rs121918697
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1PM2PP2PP3_StrongPP5_Very_Strong
The NM_001354712.2(THRB):c.1012C>T(p.Arg338Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R338Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001354712.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THRB | NM_001354712.2 | c.1012C>T | p.Arg338Trp | missense_variant | 10/11 | ENST00000646209.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THRB | ENST00000646209.2 | c.1012C>T | p.Arg338Trp | missense_variant | 10/11 | NM_001354712.2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461884Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Thyroid hormone resistance, generalized, autosomal dominant Pathogenic:4
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | May 25, 2022 | Variant summary: THRB c.1012C>T (p.Arg338Trp) results in a non-conservative amino acid change located in the Nuclear hormone receptor, ligand-binding domain (IPR000536) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251472 control chromosomes (gnomAD). c.1012C>T has been reported in the literature in multiple individuals affected with Thyroid Hormone Resistance and was shown to segregate with disease within families (e.g. Weiss_1993, Alberobello_2011, Macchia_2014, Arsov_2019). These data indicate that the variant is very likely to be associated with disease. Experimental evidence demonstrated the variant affects protein function (Sasaki_1995, Ando_1996, Wan_2005). Two ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Provincial Medical Genetics Program of British Columbia, University of British Columbia | Jan 01, 2022 | - - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital | Jun 25, 2013 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2006 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Feb 06, 2024 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Feb 20, 2023 | In the published literature, the variant has been reported in individuals affected with selective pituitary resistance to thyroid hormone (PRTH) (PMIDs: 8514853 (1993), 8384535 (1993), 8889584 (1996), 8040303 (1994), 11518118 (2001), 16804041 (2006), 25040256 (2014), 26041374 (2015), and 30430796 (2018)). This variant is located within a hotspot in the hormone-binding domain of THRB and results in significant reduction of its T3-binding activity (PMIDs: 8674808 (1995), 8384535 (1993), 25040256 (2014), and 24174637 (2014)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. - |
Selective pituitary resistance to thyroid hormone Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at