ClinVar Genomic variation as it relates to human health

Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with hereditary amyloidosis, transthyretin-related (MIM#105210) and familial carpal tunnel syndrome (MIM#115430). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. Penetrance may vary by variant, geographic region, or ethnic group (PMID: 20301373). (I) 0200 - Variant is predicted to result in a missense amino acid change from threonine to alanine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v4) <0.001 for a dominant condition (27 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v4; 4 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated transthyretin domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported multiple times as pathogenic in individuals with familial amyloid polyneuropathy and is most commonly associated with cardiac amyloidosis (ClinVar, PMID: 21992998, 28739313). This variant is also known in the literature as p.(Thr60Ala). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 80 of the TTR protein (p.Thr80Ala). This variant is present in population databases (rs121918070, gnomAD 0.0009%). This missense change has been observed in individuals with amyloidosis (PMID: 3722385, 12050338, 21992998, 25997029, 26017327). It has also been observed to segregate with disease in related individuals. This variant is also known as p.Thr60Ala. ClinVar contains an entry for this variant (Variation ID: 13421). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TTR protein function. Experimental studies have shown that this missense change affects TTR function (PMID: 15820680). For these reasons, this variant has been classified as Pathogenic.

The p.T80A pathogenic mutation (also known as c.238A>G and T60A), located in coding exon 3 of the TTR gene, results from an A to G substitution at nucleotide position 238. The threonine at codon 80 is replaced by alanine, an amino acid with similar properties. This pathogenic mutation, also known as p.T60A, has been detected in multiple individuals with familial transthyretin amyloidosis and is associated with cardiac symptoms (Wallace MR et al. J. Clin. Invest., 1986 Jul;78:6-12; Zeldenrust SR. Amyloid, 2012 Jun;19 Suppl 1:22-4; Ihse E et al. Amyloid, 2013 Sep;20:142-50; Swiecicki PL et al. Amyloid, 2015 May;22:123-31). In one study of a cohort of 60 individuals with this mutation, 42% presented primarily with cardiac symptoms; autonomic and peripheral nerve dysfunction were observed in 42% and 23% of individuals, respectively (Sattianayagam PT et al. Eur. Heart J., 2012 May;33:1120-7). In a functional study, the authors demonstrated that TTR monomers with this mutation are in an unfolded state 80% of the time in 2.5M urea (Altland K et al. Electrophoresis, 2007 Jun;28:2053-64). In addition, analysis of the crystallized structure showed that this mutation changes the conformation, suggesting that this mutation is destabilizing to the TTR protein structure (Cendron L et al. J. Biol. Chem., 2009 Sep;284:25832-41). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

DNA sequence analysis of the TTR gene demonstrated a sequence change, c.238A>G, in exon 3 that results in an amino acid change, p.Thr80Ala. The p.Thr80Ala change affects a poorly conserved amino acid residue located in a domain of the TTR protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Thr80Ala substitution. This pathogenic sequence change has previously been described in several individuals with TTR-related amyloidosis (PMID: 3722385, 12050338, 21992998, 25997029, 26017327) and has been found to segregate with disease in related individuals. This sequence change has been described in the gnomAD database with a frequency of 0.002% in the overall population (dbSNP rs121918070). The p.Thr80Ala amino acid change occurs in a region of the TTR gene where other missense sequence changes have been described in individuals with TTR-related disorders. These collective evidences indicate that this sequence change is pathogenic.

The p.Thr80Ala variant (also described as p.Thr60Ala in the literature) in TTR has been reported in >80 individuals with hereditary transthyretin amyloidosis (ATTR), many of which had cardiac involvement, and segregated with disease in 7 affected relatives from 5 families (Wallace 1986 PMID: 3722385, Benson 1987 PMID: 3030336, Koeppen 1990 PMID: 2122246, Reilly 1995 PMID: 7608709, Kotani 2002 PMID: 12000195, Lachmann 2002 PMID: 12050338, Graham 2012, Sattianayagam 2012 PMID: 21992998, Fontana 2015 PMID: 25997029, Lanoue 2016 PMID: 26959691, Auer-Grumbach 2020 PMID: 32674397, LMM data). It has also been reported by other clinical laboratories in ClinVar (Variation ID: 13421) and has been identified in 0.003% (2/68028) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). In vitro functional studies provide some evidence that this variant impacts protein function (Altland 2007 PMID: 17503405). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hereditary transthyretin amyloidosis. ACMG/AMP Criteria applied: PS4, PP1_Strong, PM2_Supporting, PS3_Supporting.

