TXNRD1

thioredoxin reductase 1, the group of Selenoproteins|Glutaredoxin domain containing

Basic information

Region (hg38): 12:104215778-104350307

Links

ENSG00000198431 ∙ NCBI:7296 ∙ OMIM:601112 ∙ HGNC:12437 ∙ Uniprot:Q16881 ∙ 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 TXNRD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNRD1 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				2	2	4
missense			30	3		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			21	3		24
Total	0	0	51	8	2

Variants in TXNRD1

This is a list of pathogenic ClinVar variants found in the TXNRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-104251538-C-G		not specified	Uncertain significance (Aug 02, 2022)
12-104251570-A-G			Likely benign (Jun 06, 2018)
12-104251602-G-C			Likely benign (Jul 21, 2018)
12-104251667-C-T		not specified	Uncertain significance (Nov 23, 2022)
12-104251668-G-A		not specified	Uncertain significance (May 26, 2024)
12-104258027-G-A			Likely benign (Dec 31, 2019)
12-104258044-G-T		not specified	Uncertain significance (Aug 04, 2021)
12-104288936-G-A			Likely benign (May 09, 2018)
12-104288942-G-A		not specified	Uncertain significance (Dec 05, 2022)
12-104289015-T-C		not specified	Uncertain significance (Oct 25, 2023)
12-104289049-G-T			Likely benign (Jan 09, 2019)
12-104303941-A-G		not specified	Likely benign (Mar 06, 2023)
12-104303959-G-C		not specified	Uncertain significance (Sep 13, 2023)
12-104303965-G-A		not specified	Uncertain significance (Mar 28, 2023)
12-104303966-G-A		not specified	Uncertain significance (Aug 02, 2023)
12-104303981-T-G		not specified	Uncertain significance (Dec 19, 2022)
12-104304035-A-G		not specified	Uncertain significance (Oct 30, 2023)
12-104304077-T-G		not specified	Uncertain significance (Jan 02, 2024)
12-104304148-G-A		not specified	Uncertain significance (Dec 28, 2023)
12-104304149-A-T		not specified	Uncertain significance (Dec 28, 2023)
12-104304189-A-T		not specified	Uncertain significance (Jan 02, 2024)
12-104304203-C-T		not specified	Uncertain significance (Jun 13, 2023)
12-104304273-C-A		not specified	Uncertain significance (Dec 18, 2023)
12-104304277-A-G		not specified	Uncertain significance (Mar 20, 2024)
12-104304295-G-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNRD1	protein_coding	protein_coding	ENST00000525566	17	134505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000161	0.998	124610	1	44	124655	0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	271	340	0.798	0.0000171	4169
Missense in Polyphen		118	164.88	0.71565		2021
Synonymous	0.889	110	123	0.898	0.00000633	1260
Loss of Function	2.79	15	32.0	0.468	0.00000152	440

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000450	0.000450
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000111
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000234	0.000230
Middle Eastern	0.000116	0.000111
South Asian	0.0000654	0.0000654
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enhances the transcriptional activity of estrogen receptors alpha and beta while isoform 5 enhances the transcriptional activity of the beta receptor only. Isoform 5 also mediates cell death induced by a combination of interferon-beta and retinoic acid. {ECO:0000269|PubMed:15199063, ECO:0000269|PubMed:18042542, ECO:0000269|PubMed:8577704, ECO:0000269|PubMed:9774665}.
• Pathway: Selenocompound metabolism - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Oxidative Stress Regulatory Pathway (Erythrocyte);Selenium Micronutrient Network;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Selenium Metabolism and Selenoproteins;Nuclear Receptors Meta-Pathway;NRF2 pathway;Oxidative Stress;Detoxification of Reactive Oxygen Species;Gene expression (Transcription);Metabolism of ingested H2SeO4 and H2SeO3 into H2Se;Generic Transcription Pathway;Metabolism of nucleotides;Cellular responses to stress;Metabolism of amino acids and derivatives;Interconversion of nucleotide di- and triphosphates;RNA Polymerase II Transcription;TCR;Metabolism;Metabolism of ingested MeSeO2H into MeSeH;Selenoamino acid metabolism;Pyrimidine metabolism;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;thioredoxin pathway;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• loftool: 0.757
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.8

Haploinsufficiency Scores

• pHI: 0.829
• hipred: N
• hipred_score: 0.380
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txnrd1
• Phenotype: cellular phenotype; growth/size/body region phenotype; embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: mesoderm formation;selenium compound metabolic process;signal transduction;cell population proliferation;nucleobase-containing small molecule interconversion;regulation of lipid metabolic process;electron transport chain;cellular response to oxidative stress;cell redox homeostasis;cellular oxidant detoxification
• Cellular component: fibrillar center;nucleoplasm;cytoplasm;mitochondrion;cytosol;extracellular exosome
• Molecular function: thioredoxin-disulfide reductase activity;protein binding;electron transfer activity;protein disulfide oxidoreductase activity;flavin adenine dinucleotide binding;methylselenol reductase activity;methylseleninic acid reductase activity