chr14-81062179-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP5BP4BS1_SupportingBS2
The NM_000369.5(TSHR):c.202C>T(p.Pro68Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000359 in 1,611,868 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00037 ( 2 hom. )
Consequence
TSHR
NM_000369.5 missense
NM_000369.5 missense
Scores
3
10
6
Clinical Significance
Conservation
PhyloP100: 4.69
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 Likely_benign. Variant got -5 ACMG points.
PP5
Variant 14-81062179-C-T is Pathogenic according to our data. Variant chr14-81062179-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 437071.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=5, Pathogenic=2, Likely_pathogenic=3}. Variant chr14-81062179-C-T is described in Lovd as [Likely_pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.23717248). . Strength limited to SUPPORTING due to the PP5.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.000366 (534/1459658) while in subpopulation MID AF= 0.00435 (25/5750). AF 95% confidence interval is 0.00302. There are 2 homozygotes in gnomad4_exome. There are 294 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAdExome4 at 2 AD,AR gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TSHR | NM_000369.5 | c.202C>T | p.Pro68Ser | missense_variant | Exon 2 of 10 | ENST00000298171.7 | NP_000360.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TSHR | ENST00000298171.7 | c.202C>T | p.Pro68Ser | missense_variant | Exon 2 of 10 | 1 | NM_000369.5 | ENSP00000298171.2 |
Frequencies
GnomAD3 genomes 0.000302 AC: 46AN: 152092Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000543 AC: 136AN: 250508Hom.: 1 AF XY: 0.000635 AC XY: 86AN XY: 135410
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GnomAD4 exome AF: 0.000366 AC: 534AN: 1459658Hom.: 2 Cov.: 30 AF XY: 0.000405 AC XY: 294AN XY: 726136
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GnomAD4 genome 0.000296 AC: 45AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74440
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:6Uncertain:7
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Pathogenic:1Uncertain:3
| Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The TSHR p.P68S variant was identified in 2 of 382 proband chromosomes (frequency: 0.0052) from individuals with non-autoimmune subclinical hypothyroidism non-autoimmune hyperthyrotropinemia (Nicoletti_2009_PMID:19820021; Calebiro_2012_PMID:22049173). In a large consanguineous family with resistance to TSH, the p.P68S variant was found in 4 family members in the heterozygous state (1 mildly affected, 3 unaffected) and in 4 family members in the compound heterozygous state (2 affected, 2 mildly affected). Functional assays showed a decrease in TSHR activity when the p.P68S TSHR variant was transfected into HEK-293 cells alone, but not when transfected as wildtype-TSHR/p.P68S (mimicking heterozygosity) (Tenenbaum-Rakover_2009_PMID:19240155). The p.P68S variant was also identified in 4 of 111 pediatric patients; 3 patients had subclinical hypothyroidism (2 heterozygous, 1 compound heterozygous) and 1 patient had congenital hypothyroidism (heterozygous) (Vigone_2017_PMID:28561265). The variant was identified in dbSNP (ID: rs142063461), ClinVar (classified as uncertain significance by Illumina and as likely pathogenic by Genetic Services Laboratory, University of Chicago) and LOVD 3.0 (classified as likely pathogenic). The variant was identified in control databases in 140 of 281886 chromosomes (1 homozygous) at a frequency of 0.0004967 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Ashkenazi Jewish in 18 of 10358 chromosomes (freq: 0.001738), South Asian in 37 of 30534 chromosomes (freq: 0.001212), Other in 5 of 7178 chromosomes (freq: 0.000697), Latino in 24 of 35272 chromosomes (freq: 0.00068), European (non-Finnish) in 55 of 128682 chromosomes (freq: 0.000427) and African in 1 of 24926 chromosomes (freq: 0.00004), but was not observed in the East Asian or European (Finnish) populations. The p.P68 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the potential impact to the protein. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. Functional in vitro assays showed a decrease in cell surface expression of TSHR with the p.P68S compared to wildtype but no significant difference in biological activity (Nicoletti_2009_PMID:19820021). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. - |
| Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 16, 2024 | Identified in the heterozygous state in a patient with congenital hypothyroidism in the published literature, although this variant was inherited from a parent with unknown clinical status (PMID: 34248839); Published functional studies suggest this variant is associated with decreased TSH binding capacity and a reduction in cell-surface expression, but no overall effect on biological activity (PMID: 19820021, 19240155); Additional functional studies suggest this variant reduces TSH-stimulated downstream activity in cells transfected with P68S alone (simulating homozygosity) but no effect noted when cotransfecting P68S and wild-type TSHR (simulating heterozygosity) (PMID: 19240155); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in homozygous state in one clinically unaffected adult relative of an individual referred for genetic testing at GeneDx; This variant is associated with the following publications: (PMID: 27060741, 31589614, 34248839, 34426522, 26556299, 33558524, 34200080, 26990548, 28444304, 22049173, 34308104, 36913313, 36964991, 28561265, 34780050, 39337518, 25557138, 19820021, 19240155) - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 01, 2023 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 02, 2021 | This sequence change replaces proline with serine at codon 68 of the TSHR protein (p.Pro68Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine. This variant is present in population databases (rs142063461, ExAC 0.1%). This missense change has been observed in individual(s) with clinical features of hypothyroidism (PMID: 19240155, 25557138). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 437071). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects TSHR function (PMID: 19240155, 19820021). For these reasons, this variant has been classified as Pathogenic. - |
