ClinVar Genomic variation as it relates to human health
NM_000138.5(FBN1):c.5368C>T (p.Arg1790Ter)
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_000138.5(FBN1):c.5368C>T (p.Arg1790Ter)
Variation ID: 42382 Accession: VCV000042382.32
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 15q21.1 15: 48456691 (GRCh38) [ NCBI UCSC ] 15: 48748888 (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 Jan 31, 2015 May 1, 2024 Nov 8, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000138.5:c.5368C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000129.3:p.Arg1790Ter nonsense NC_000015.10:g.48456691G>A NC_000015.9:g.48748888G>A NG_008805.2:g.194098C>T LRG_778:g.194098C>T LRG_778t1:c.5368C>T LRG_778p1:p.Arg1790Ter - Protein change
- R1790*
- Other names
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p.R1790X:CGA>TGA
- Canonical SPDI
- NC_000015.10:48456690:G:A
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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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FBN1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
7806 | 8149 |
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
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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 (6) |
criteria provided, multiple submitters, no conflicts
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Nov 8, 2023 | RCV000035224.18 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 1, 2022 | RCV000181541.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 27, 2023 | RCV000684816.12 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 25, 2022 | RCV002310642.9 |
Submissions - Germline
Classification
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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
(Nov 01, 2016)
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criteria provided, single submitter
Method: clinical testing
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Marfan syndrome
Affected status: yes
Allele origin:
germline
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Center for Human Genetics, Inc, Center for Human Genetics, Inc
Accession: SCV000781385.1
First in ClinVar: Jan 31, 2015 Last updated: Jan 31, 2015 |
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Pathogenic
(Mar 01, 2021)
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criteria provided, single submitter
Method: research
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Marfan syndrome
Affected status: yes
Allele origin:
unknown
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Centre of Medical Genetics, University of Antwerp
Accession: SCV002025343.1
First in ClinVar: May 24, 2022 Last updated: May 24, 2022 |
Comment:
PM2, PVS1, PP4
Sex: male
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Pathogenic
(Jun 05, 2023)
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criteria provided, single submitter
Method: clinical testing
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Marfan syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000058869.6
First in ClinVar: May 03, 2013 Last updated: Apr 20, 2024 |
Comment:
The p.Arg1790X variant in FBN1 has been reported in 6 individuals with clinically diagnosed Marfan Syndrome (fulfilled Ghent criteria) and 3 individuals with clinical features … (more)
The p.Arg1790X variant in FBN1 has been reported in 6 individuals with clinically diagnosed Marfan Syndrome (fulfilled Ghent criteria) and 3 individuals with clinical features of Marfan-like phenotypes (Marfan syndrome suspected, but not fulfilling Ghent criteria; Arbustini 2005 PMID: 16222657, Sakai 2006 PMID: 16835936, Chung 2009 PMID: 19533785, Magyar 2009 PMID: 19618372, Yoo 2010 PMID: 19863550, Zhurayev 2016 PMID: 27724990, Stengl 2020 PMID: 33059708, Meester 2022 PMID: 35058154. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 42382) and was absent from large population studies (gnomAD, v.3.1.2). This nonsense variant leads to a premature termination codon at position 1790, which is predicted to lead to a truncated or absent protein. Heterozygous loss of function of the FBN1 gene is an established disease mechanism of autosomal dominant Marfan syndrome. In summary, this variant meets criterion to be classified as pathogenic for autosomal dominant Marfan Syndrome. ACMG/AMP Criteria applied: PM2_supporting, PSV1, PS4_Moderate. (less)
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Pathogenic
(Jul 25, 2022)
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criteria provided, single submitter
Method: clinical testing
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Familial thoracic aortic aneurysm and aortic dissection
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000319217.7
First in ClinVar: Oct 02, 2016 Last updated: May 01, 2024 |
Comment:
The p.R1790* pathogenic mutation (also known as c.5368C>T), located in coding exon 43 of the FBN1 gene, results from a C to T substitution at … (more)
The p.R1790* pathogenic mutation (also known as c.5368C>T), located in coding exon 43 of the FBN1 gene, results from a C to T substitution at nucleotide position 5368. This alteration changes the amino acid from an arginine to a stop codon within coding exon 43. This mutation has been reported in numerous Marfan syndrome cohorts (e.g., Arbustini E et al. Hum Mutat. 2005;26(5):494; Magyar I et al. Hum. Mutat. 2009;30:1355-64; Stheneur C et al. Eur. J. Hum. Genet. 2009;17:1121-8; Franken R et al. Eur. Heart J, 2016;37:3285-3290). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Oct 05, 2021)
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criteria provided, single submitter
Method: clinical testing
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Marfan syndrome
Affected status: yes
Allele origin:
unknown
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Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Accession: SCV001976805.1
First in ClinVar: Oct 16, 2021 Last updated: Oct 16, 2021 |
Comment:
PVS1, PM2, PP5
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Pathogenic
(Mar 01, 2022)
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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: SCV000233844.12
First in ClinVar: Jul 05, 2015 Last updated: Mar 04, 2023 |
Comment:
Has been reported several times in association with Marfan syndrome or other Marfan-like syndrome in unrelated patients referred for genetic testing at GeneDx and in … (more)
