ClinVar Genomic variation as it relates to human health
NM_000371.4(TTR):c.157T>C (p.Phe53Leu)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000371.4(TTR):c.157T>C (p.Phe53Leu)
Variation ID: 13456 Accession: VCV000013456.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 18q12.1 18: 31592983 (GRCh38) [ NCBI UCSC ] 18: 29172946 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Aug 29, 2016 May 26, 2024 Oct 12, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000371.4:c.157T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000362.1:p.Phe53Leu missense NC_000018.10:g.31592983T>C NC_000018.9:g.29172946T>C NG_009490.1:g.6217T>C LRG_416:g.6217T>C LRG_416t1:c.157T>C LRG_416p1:p.Phe53Leu P02766:p.Phe53Leu - Protein change
- F53L
- Other names
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F33L
- Canonical SPDI
- NC_000018.10:31592982:T:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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TTR | - | - |
GRCh38 GRCh37 |
375 | 422 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (2) |
criteria provided, single submitter
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Oct 12, 2023 | RCV000014398.40 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Jan 9, 2023 | RCV001810860.15 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 10, 2023 | RCV002390108.10 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Feb 13, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001473955.1
First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021 |
Comment:
The TTR c.157T>C; p.Phe53Leu variant (rs121918068), also known as Phe33Leu, is reported in the literature in multiple individuals affected with TTR amyloidosis or amyloid polyneuropathy … (more)
The TTR c.157T>C; p.Phe53Leu variant (rs121918068), also known as Phe33Leu, is reported in the literature in multiple individuals affected with TTR amyloidosis or amyloid polyneuropathy (Altland 2007, Barreiros 2010, Chen 2014, Connors 2003, Ihse 2013, Ii 1991). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The phenylalanine at codon 53 is moderately conserved, and functional studies show altered multimerization properties (Altland 2007). Additionally, other amino acid substitutions at this codon (Cys, Ile, and Val) have been reported in individuals with TTR amyloidosis and are considered disease-causing (Altland 2007, Connors 2003, Venkatesh 2017). Based on available information, the p.Phe53Leu 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. Barreiros AP et al. Liver transplantation and combined liver-heart transplantation in patients with familial amyloid polyneuropathy: a single-center experience. Liver Transpl. 2010 Mar;16(3):314-23. Chen CH et al. A case of familial amyloidotic polyneuropathy with a rare Phe33Leu mutation in the TTR gene. J Formos Med Assoc. 2014 Aug;113(8):575-6. Connors LH et al. Tabulation of human transthyretin (TTR) variants, 2003. Amyloid. 2003 Sep;10(3):160-84. 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. Ii S et al. Two-tiered DNA-based diagnosis of transthyretin amyloidosis reveals two novel point mutations. Neurology. 1991 Jun;41(6):893-8. Venkatesh P et al. Vitreous Amyloidosis: Ocular, Systemic, and Genetic Insights. Ophthalmology. 2017 Jul;124(7):1014-1022. (less)
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Pathogenic
(Jul 20, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV002771670.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
Comment:
This variant has been identified in multiple individuals with transthyretin-related amyloidosis and/or amyloid cardiomyopathy. In some published literature, this variant is referred to as Phe33Leu. … (more)
This variant has been identified in multiple individuals with transthyretin-related amyloidosis and/or amyloid cardiomyopathy. In some published literature, this variant is referred to as Phe33Leu. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Computational tools predict this variant is damaging. (less)
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Pathogenic
(Jan 09, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV002820740.1
First in ClinVar: Jan 21, 2023 Last updated: Jan 21, 2023 |
Comment:
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; … (more)
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate a damaging effect; the variant destabilizes TTR monomers (Altland et al., 2007); This variant is associated with the following publications: (PMID: 9798666, 26521788, 31932463, 1932142, 20209591, 2046936, 33373035, 32789836, 34440326, 33739616, 23713495, 17503405) (less)
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Pathogenic
(Oct 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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Amyloidosis, hereditary systemic 1
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001202374.5
First in ClinVar: Apr 15, 2020 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 53 of the TTR protein (p.Phe53Leu). … (more)
This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 53 of the TTR protein (p.Phe53Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hereditary transthyretin-mediated (hATTR) amyloidosis (PMID: 1932142, 2046936, 9798666, 17503405, 20209591, 23713495). This variant is also known as Phe33Leu (F33L). ClinVar contains an entry for this variant (Variation ID: 13456). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TTR protein function. This variant disrupts the p.Phe53 amino acid residue in TTR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15478468, 17503405, 20558946, 22745357). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jan 10, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002703386.3
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.F53L pathogenic mutation (also known as c.157T>C), located in coding exon 2 of the TTR gene, results from a T to C substitution at … (more)
