TXN

thioredoxin

Basic information

Region (hg38): 9:110243810-110256507

Links

ENSG00000136810

∙ NCBI:7295 ∙ OMIM:187700 ∙ HGNC:12435 ∙ Uniprot:P10599 ∙ 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 TXN gene.

Variants pathogenicity by type

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

Variants in TXN

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

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

Position	Type	Phenotype	Significance	ClinVar
9-110244173-A-G		not specified	Uncertain significance (Nov 13, 2023)	3185132
9-110251438-C-T		not specified	Likely benign (Mar 28, 2023)	2530547

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXN	protein_coding	protein_coding	ENST00000374517	5	12830

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.201	0.759	125704	0	3	125707	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	30	53.4	0.562	0.00000254	699
Missense in Polyphen		4	9.584	0.41736		167
Synonymous	0.142	18	18.8	0.958	0.00000111	175
Loss of Function	1.71	2	6.82	0.293	2.88e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions. Plays a role in the reversible S-nitrosylation of cysteine residues in target proteins, and thereby contributes to the response to intracellular nitric oxide. Nitrosylates the active site Cys of CASP3 in response to nitric oxide (NO), and thereby inhibits caspase-3 activity. Induces the FOS/JUN AP-1 DNA-binding activity in ionizing radiation (IR) cells through its oxidation/reduction status and stimulates AP-1 transcriptional activity.;
Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Oxidative Stress Regulatory Pathway (Erythrocyte);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Selenium Micronutrient Network;TNF alpha Signaling Pathway;Human Complement System;Nuclear Receptors Meta-Pathway;NRF2 pathway;VEGFA-VEGFR2 Signaling Pathway;Detoxification of Reactive Oxygen Species;Gene expression (Transcription);Generic Transcription Pathway;Oxidative Stress Induced Senescence;The NLRP3 inflammasome;Metabolism of nucleotides;Cellular Senescence;Inflammasomes;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;Cellular responses to stress;Metabolism of proteins;Interconversion of nucleotide di- and triphosphates;RNA Polymerase II Transcription;Protein repair;Innate Immune System;Immune System;Metabolism;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;Transcriptional Regulation by TP53;TNFalpha;TNF receptor signaling pathway ;p38 MAPK signaling pathway;Signaling events mediated by PTP1B (Consensus)

Recessive Scores

pRec: 0.729

Intolerance Scores

loftool: 0.260
rvis_EVS: 0.01
rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

pHI: 0.346
hipred: Y
hipred_score: 0.567
ghis: 0.520

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Txn1
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); embryo phenotype; cellular phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;glycerol ether metabolic process;signal transduction;cell-cell signaling;cell population proliferation;response to radiation;activation of protein kinase B activity;positive regulation of peptidyl-serine phosphorylation;obsolete regulation of protein import into nucleus, translocation;positive regulation of DNA binding;cell redox homeostasis;negative regulation of protein export from nucleus;positive regulation of protein kinase B signaling;oxidation-reduction process;negative regulation of hydrogen peroxide-induced cell death
Cellular component: nucleus;cytosol;extracellular exosome
Molecular function: RNA binding;protein binding;protein disulfide oxidoreductase activity;peptide disulfide oxidoreductase activity