The TTR c.238A>G; p.Thr80Ala variant (rs121918070), also known as p.Thr60Ala, is reported in the literature in multiple individuals and families affected with hereditary amyloidosis, associated mainly with amyloidotic cardiomyopathy at a late age of onset and a poor prognosis (Altland 2007, Dohrn 2013, Fontana 2015, Ihse 2013, Lachmann 2002, Pilebro 2016, Swiecicki 2015, Waits 1995, Wallace 1986). This variant is the most common pathogenic TTR variant in the United Kingdom, and has high prevalence in northwest Ireland (Reilly 1995, Sattianayagam 2012). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 13421), and is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. The threonine at codon 80 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.675). However, functional analyses of the variant protein show a reduction in stability compared to the wild-type protein (Cendron 2009, Sekijima 2005). Based on available information, the p.Thr80Ala variant is considered to be pathogenic. References: Altland K et al. Genetic microheterogeneity of human transthyretin detected by IEF. Electrophoresis. 2007 Jun;28(12):2053-64. PMID: 17503405. Cendron L et al. Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses. J Biol Chem. 2009 Sep 18;284(38):25832-41. PMID: 19602727. Dohrn MF et al. Diagnostic hallmarks and pitfalls in late-onset progressive transthyretin-related amyloid-neuropathy. J Neurol. 2013 Dec;260(12):3093-108. PMID: 24101130. Fontana M et al. Differential Myocyte Responses in Patients with Cardiac Transthyretin Amyloidosis and Light-Chain Amyloidosis: A Cardiac MR Imaging Study. Radiology. 2015 Nov;277(2):388-97. PMID: 25997029. Ihse E et al. Amyloid fibrils containing fragmented ATTR may be the standard fibril composition in ATTR amyloidosis. Amyloid. 2013 Sep;20(3):142-50. PMID: 23713495. Lachmann HJ et al. Misdiagnosis of hereditary amyloidosis as AL (primary) amyloidosis. N Engl J Med. 2002 Jun 6;346(23):1786-91. PMID: 12050338. Pilebro B et al. (99m)Tc-DPD uptake reflects amyloid fibril composition in hereditary transthyretin amyloidosis. Ups J Med Sci. 2016;121(1):17-24. PMID: 26849806. Reilly MM et al. Familial amyloid polyneuropathy (TTR ala 60) in north west Ireland: a clinical, genetic, and epidemiological study. J Neurol Neurosurg Psychiatry. 1995 Jul;59(1):45-9. PMID: 7608709. Sattianayagam PT et al. Cardiac phenotype and clinical outcome of familial amyloid polyneuropathy associated with transthyretin alanine 60 variant. Eur Heart J. 2012 May;33(9):1120-7. PMID: 21992998. Sekijima Y et al. The biological and chemical basis for tissue-selective amyloid disease. Cell. 2005 Apr 8;121(1):73-85. PMID: 15820680. Swiecicki PL et al. Hereditary ATTR amyloidosis: a single-institution experience with 266 patients. Amyloid. 2015;22(2):123-31. PMID: 26017327. Waits RP et al. Low plasma concentrations of retinol-binding protein in individuals with mutations affecting position 84 of the transthyretin molecule. Clin Chem. 1995 Sep;41(9):1288-91. PMID: 7656439. Wallace MR et al. Biochemical and molecular genetic characterization of a new variant prealbumin associated with hereditary amyloidosis. J Clin Invest. 1986 Jul;78(1):6-12. PMID: 3722385.

Converted during submission from pathogenic to Pathogenic.

Common pathogenic variant in the TTR gene, which has been reported in populations around the world in association with hereditary amyloidosis, amyloidotic cardiomyopathy, and polyneuropathy, and is the most common TTR variant in the UK and North-West Ireland (Wallace et al., 1986; Benson et al., 1987; Koeppen et al., 1990; Saunton et al., 1991; Kotani et al., 2002; Lachmann et al., 2002; Connors et al., 2011; Sattianayagam et al., 2012; Arruda-Olso et al., 2013; Ihse et al., 2013; Swiecicki et al., 2015; Reilly 1995); Observed in 58 patients with a clinical diagnosis of TTR amyloidosis; all had histological evidence of amyloid deposition, two had a cardiac transplant, and ten had a liver transplant (Swiecicki et al., 2015); Reported to segregate with amyloidosis in several families (Wallace et al., 1986; Koeppen et al., 1990; Reilly et al., 1995); Also reported as T60A due to a difference in cDNA numbering; Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Functional studies demonstrate this variant induces conformational changes within the TTR monomers that result in the destablization of the native structure of these monomers compared to wildtype, leading to amyloidogenic potential (Altland et al., 2007; Cendron et al., 2009); Reported in ClinVar as pathogenic (ClinVar Variant ID #13421; ClinVar); This variant is associated with the following publications: (PMID: 19602727, 26894299, 17968687, 24517438, 25604431, 1644839, 3722385, 21992998, 23713495, 12050338, 12000195, 24131106, 1664269, 3030336, 2122246, 15820680, 21838471, 22620962, 27033334, 26610878, 25997029, 24101130, 26959691, 26849806, 32674397, 26017327, 7608709, 26656838, 17503405)

The frequency of this variant in the general population is consistent with pathogenicity. (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)) This variant has been identified in multiple unrelated individuals with clinical features associated with this gene. Assessment of experimental evidence regarding the effect of this variant on protein function is inconclusive. The structural, stability, folding, thermodynamic, and thyroxine affinity assays are not inconsistent with, but not conclusively demonstrative of, pathogenicity (PMID: 3097057, 9818054, 15820680, 17503405, 19602727). This variant is mainly associated with hereditary TTR amyloid cardiomyopathy, formerly known as familial amyloidotic cardiomyopathy (FAC). In some published literature, this variant is referred to as p.Thr60Ala.

Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. p.Thr60Ala variant (aka p.Thr80Ala). This variant has been reported in many cases of amyloidosis. It has been associated with carpel tunnel syndrome, cardiac amyloidosis, and polyneuropathy.

Variant interpretted as Pathogenic and reported on 11-13-2019 by Lab or GTR ID 500068. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.