The p.F53L pathogenic mutation (also known as c.157T>C), located in coding exon 2 of the TTR gene, results from a T to C substitution at nucleotide position 157. The phenylalanine at codon 53 is replaced by leucine, an amino acid with highly similar properties. This alteration, which is also known as p.F33L, was first reported in a Polish-American individual who developed symptoms of autonomic dysfunction and neuropathy at 53 years of age; a sural nerve biopsy showed the presence of amyloid and immunohistochemistry revealed transthyretin (Ii S et al. Neurology, 1991 Jun;41:893-8). This variant has been identified in individuals of Polish, Swedish, Ashkenazi Jewish, and Asian ancestry with symptoms of familial amyloidotic polyneuropathy (Harding J et al. Biochim Biophys Acta. 1991; 1097(3):183-6; Holmgren G et al. Amyloid. 2005; 12(3):189-92; Leibou L et al. Isr Med Assoc J. 2012; 14(11):662-5; Chen CH et al. J Formos Med Assoc. 2014; 113(8):575-6). A functional study of urea gradients found this alteration resulted in decreased conformational stability of the monomer molecule (Altland K et al. Electrophoresis. 2007; 28(12):2053-64). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by BayesDel in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Nov 01, 1998)
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no assertion criteria provided
Method: literature only
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AMYLOIDOSIS, HEREDITARY SYSTEMIC 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000034647.3
First in ClinVar: Apr 04, 2013 Last updated: May 26, 2024 |
Comment on evidence:
Amyloid polyneuropathy has been related to a phe33-to-ile mutation in transthyretin (F33I; 176300.0002). Familial amyloidosis (AMYLD1; 105210) due to a phe33-to-leu (F33L) mutation was reported … (more)
Amyloid polyneuropathy has been related to a phe33-to-ile mutation in transthyretin (F33I; 176300.0002). Familial amyloidosis (AMYLD1; 105210) due to a phe33-to-leu (F33L) mutation was reported in one patient by Ii et al. (1991) and Harding et al. (1991) and in another patient by Myers et al. (1998). In both instances the patient was of Polish-American ethnicity, had no family history of amyloidosis, and had a late onset of symptoms. In the patient who was doubly reported, onset was at age 53 with paresthesias, sensory loss, and areflexia of the lower limbs due to a sensorimotor polyneuropathy along with constipation, impotence, and orthostatic hypotension due to autonomic neuropathy. The patient progressed to upper- and lower-limb sensorimotor polyneuropathy and an infiltrative cardiomyopathy. The patient reported by Myers et al. (1998) initially presented with symptomatic ascites and showed asymptomatic mild peripheral neuropathy, carpal tunnel syndrome, and mild cardiomyopathy at the age of 65 years. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Spectrum of transthyretin gene mutations and clinical characteristics of Polish patients with cardiac transthyretin amyloidosis. | Gawor M | Cardiology journal | 2022 | PMID: 32789836 |
Variant Transthyretin Amyloidosis (ATTRv) in Hungary: First Data on Epidemiology and Clinical Features. | Pozsonyi Z | Genes | 2021 | PMID: 34440326 |
Transthyretin-related familial amyloid polyneuropathy (ATTR-FAP) in Poland - genetic and clinical presentation. | Lipowska M | Neurologia i neurochirurgia polska | 2020 | PMID: 33373035 |
Hereditary transthyretin amyloidosis caused by the rare Phe33Leu mutation. | Björkenheim A | BMJ case reports | 2020 | PMID: 31932463 |
Clinical features of familial amyloid polyneuropathy carrying transthyretin mutations in four Chinese kindreds. | Liu G | Journal of the peripheral nervous system : JPNS | 2017 | PMID: 27859927 |
Hereditary Transthyretin Amyloidosis in Eight Chinese Families. | Meng LC | Chinese medical journal | 2015 | PMID: 26521788 |
A case of familial amyloidotic polyneuropathy with a rare Phe33Leu mutation in the TTR gene. | Chen CH | Journal of the Formosan Medical Association = Taiwan yi zhi | 2014 | PMID: 25037766 |
Amyloid fibrils containing fragmented ATTR may be the standard fibril composition in ATTR amyloidosis. | Ihse E | Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis | 2013 | PMID: 23713495 |
Disease profile and differential diagnosis of hereditary transthyretin-related amyloidosis with exclusively cardiac phenotype: an Italian perspective. | Rapezzi C | European heart journal | 2013 | PMID: 22745357 |
Clinical and genetic findings in eight Israeli patients with transthyretin-associated familial amyloid polyneuropathy. | Leibou L | The Israel Medical Association journal : IMAJ | 2012 | PMID: 23240369 |
A case of familial amyloid polyneuropathy due to Phe33Val TTR with vitreous involvement as the initial manifestation. | Kono S | Internal medicine (Tokyo, Japan) | 2010 | PMID: 20558946 |
Liver transplantation and combined liver-heart transplantation in patients with familial amyloid polyneuropathy: a single-center experience. | Barreiros AP | Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society | 2010 | PMID: 20209591 |
Genetic microheterogeneity of human transthyretin detected by IEF. | Altland K | Electrophoresis | 2007 | PMID: 17503405 |
Transthyretin RNA profiling in livers from transplanted patients affected by familial amyloidotic polyneuropathy, and identification of a dual transcription start point. | Rimessi P | Liver international : official journal of the International Association for the Study of the Liver | 2006 | PMID: 16448460 |
A Swedish family with the rare Phe33Leu transthyretin mutation. | Holmgren G | Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis | 2005 | PMID: 16194875 |
An unusual transthyretin gene missense mutation (TTR Phe33Val) linked to familial amyloidotic polyneuropathy. | Frigerio R | Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis | 2004 | PMID: 15478468 |
Familial amyloid with a transthyretin leucine 33 mutation presenting with ascites. | Myers TJ | American journal of hematology | 1998 | PMID: 9798666 |
Two-tiered DNA-based diagnosis of transthyretin amyloidosis reveals two novel point mutations. | Ii S | Neurology | 1991 | PMID: 2046936 |
A second transthyretin mutation at position 33 (Leu/Phe) associated with familial amyloidotic polyneuropathy. | Harding J | Biochimica et biophysica acta | 1991 | PMID: 1932142 |
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Text-mined citations for rs121918068 ...
HelpRecord last updated Nov 10, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.