DIO2
Basic information
Region (hg38): 14:80197526-80387757
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DIO2 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 | 7 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 6 | 1 | 1 |
Variants in DIO2
This is a list of pathogenic ClinVar variants found in the DIO2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
14-80201236-G-A | Levothyroxine response | other (-) | ||
14-80202694-C-A | not specified | Uncertain significance (Nov 04, 2022) | ||
14-80202706-T-C | not specified | Uncertain significance (Feb 27, 2023) | ||
14-80202748-G-A | not specified | Uncertain significance (Oct 06, 2023) | ||
14-80202870-C-A | not specified | Uncertain significance (Mar 15, 2024) | ||
14-80202892-G-C | not specified | Uncertain significance (Feb 02, 2022) | ||
14-80202894-G-A | not specified | Uncertain significance (Apr 17, 2023) | ||
14-80203065-T-G | not specified | Uncertain significance (Dec 19, 2023) | ||
14-80203237-T-C | Levothyroxine response | other (-) | ||
14-80203244-G-C | Benign (Aug 16, 2018) | |||
14-80211286-C-T | not specified | Likely benign (Jun 24, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DIO2 | protein_coding | protein_coding | ENST00000555750 | 3 | 190228 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.620 | 0.379 | 124599 | 0 | 3 | 124602 | 0.0000120 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.935 | 137 | 171 | 0.799 | 0.00000981 | 1984 |
Missense in Polyphen | 46 | 67.988 | 0.67659 | 772 | ||
Synonymous | 0.987 | 58 | 68.4 | 0.848 | 0.00000380 | 627 |
Loss of Function | 2.63 | 2 | 11.7 | 0.171 | 6.49e-7 | 136 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
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 | 0.0000654 | 0.0000654 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Responsible for the deiodination of T4 (3,5,3',5'- tetraiodothyronine) into T3 (3,5,3'-triiodothyronine). Essential for providing the brain with appropriate levels of T3 during the critical period of development.;
- Pathway
- Thyroid hormone signaling pathway - Homo sapiens (human);Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins;Angiopoietin Like Protein 8 Regulatory Pathway;Regulation of thyroid hormone activity;Metabolism of amino acids and derivatives;Metabolism;thyroid hormone metabolism II (via conjugation and/or degradation);thyroid hormone metabolism I (via deiodination);thyronamine and iodothyronamine metabolism;Thyroxine biosynthesis;Amine-derived hormones
(Consensus)
Intolerance Scores
- loftool
- 0.715
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.125
- hipred
- N
- hipred_score
- 0.269
- ghis
- 0.487
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.122
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dio2
- Phenotype
- homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; renal/urinary system phenotype; skeleton phenotype; digestive/alimentary phenotype;
Zebrafish Information Network
- Gene name
- dio2
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- orientation
Gene ontology
- Biological process
- selenocysteine incorporation;thyroid hormone generation;thyroid hormone metabolic process;hormone biosynthetic process;oxidation-reduction process;positive regulation of cold-induced thermogenesis
- Cellular component
- plasma membrane;membrane;integral component of membrane
- Molecular function
- thyroxine 5'-deiodinase activity;selenium binding;ubiquitin protein ligase binding