THTPA

thiamine triphosphatase

Basic information

Region (hg38): 14:23555988-23560271

Links

ENSG00000259431 ∙ NCBI:79178 ∙ OMIM:611612 ∙ HGNC:18987 ∙ Uniprot:Q9BU02 ∙ 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 THTPA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THTPA 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						0
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	1		4
Total	0	0	19	1	0

Variants in THTPA

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

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

Position	Type	Phenotype	Significance	ClinVar
14-23556786-G-T		not specified	Uncertain significance (Jun 23, 2023)
14-23556789-A-G		not specified	Uncertain significance (Sep 16, 2021)
14-23556798-C-T		not specified	Uncertain significance (Aug 22, 2023)
14-23556814-G-T		not specified	Uncertain significance (Dec 21, 2021)
14-23556822-T-C		not specified	Uncertain significance (Feb 06, 2023)
14-23556876-A-G		not specified	Uncertain significance (Sep 14, 2023)
14-23556882-C-T		not specified	Uncertain significance (May 04, 2022)
14-23556918-T-A		not specified	Uncertain significance (Mar 19, 2024)
14-23557007-G-A		not specified	Uncertain significance (Mar 07, 2024)
14-23557148-G-A		not specified	Uncertain significance (May 03, 2023)
14-23557200-C-G		not specified	Uncertain significance (Jun 02, 2023)
14-23557208-T-G		not specified	Uncertain significance (May 30, 2024)
14-23557229-G-A		not specified	Uncertain significance (May 08, 2023)
14-23557277-A-C		not specified	Uncertain significance (May 04, 2023)
14-23557296-G-A		not specified	Uncertain significance (Jun 02, 2024)
14-23557297-C-A		not specified	Uncertain significance (Jun 02, 2024)
14-23558709-G-C		not specified	Uncertain significance (Feb 27, 2023)
14-23558713-C-T		not specified	Uncertain significance (Mar 31, 2022)
14-23558751-C-T		not specified	Uncertain significance (Dec 13, 2023)
14-23558785-A-G		not specified	Uncertain significance (Dec 21, 2022)
14-23559778-T-G		not specified	Uncertain significance (Aug 02, 2022)
14-23559813-T-C		not specified	Uncertain significance (Jan 16, 2024)
14-23559948-T-C		not specified	Uncertain significance (Mar 16, 2022)
14-23559987-C-T		not specified	Likely benign (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THTPA	protein_coding	protein_coding	ENST00000288014	2	4265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000277	0.326	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.334	143	132	1.08	0.00000721	1455
Missense in Polyphen		44	41.34	1.0643		484
Synonymous	0.810	46	53.5	0.859	0.00000267	500
Loss of Function	0.298	9	10.0	0.899	7.49e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000975	0.0000967
Middle Eastern	0.000218	0.000217
South Asian	0.000273	0.000261
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolase highly specific for thiamine triphosphate (ThTP). {ECO:0000269|PubMed:11827967, ECO:0000269|PubMed:23707715}.
• Pathway: Thiamine metabolism - Homo sapiens (human);Thiamine Metabolism;Vitamin B1 (thiamin) metabolism;Metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.892
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.0724
• hipred: N
• hipred_score: 0.146
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thtpa

Gene ontology

• Biological process: generation of precursor metabolites and energy;thiamine metabolic process;dephosphorylation;thiamine diphosphate metabolic process;thiamine-containing compound metabolic process
• Cellular component: cytosol
• Molecular function: magnesium ion binding;hydrolase activity;thiamin-triphosphatase activity