Hypothyroidism due to TSH receptor mutations Pathogenic:1Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 18, 2018 | The TSHR c.202C>T (p.Pro68Ser) variant has been reported in five studies in which it is found in at least 16 individuals affected with high TSH levels, including in five in a compound heterozygous state (two of whom were unrelated) and eleven in a heterozygous state (seven of whom were unrelated) (Tenenbaum-Rakover et al. 2009; Nicoletti et al. 2009; Calebiro et al. 2012; Deeb et al. 2016; Vignone et al. 2017). Only two of the above individuals had clinical symptoms of congenital hypothyroidism, and both individuals carried the p.Pro68Ser variant in a heterozygous state (Deeb et al. 2016; Vignone et al. 2017). The other individuals were classified as mildly affected with congenital hypothyroidism. The p.Pro68Ser variant was identified in a heterozygous state in three of 213 controls (Tenenbaum-Rakover et al. 2009; Nicoletti et al. 2009) and is reported at a frequency of 0.00332 in the Other population of the Exome Aggregation Consortium. One homozygote is reported in the South Asian population in the Genome Aggregation Database. Surface expression of the p.Pro68Ser variant was found to be reduced by 80% in HEK-293 cells and by 50% in COS-7 cells compared to wild type, but the biological activity as measured by cAMP production was not affected (Tenenbaum-Rakover et al. 2009; Nicoletti et al. 2009). Based on the collective evidence supporting a mild phenotype, the p.Pro68Ser variant is classified as a variant of unknown significance, but suspicious for pathogenicity for congenital hypothyroidism. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 01, 2016 | - - |
Familial hyperthyroidism due to mutations in TSH receptor Uncertain:2
| Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | Apr 21, 2023 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jan 27, 2022 | - - |
Familial gestational hyperthyroidism Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 28, 2024 | - - |
Inborn genetic diseases Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2021 | The c.202C>T (p.P68S) alteration is located in exon 2 (coding exon 2) of the TSHR gene. This alteration results from a C to T substitution at nucleotide position 202, causing the proline (P) at amino acid position 68 to be replaced by a serine (S)._x000D_ _x000D_ Based on the available evidence, this alteration is likely pathogenic for autosomal recessive congenital nongoitrous hypothyroidism; however, the association of this alteration with autosomal dominant nonautoimmune hyperthyroidism is unlikely. Based on data from the Genome Aggregation Database (gnomAD), the TSHR c.202C>T alteration was observed in 0.05% (140/281886) of total alleles studied, with a frequency of 0.17% (18/10358) in the Ashkenazi Jewish subpopulation. This variant has been observed as compound heterozygous with other TSHR variants in several individuals with elevated TSH levels and it has been reported to segregate with elevated TSH in multiple families (Tennenbaum-Rakover, 2009; Tennenbaum-Rakover, 2015; Vigone, 2017). This amino acid position is highly conserved in available vertebrate species. In vitro functional studies show that in the homozygous and compound heterozygous states, this alteration leads to a significant reduction in TSHR activity compared to wild-type (Tennenbaum-Rakover, 2009). Based on the available evidence, this alteration is classified as likely pathogenic. - |
TSHR-related disorder Pathogenic:1
| Likely pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 2024 | The TSHR c.202C>T variant is predicted to result in the amino acid substitution p.Pro68Ser. This variant has been reported in the homozygous and compound heterozygous states in individuals with hyperthyrotropinemia and mild hyperthyrotropinemia, and functional studies have found that this amino acid substitution decreases substrate binding capacity of the protein (Tenenbaum-Rakover et al., 2009. PubMed ID: 19240155; Nicoletti et al. 2009. PubMed ID: 19820021; Tenenbaum-Rakover et al. 2015. PubMed ID: 25557138). This variant is reported in 0.17% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. This variant is interpreted as likely pathogenic. - |
Familial hyperthyroidism due to mutations in TSH receptor;C1863959:Familial gestational hyperthyroidism;C3493776:Hypothyroidism due to TSH receptor mutations Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jun 22, 2024 | - - |
Malignant tumor of breast Uncertain:1
| Uncertain significance, no assertion criteria provided | research | Center of Medical Genetics and Primary Health Care | Apr 08, 2020 | ACMG Guidelines 2015 criteria PP2 Pathogenic Supporting: 38 out of 52 non-VUS missense variants in gene TSHR are PATH = 73.1% > threshold of 51.0%, and 44 out of 118 clinically reported variants in gene TSHR are PATH = 37.3% > threshold of 12.0%. PP3 Pathogenic Supporting: 9 pathogenic predictions from DANN, DEOGEN2, EIGEN, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster and REVEL vs 2 benign predictions from PrimateAI and SIFT. PP4 Pathogenic Supporting: The variant was detected in a female patient diagnosed with breast cancer at the age of 28 y.o. However, the current data are insufficient to assess the role of the variant in the development of breast cancer. Therefore, this variant was classified as a Variant of Unknown Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
.;.;.;D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;D;T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
.;M;.;.;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Pathogenic
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;D;T;D;D
Polyphen
0.99
.;D;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at