TXN2

thioredoxin 2

Basic information

Region (hg38): 22:36467046-36481640

Links

ENSG00000100348

∙ NCBI:25828 ∙ OMIM:609063 ∙ HGNC:17772 ∙ Uniprot:Q99757 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

combined oxidative phosphorylation defect type 29 (Supportive), mode of inheritance: AR
combined oxidative phosphorylation deficiency 29 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 29	AR	Biochemical	Medical management (with coenzyme Q10) has been described as beneficial	Biochemical; Neurologic	26626369

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TXN2 gene.

not_provided (46 variants)
not_specified (18 variants)
Combined_oxidative_phosphorylation_deficiency_29 (3 variants)
TXN2-related_disorder (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012473.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				16 clinvar	1 clinvar	17
missense			33 clinvar	1 clinvar		34
nonsense	1 clinvar		1 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	35	17	1

Highest pathogenic variant AF is 0.0000150556

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXN2	protein_coding	protein_coding	ENST00000216185	3	14995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000256	0.325	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.615	79	95.9	0.823	0.00000499	1078
Missense in Polyphen		17	30.716	0.55347		371
Synonymous	-0.624	44	39.0	1.13	0.00000219	345
Loss of Function	0.0508	7	7.15	0.979	4.65e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Important for the control of mitochondrial reactive oxygen species homeostasis, apoptosis regulation and cell viability. Possesses a dithiol-reducing activity. {ECO:0000269|PubMed:12032145, ECO:0000269|PubMed:12080052, ECO:0000269|PubMed:26626369}.;
Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Oxidative Stress;Detoxification of Reactive Oxygen Species;Cellular responses to stress;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;Metabolism;Cellular responses to external stimuli;Sulfur amino acid metabolism (Consensus)

Intolerance Scores

loftool: 0.605
rvis_EVS: -0.36
rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

pHI: 0.305
hipred: N
hipred_score: 0.219
ghis: 0.625

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Txn2
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; 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); growth/size/body region phenotype; cellular phenotype;

Gene ontology

Biological process: sulfur amino acid catabolic process;response to hypoxia;glycerol ether metabolic process;response to oxidative stress;response to hormone;response to glucose;response to organic cyclic compound;cellular response to nutrient levels;response to drug;cell redox homeostasis;response to axon injury;oxidation-reduction process
Cellular component: nucleolus;mitochondrion;mitochondrial matrix;dendrite;neuronal cell body
Molecular function: protein binding;peptide-methionine (S)-S-oxide reductase activity;protein disulfide oxidoreductase activity;peptide-methionine (R)-S-oxide reductase activity;protein-containing complex binding