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NM_000371.4(TTR):c.88T>C (p.Cys30Arg) AND Amyloidosis, hereditary systemic 1

Germline classification:
Pathogenic/Likely pathogenic (4 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:
RCV000014386.40

Allele description [Variation Report for NM_000371.4(TTR):c.88T>C (p.Cys30Arg)]

NM_000371.4(TTR):c.88T>C (p.Cys30Arg)

Gene:
TTR:transthyretin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q12.1
Genomic location:
Preferred name:
NM_000371.4(TTR):c.88T>C (p.Cys30Arg)
Other names:
C10R
HGVS:
  • NC_000018.10:g.31592914T>C
  • NG_009490.1:g.6148T>C
  • NM_000371.4:c.88T>CMANE SELECT
  • NP_000362.1:p.Cys30Arg
  • NP_000362.1:p.Cys30Arg
  • LRG_416t1:c.88T>C
  • LRG_416:g.6148T>C
  • LRG_416p1:p.Cys30Arg
  • NC_000018.9:g.29172877T>C
  • NM_000371.3:c.88T>C
  • P02766:p.Cys30Arg
Protein change:
C30R; CYS10ARG
Links:
UniProtKB: P02766#VAR_007547; OMIM: 176300.0028; dbSNP: rs121918083
NCBI 1000 Genomes Browser:
rs121918083
Molecular consequence:
  • NM_000371.4:c.88T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

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
SCV000034635OMIM
no assertion criteria provided
Pathogenic
(Dec 1, 1992)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

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

SCV000696637Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely pathogenic
(Apr 5, 2016)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001575268Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

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

PubMed (3)
[See all records that cite these PMIDs]

SCV002580651MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 24, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Low plasma concentrations of retinol-binding protein in individuals with mutations affecting position 84 of the transthyretin molecule.

Waits RP, Yamada T, Uemichi T, Benson MD.

Clin Chem. 1995 Sep;41(9):1288-91.

PubMed [citation]
PMID:
7656439

Cysteine 10 is a key residue in amyloidogenesis of human transthyretin Val30Met.

Takaoka Y, Ohta M, Miyakawa K, Nakamura O, Suzuki M, Takahashi K, Yamamura K, Sakaki Y.

Am J Pathol. 2004 Jan;164(1):337-45.

PubMed [citation]
PMID:
14695346
PMCID:
PMC1602210
See all PubMed Citations (8)

Details of each submission

From OMIM, SCV000034635.5

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

Description

In a kindred with systemic amyloidosis (AMYLD1; 105210) presenting as peripheral neuropathy in the sixth and seventh decades of life, Uemichi et al. (1992) demonstrated a T-to-C transition at nucleotide 1038 of the TTR gene leading to substitution of arginine for cysteine at position 10 of the TTR protein molecule (C10R). The mutation created a new restriction recognition site, thus allowing easy diagnosis. The mutation was identified in 7 persons: none of 3 female mutant gene carriers, who were 87, 85, and 76 years old, had symptoms of the disease, while 4 of 5 male carriers, including 1 patient whose DNA was not available for testing, developed the disease in their fifties or sixties. It had been observed in other types of FAP that males are affected predominantly or at earlier ages than females. Affected subjects showed sensory and motor neuropathy, bowel disorder, sexual impotence, cardiomyopathy, and vitreous opacity, but no kidney dysfunction. Benson (2001) noted that arg10 replaces the only cysteine in the transthyretin molecule.

#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, SCV000696637.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Variant Summary: The c.88T>C variant involves the alteration of a conserved nucleotide and 4/4 in silico tools predict a pathogenic outcome. The variant, also known as Cys10Arg, involves the only free Cysteine in TTR and is hypothesized to cause structural changes in the heterozygous TTR dimer and tetramer that lead to polymerization of TTR molecules (Uemichi_1992). The variant is absent from the large, broad ExAC control population. The variant was found in multiple affected individuals in the literature, including a family in which all tested affected males carried the variant while three unaffected females also carried the variant, suggesting some role of sex in the occurrence of disease (Uemichi_1992). One clinical lab has classified the variant as "pathogenic". Therefore, taken together, this variant has been classified as Likely Pathogenic.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001575268.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 30 of the TTR protein (p.Cys30Arg). This variant is present in population databases (rs121918083, gnomAD 0.007%). This missense change has been observed in individual(s) with clinical features of hereditary transthyretin-mediated amyloidosis (hATTR amyloidosis) (PMID: 1362222, 24664531; Invitae). It has also been observed to segregate with disease in related individuals. This variant is also known as Cys10Arg. ClinVar contains an entry for this variant (Variation ID: 13444). 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 with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

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

From MGZ Medical Genetics Center, SCV002580651.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Oct 20, 2024