Has been reported several times in association with Marfan syndrome or other Marfan-like syndrome in unrelated patients referred for genetic testing at GeneDx and in the published literature (Arbustini et al., 2005; Sakai et al., 2006; Howarth et al., 2007; Chung et al., 2009; Magyar et al., 2009; Yoo et al., 2010; Stengl et al., 2020); Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 16222657, 19533785, 16835936, 17627385, 19293843, 26787436, 19863550, 19618372, 33059708) (less)
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Pathogenic
(Jul 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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Marfan syndrome
Familial thoracic aortic aneurysm and aortic dissection
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000544859.6
First in ClinVar: Jan 31, 2015 Last updated: Feb 28, 2024 |
Comment:
This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg1790*) in the FBN1 gene. … (more)
This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg1790*) in the FBN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FBN1 are known to be pathogenic (PMID: 17657824, 19293843). This premature translational stop signal has been observed in individuals with Marfan syndrome (PMID: 16222657, 16835936, 19533785, 19618372, 19863550, 26787436). ClinVar contains an entry for this variant (Variation ID: 42382). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Nov 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Marfan syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004827283.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
The c.5368C>T (p.Arg1790*) variant in of the FBN1 gene creates a premature termination codon that is predicted to lead to an absent or truncated protein … (more)
The c.5368C>T (p.Arg1790*) variant in of the FBN1 gene creates a premature termination codon that is predicted to lead to an absent or truncated protein product. This variant has been identified in numerous individuals (>10) affected with clinical features of Marfan syndrome (PMID:16222657, 19618372, 16835936, 19533785, 19863550, 19293843, 17627385, 26787436). Loss of function variants are known to be pathogenic for FBN1 (PMID: 17701892, 30286810, 21063442, 17657824, 19293843). Truncating variants downstream of this variant are reported in individuals with Marfan syndrome (PMID: 27906200, 31730815, 24793577). This variant is found to be absent in the general population database (gnomAD) and interpreted as pathogenic by several submitters in the ClinVar database (ClinVar ID: 42382). Therefore, the c.5368C>T (p.Arg1790*) variant in the FBN1 gene is classified as pathogenic. (less)
Number of individuals with the variant: 1
Zygosity: Single Heterozygote
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Pathogenic
(Nov 07, 2017)
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no assertion criteria provided
Method: clinical testing
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Marfan syndrome
Affected status: yes
Allele origin:
germline
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Center for Medical Genetics Ghent, University of Ghent
Accession: SCV000787127.1
First in ClinVar: Jul 21, 2018 Last updated: Jul 21, 2018 |
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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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Mutation analysis of the FBN1 gene in a cohort of patients with Marfan Syndrome: A 10-year single center experience. | Mannucci L | Clinica chimica acta; international journal of clinical chemistry | 2020 | PMID: 31730815 |
Identification of gross deletions in FBN1 gene by MLPA. | Yang H | Human genomics | 2018 | PMID: 30286810 |
Evaluating the quality of Marfan genotype-phenotype correlations in existing FBN1 databases. | Groth KA | Genetics in medicine : official journal of the American College of Medical Genetics | 2017 | PMID: 27906200 |
Genotype impacts survival in Marfan syndrome. | Franken R | European heart journal | 2016 | PMID: 26787436 |
The spectrum of FBN1, TGFβR1, TGFβR2 and ACTA2 variants in 594 individuals with suspected Marfan Syndrome, Loeys-Dietz Syndrome or Thoracic Aortic Aneurysms and Dissections (TAAD). | Lerner-Ellis JP | Molecular genetics and metabolism | 2014 | PMID: 24793577 |
The clinical spectrum of complete FBN1 allele deletions. | Hilhorst-Hofstee Y | European journal of human genetics : EJHG | 2011 | PMID: 21063442 |
Clinical and genetic analysis of Korean patients with Marfan syndrome: possible ethnic differences in clinical manifestation. | Yoo EH | Clinical genetics | 2010 | PMID: 19863550 |
Quantitative sequence analysis of FBN1 premature termination codons provides evidence for incomplete NMD in leukocytes. | Magyar I | Human mutation | 2009 | PMID: 19618372 |
Identification of novel FBN1 and TGFBR2 mutations in 65 probands with Marfan syndrome or Marfan-like phenotypes. | Chung BH | American journal of medical genetics. Part A | 2009 | PMID: 19533785 |
Identification of the minimal combination of clinical features in probands for efficient mutation detection in the FBN1 gene. | Stheneur C | European journal of human genetics : EJHG | 2009 | PMID: 19293843 |
Effect of mutation type and location on clinical outcome in 1,013 probands with Marfan syndrome or related phenotypes and FBN1 mutations: an international study. | Faivre L | American journal of human genetics | 2007 | PMID: 17701892 |
The importance of mutation detection in Marfan syndrome and Marfan-related disorders: report of 193 FBN1 mutations. | Comeglio P | Human mutation | 2007 | PMID: 17657824 |
Application of dHPLC for mutation detection of the fibrillin-1 gene for the diagnosis of Marfan syndrome in a National Health Service Laboratory. | Howarth R | Genetic testing | 2007 | PMID: 17627385 |
Comprehensive genetic analysis of relevant four genes in 49 patients with Marfan syndrome or Marfan-related phenotypes. | Sakai H | American journal of medical genetics. Part A | 2006 | PMID: 16835936 |
Identification of sixty-two novel and twelve known FBN1 mutations in eighty-one unrelated probands with Marfan syndrome and other fibrillinopathies. | Arbustini E | Human mutation | 2005 | PMID: 16222657 |
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Text-mined citations for rs113249837 ...
HelpRecord last updated Nov 25, 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.