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NM_000371.4(TTR):c.238A>G (p.Thr80Ala) AND Amyloidosis, hereditary systemic 1

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Jan 31, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000014363.59

Allele description [Variation Report for NM_000371.4(TTR):c.238A>G (p.Thr80Ala)]

NM_000371.4(TTR):c.238A>G (p.Thr80Ala)

Gene:
TTR:transthyretin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q12.1
Genomic location:
Preferred name:
NM_000371.4(TTR):c.238A>G (p.Thr80Ala)
Other names:
T60A; p.T80A:ACT>GCT
HGVS:
  • NC_000018.10:g.31595157A>G
  • NG_009490.1:g.8391A>G
  • NM_000371.4:c.238A>GMANE SELECT
  • NP_000362.1:p.Thr80Ala
  • NP_000362.1:p.Thr80Ala
  • LRG_416t1:c.238A>G
  • LRG_416:g.8391A>G
  • LRG_416p1:p.Thr80Ala
  • NC_000018.9:g.29175120A>G
  • NM_000371.3:c.238A>G
  • P02766:p.Thr80Ala
  • c.238A>G
  • p.THR80ALA
Protein change:
T80A; THR60ALA
Links:
UniProtKB: P02766#VAR_007573; OMIM: 176300.0004; dbSNP: rs121918070
NCBI 1000 Genomes Browser:
rs121918070
Molecular consequence:
  • NM_000371.4:c.238A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Amyloidosis, hereditary systemic 1 (AMYLD1)
Synonyms:
Amyloidosis Transthyretin related; Amyloid polyneuropathy transthyretin related; Transthyretin amyloidosis; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0971004; MedGen: C2751492; Orphanet: 85447; Orphanet: 85451; OMIM: 105210

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000034612OMIM
no assertion criteria provided
Pathogenic
(Jun 6, 2002)
germlineliterature only

PubMed (9)
[See all records that cite these PMIDs]

Benson, M. D. Characterization of an amyloid fibril protein in heredofamilial amyloidosis. (Abstract) Clin. Res. 28: 340A, 1980.,

SCV000053246Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
pathogenic
(Aug 18, 2011)
germlinecuration, clinical testing

PubMed (14)
[See all records that cite these PMIDs]

Citation Link,

SCV000060026Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 27, 2023)
germlineclinical testing

PubMed (21)
[See all records that cite these PMIDs]

SCV000541954Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 31, 2024)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV001423371GenomeConnect, ClinGen
no classification provided
not providedunknownphenotyping only

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedphenotyping only
not providedgermlineyes13not providednot provided13not providedcuration
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Hereditary amyloidosis and cardiomyopathy.

Benson MD.

Am J Med. 1992 Jul;93(1):1-2. No abstract available.

PubMed [citation]
PMID:
1626556

Identification of carriers of a variant plasma prealbumin (transthyretin) associated with familial amyloidotic polyneuropathy type I.

Benson MD, Dwulet FE.

J Clin Invest. 1985 Jan;75(1):71-5.

PubMed [citation]
PMID:
2981253
PMCID:
PMC423403
See all PubMed Citations (38)

Details of each submission

From OMIM, SCV000034612.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (9)

Description

Wallace et al. (1986) found substitution of alanine for threonine at position 60 of transthyretin (T60A) in an Irish kindred with familial amyloid polyneuropathy (AMYLD1; 105210) from the Appalachian region of the United States. As in the Indiana form (176300.0006), major deposits of amyloid occurred in the heart, but otherwise the disorder appeared 'to have a unique disease progression.' Benson et al. (1987) gave the clinical description of the Appalachian kindred with hereditary amyloidosis and late-onset cardiomyopathy. The family was partially of Irish ancestry (Benson, 1988). The proband of the family was 65 years old when he died of cardiomyopathy. For several years he had symptoms of peripheral neuropathy, including chronic diarrhea, bladder dysfunction, and sexual impotence. Bladder and prostatic biopsies were positive for amyloid. During the last few months of his life, he developed severe congestive heart failure and heart block that required a pacemaker. There were at least 22 affected individuals in the family. Although in general the late onset of the ailment placed it in type II amyloid polyneuropathy, the authors believed that the lack of eye involvement set the entity apart from the Indiana form of the disease. They pointed out the hazard that patients with this disorder will be misdiagnosed as having the immunoglobulin type of systemic amyloidosis, an error that might lead to chemotherapy and unjustified risk to the patient.

Amyloidosis resulting from this variant has been referred to as the Appalachian type (Wallace et al., 1988; Benson, 2001).

Koeppen et al. (1990) restudied the family reported by Koeppen et al. (1985). They updated and revised the pedigree and determined that the underlying mutation was thr60-to-ala, the Appalachian mutation.

Staunton et al. (1987) described transthyretin-derived amyloid polyneuropathy of a hereditary nature in County Donegal, Ireland. The clinical picture was most consistent with that of the Portuguese type, although the age of onset was somewhat older. In fact, however, as reported by Staunton et al. (1991), the mutation proved to be the thr60-to-ala Appalachian mutation which had been found in a family of Irish ancestry living in the Appalachian region of the U.S.

In 5 patients with cardiac amyloidosis, 3 of whom also had renal and or splenic involvement, Lachmann et al. (2002) identified heterozygosity for the T60A mutation in the TTR gene. The predominant clinical feature in these patients was cardiomyopathy and/or neuropathy.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000053246.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedcuration PubMed (14)
2not provided9not providednot providedcuration PubMed (14)
3not provided2not providednot providedcuration PubMed (14)
4not providednot providednot providednot providedclinical testing PubMed (14)

Description

"Proband with ATTR and his affected brother carried this variant; 5 other family members also carried this variant (sister, niece, grandson, and two children of the proband); only sister was specified to be "as yet unaffected" while the affectation status of the other family members (excluding the affected brother) was not specified; likely that the niece, grandson, and two children are below the average onset age and are therefore asymptomatic."
"9 affected members from 7 ATTR families in Ireland carried the variant; considered a low penetrance mutation since there is a high carrier frequency in this region (see pbGP)."
"2 ATTR pts with variant who underwent liver transplantation; both developed cardiac complications; see additional comments section."

Description

Converted during submission to Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes2not providednot provided2not providednot providednot provided
2germlineyes9not providednot provided9not providednot providednot provided
3germlineyes2not providednot provided2not providednot providednot provided
4germlineunknownnot providedBloodassert pathogenicitynot providednot providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000060026.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (21)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000541954.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

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). 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) has been performed at Invitae 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GenomeConnect, ClinGen, SCV001423371.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedphenotyping onlynot provided

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024