DIO3
iodothyronine deiodinase 3, the group of Selenoproteins
Basic information
Region (hg38): 14:101560139-101563452
Previous symbols: [ "TXDI3" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (13 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DIO3 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 | 1 | |||||
| missense | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 1 |
Variants in DIO3
This is a list of pathogenic ClinVar variants found in the DIO3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-101561503-C-A | not specified | Likely benign (May 23, 2024) | ||
| 14-101561515-T-C | not specified | Likely benign (Aug 02, 2022) | ||
| 14-101561554-G-A | not specified | Uncertain significance (Jul 12, 2022) | ||
| 14-101561558-C-T | not specified | Uncertain significance (Jan 24, 2024) | ||
| 14-101561615-C-T | not specified | Uncertain significance (Sep 22, 2022) | ||
| 14-101561719-C-T | not specified | Uncertain significance (Aug 17, 2022) | ||
| 14-101561776-C-G | not specified | Uncertain significance (Apr 13, 2022) | ||
| 14-101561940-C-A | not specified | Uncertain significance (Aug 19, 2023) | ||
| 14-101561940-C-G | not specified | Uncertain significance (Jan 17, 2023) | ||
| 14-101562081-C-G | not specified | Uncertain significance (Jul 08, 2022) | ||
| 14-101562109-G-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 14-101562195-G-T | not specified | Uncertain significance (May 18, 2023) | ||
| 14-101562208-G-A | not specified | Uncertain significance (Nov 15, 2021) | ||
| 14-101562214-G-A | not specified | Uncertain significance (Aug 22, 2023) | ||
| 14-101562327-C-T | Benign (Jun 15, 2018) | |||
| 14-101562394-C-T | not specified | Uncertain significance (Jan 06, 2023) | ||
| 14-101562395-G-A | not specified | Likely benign (May 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DIO3 | protein_coding | protein_coding | ENST00000510508 | 1 | 2102 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.623 | 0.370 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.97 | 132 | 213 | 0.620 | 0.0000143 | 1947 |
| Missense in Polyphen | 45 | 100.08 | 0.44965 | 858 | ||
| Synonymous | -0.0166 | 101 | 101 | 1.00 | 0.00000763 | 637 |
| Loss of Function | 2.17 | 1 | 7.36 | 0.136 | 3.20e-7 | 70 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Responsible for the deiodination of T4 (3,5,3',5'- tetraiodothyronine) into RT3 (3,3',5'-triiodothyronine) and of T3 (3,5,3'-triiodothyronine) into T2 (3,3'-diiodothyronine). RT3 and T2 are inactive metabolites. May play a role in preventing premature exposure of developing fetal tissues to adult levels of thyroid hormones. Can regulate circulating fetal thyroid hormone concentrations throughout gestation. Essential role for regulation of thyroid hormone inactivation during embryological development. {ECO:0000269|PubMed:7593630}.;
- Pathway
- Thyroid hormone signaling pathway - Homo sapiens (human);Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins;Regulation of thyroid hormone activity;Metabolism of amino acids and derivatives;Tyrosine metabolism;Metabolism;thyroid hormone metabolism I (via deiodination);thyronamine and iodothyronamine metabolism;Thyroxine biosynthesis;Amine-derived hormones
(Consensus)
Intolerance Scores
- loftool
- 0.0557
- rvis_EVS
- -0.29
- rvis_percentile_EVS
- 32.94
Haploinsufficiency Scores
- pHI
- 0.299
- hipred
- N
- hipred_score
- 0.464
- ghis
- 0.432
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- 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
- Dio3
- Phenotype
- liver/biliary system phenotype; reproductive system 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); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- dio3a
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- thyroid hormone generation;biological_process;positive regulation of multicellular organism growth;thyroid hormone metabolic process;thyroid hormone catabolic process;hormone biosynthetic process;negative regulation of eye photoreceptor cell development;macromolecule metabolic process;retinal cone cell development;oxidation-reduction process;retinal cone cell apoptotic process
- Cellular component
- plasma membrane;endosome membrane;integral component of membrane
- Molecular function
- thyroxine 5'-deiodinase activity;thyroxine 5-deiodinase activity