rs730881164
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PP3_ModerateBS2_Supporting
The ENST00000237014.8(TTR):āc.280G>Cā(p.Asp94His) variant causes a missense change. The variant allele was found at a frequency of 0.0000589 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.000066 ( 0 hom., cov: 32)
Exomes š: 0.000058 ( 0 hom. )
Consequence
TTR
ENST00000237014.8 missense
ENST00000237014.8 missense
Scores
8
10
1
Clinical Significance
Conservation
PhyloP100: 5.80
Genes affected
TTR (HGNC:12405): (transthyretin) This gene encodes one of the three prealbumins, which include alpha-1-antitrypsin, transthyretin and orosomucoid. The encoded protein, transthyretin, is a homo-tetrameric carrier protein, which transports thyroid hormones in the plasma and cerebrospinal fluid. It is also involved in the transport of retinol (vitamin A) in the plasma by associating with retinol-binding protein. The protein may also be involved in other intracellular processes including proteolysis, nerve regeneration, autophagy and glucose homeostasis. Mutations in this gene are associated with amyloid deposition, predominantly affecting peripheral nerves or the heart, while a small percentage of the gene mutations are non-amyloidogenic. The mutations are implicated in the etiology of several diseases, including amyloidotic polyneuropathy, euthyroid hyperthyroxinaemia, amyloidotic vitreous opacities, cardiomyopathy, oculoleptomeningeal amyloidosis, meningocerebrovascular amyloidosis and carpal tunnel syndrome. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM1
In a hotspot region, there are 10 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 5 uncertain in ENST00000237014.8
PP3
MetaRNN computational evidence supports a deleterious effect, 0.865
BS2
High AC in GnomAd4 at 10 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTR | NM_000371.4 | c.280G>C | p.Asp94His | missense_variant | 3/4 | ENST00000237014.8 | NP_000362.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTR | ENST00000237014.8 | c.280G>C | p.Asp94His | missense_variant | 3/4 | 1 | NM_000371.4 | ENSP00000237014 | P1 | |
TTR | ENST00000649620.1 | c.280G>C | p.Asp94His | missense_variant | 5/6 | ENSP00000497927 | P1 | |||
TTR | ENST00000610404.5 | c.184G>C | p.Asp62His | missense_variant | 3/4 | 5 | ENSP00000477599 | |||
TTR | ENST00000541025.2 | n.306G>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152178Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251446Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135892
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GnomAD4 exome AF: 0.0000581 AC: 85AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 727236
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74338
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:9
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:5
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2024 | Reported in one individual with hypertrophic cardiomyopathy (HCM) and one individual with suspected Charcot-Marie-Tooth disease (CMT) (PMID: 29121657, 32376792); Identified in 7 out of 4,000 pregnant German women with no family history of amyloidosis or thyroid disorder; reported as a common variant in the German population; denoted as D74H by alternative nomenclature (Uemichi et al. (1994) Amyloid: The Journal of Protein Folding Disorders 1 (3) :149-53 (http://www.tandfonline.com/doi/abs/10.3109/13506129409148445)); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 14640030, 32376792, 34658264, 29121657) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 05, 2016 | - - |
Amyloidosis, hereditary systemic 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | This sequence change replaces aspartic acid, which is acidic and polar, with histidine, which is basic and polar, at codon 94 of the TTR protein (p.Asp94His). This variant is present in population databases (rs730881164, gnomAD 0.009%). This missense change has been observed in individual(s) with clinical features of hATTR amyloidosis and/or hereditary transthyretin-mediated amyloidosis (hATTR amyloidosis) (PMID: 29121657, 32376792, 34658264; Invitae). ClinVar contains an entry for this variant (Variation ID: 181695). 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%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 26, 2021 | Variant summary: TTR c.280G>C (p.Asp94His) (legacy name p.Asp74His) results in a non-conservative amino acid change located in the Transthyretin/hydroxyisourate hydrolase domain (IPR023416) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.4e-05 in 251446 control chromosomes. The observed variant frequency is approximately 1.4 fold of the estimated maximal expected allele frequency for a pathogenic variant in TTR causing Transthyretin Amyloidosis phenotype (3.1e-05), strongly suggesting that the variant is benign. c.280G>C has been reported in the literature as a non-amyloidogenic variant that was found in seven unrelated families with no personal history of amyloidosis nor thyroid disorders and was considered as a frequent polymorphism in the German population (example, Uemichi_1994). It has subsequently been reported in settings of multigene panel testing within within cohorts of individuals with hypertrophic cardiomyopathy (HCM) and Charcot-Marie -Tooth disease (example, Viswanathan_2017, Volodarsky_2021). Furthermore, recent reports have categorized this among TTR gene variants that do not affect function (example, Pueyo_2019). In summary, these report(s) do not provide unequivocal conclusions about association of the variant with Transthyretin Amyloidosis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly benign. - |
Charcot-Marie-Tooth disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
Hyperthyroxinemia, dystransthyretinemic;C2751492:Amyloidosis, hereditary systemic 1;C5779776:Carpal tunnel syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 06, 2022 | - - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 29, 2024 | The p.D94H variant (also known as c.280G>C), located in coding exon 3 of the TTR gene, results from a G to C substitution at nucleotide position 280. The aspartic acid at codon 94 is replaced by histidine, an amino acid with similar properties. This variant was first reported in 7 German individuals with no family history of amyloidosis (Umechi T et al. Amyloid, 1994;1(3):149-53). This variant was reported in an individual with hypertrophic cardiomyopathy in conjunction with a variant in another cardiac gene, and has also been detected in a Charcot-Marie-Tooth disease cohort (Viswanathan SK et al. PLoS ONE, 2017 Nov;12:e0187948; Volodarsky M et al. J Med Genet. 2021 04;58(4):284-288). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on available evidence to date, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Pathogenic
D;D;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;M;.;.
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
.;D;.;.
REVEL
Pathogenic
Sift
Uncertain
.;D;.;.
Sift4G
Uncertain
.;T;D;D
Polyphen
D;D;.;.
Vest4
0.71, 0.73, 0.68
MutPred
Gain of MoRF binding (P = 0.0968);Gain of MoRF binding (P = 0.0968);Gain of MoRF binding (P = 0.0968);Gain of MoRF binding (P = 0.0968);
MVP
1.0
MPC
1.5
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
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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