rs786204790
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePP5_Very_Strong
The NM_000369.5(TSHR):c.545+2_545+3del variant causes a splice donor, coding sequence change. The variant allele was found at a frequency of 0.0000149 in 1,613,684 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
TSHR
NM_000369.5 splice_donor, coding_sequence
NM_000369.5 splice_donor, coding_sequence
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.93
Genes affected
TSHR (HGNC:12373): (thyroid stimulating hormone receptor) The protein encoded by this gene is a membrane protein and a major controller of thyroid cell metabolism. The encoded protein is a receptor for thyrothropin and thyrostimulin, and its activity is mediated by adenylate cyclase. Defects in this gene are a cause of several types of hyperthyroidism. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.033551197 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
PP5
?
Variant 14-81092607-CTG-C is Pathogenic according to our data. Variant chr14-81092607-CTG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 189249.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSHR | NM_000369.5 | c.545+2_545+3del | splice_donor_variant, coding_sequence_variant | 6/10 | ENST00000298171.7 | ||
LOC101928462 | XR_001751022.2 | n.881+973_881+974del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSHR | ENST00000298171.7 | c.545+2_545+3del | splice_donor_variant, coding_sequence_variant | 6/10 | 1 | NM_000369.5 | P1 | ||
ENST00000646052.2 | n.904+973_904+974del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461504Hom.: 0 AF XY: 0.0000124 AC XY: 9AN XY: 727064
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hypothyroidism due to TSH receptor mutations Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 18, 2014 | The c.545+2_545+3del variant in TSHR has not been reported in individuals with disease or in large population studies. This variant occurs in the invariant region (+/- 1/2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. Biallelic loss-of-function variants in the TSHR gene have been shown to cause thyroid-stimulating hormone resistance (see review by Cassio 2013). Although there are multiple cases identified with only a single heterozygous pathogenic variant, insufficient evidence exists to determine if a true carrier phenotype is possible or if these studies simply did not find the second variant. In summary, this novel variant is likely to be pathogenic in a recessive manner for TSH resistance, though additional studies are required to fully establish its clinical significance. - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 20, 2023 | This sequence change affects a splice site in intron 6 of the TSHR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TSHR are known to be pathogenic (PMID: 8954020). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSHR-related conditions. ClinVar contains an entry for this variant (Variation ID: 189249). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
Computational scores
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SpliceAI score (max)
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DS_DL_spliceai
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at