE METABOLISM DYSFUNCTION SYNDROME 5 (EPISODIC ENCEPHALOPATHY TYPE)	THIAMINE METABOLISM DYSFUNCTION SYNDROME	GENOMICS_ENGLAND_DG	28431625		★★★★★ ★☆☆☆☆ Found in Text Mining only
THIAMINE METABOLISM DYSFUNCTION SYNDROME 5 (EPISODIC ENCEPHALOPATHY TYPE)	THIAMINE METABOLISM DYSFUNCTION SYNDROME	BEFREE	30789823		★★★★★ ★☆☆☆☆ Found in Text Mining only
THIAMINE METABOLISM DYSFUNCTION SYNDROME 5 (EPISODIC ENCEPHALOPATHY TYPE)	THIAMINE METABOLISM DYSFUNCTION SYNDROME	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

TPK1 (thiamin pyrophosphokinase 1)