ClinVar Genomic variation as it relates to human health
NM_000508.3(FGA):c.103C>T (p.Arg35Cys)
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_000508.3(FGA):c.103C>T (p.Arg35Cys)
Variation ID: 16399 Accession: VCV000016399.9
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4q31.3 4: 154589514 (GRCh38) [ NCBI UCSC ] 4: 155510666 (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 Nov 9, 2018 Oct 8, 2024 Aug 7, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_021871.4:c.103C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_068657.1:p.Arg35Cys missense NM_000508.4:c.103C>T NM_000508.5:c.103C>T NP_000499.1:p.Arg35Cys missense NM_021871.3:c.103C>T NC_000004.12:g.154589514G>A NC_000004.11:g.155510666G>A NG_008832.1:g.6232C>T LRG_557:g.6232C>T LRG_557t1:c.103C>T LRG_557p1:p.Arg35Cys LRG_557t2:c.103C>T P02671:p.Arg35Cys - Protein change
- R35C
- Other names
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R16C
FIBRINOGEN HERSHEY 2
FIBRINOGEN HOMBURG 2
FIBRINOGEN HOMBURG 3
FIBRINOGEN KAWAGUCHI 1
FIBRINOGEN LEOGAN
FIBRINOGEN METZ 1
FIBRINOGEN NEW ALBANY
FIBRINOGEN OSAKA 1
FIBRINOGEN SCHWARZACH 1
FIBRINOGEN STONY BROOK 1
FIBRINOGEN ZURICH 1
FIBRINOGEN TORINO 1
FIBRINOGEN LEDYARD
FIBRINOGEN HERSHEY 3
- Canonical SPDI
- NC_000004.12:154589513: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
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD), exomes 0.00000
The Genome Aggregation Database (gnomAD) 0.00001
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
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
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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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FGA | - | - |
GRCh38 GRCh37 |
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Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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 (1) |
no assertion criteria provided
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Jul 1, 2006 | RCV000017825.8 | |
Pathogenic (1) |
criteria provided, single submitter
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May 27, 2022 | RCV002284176.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 7, 2023 | RCV003330394.1 | |
FGA-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Jan 4, 2024 | RCV004532378.2 |
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
Help
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
Help
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
Help
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
(Aug 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Familial dysfibrinogenemia
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004038337.1
First in ClinVar: Oct 07, 2023 Last updated: Oct 07, 2023 |
Comment:
Variant summary: FGA c.103C>T (p.Arg35Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging … (more)
Variant summary: FGA c.103C>T (p.Arg35Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251232 control chromosomes. In a cross-sectional review of the literature, c.103C>T has been reported as the "A alpha Arg16Cys" variant in heterozygous or homozygous genotypes in multple individuals affected with features of Dysfibrinogenemia, some of whom reported multiple coagulation factor deficiencies (example, Galanakis_1993, Miesbach_2010, Preisler_2021). The inheritance of dysfibrinogemia is most often autosomal dominant with reports of severely affected homozygotes as well some variably affected heterozygotes and some reportedly asymptomatic heterozygotes. The range of phenotypes encountered can vary from undue bleeding, easy bruising to those experienced thrombotic events (Miesbach_2010). These data indicate that the variant is very likely to be associated with disease. Experimental evidence demonstrating an impact on protein function was not ascertained in the context of this evaluation. The following publications have been ascertained in the context of this evaluation (PMID: 8457654, 15009465, 19923982, 33477601). One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(May 27, 2022)
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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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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV002573728.2
First in ClinVar: Sep 24, 2022 Last updated: Jan 26, 2024 |
Comment:
PM1, PM2, PM5, PS3, PS4_moderate
Number of individuals with the variant: 3
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Pathogenic
(Jul 01, 2006)
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no assertion criteria provided
Method: literature only
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FIBRINOGEN METZ 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000038104.6
First in ClinVar: Apr 04, 2013 Last updated: Nov 09, 2018 |
Comment on evidence:
Fibrinogen Metz has also been called fibrinogen Bergamo-1, Hershey-2, Hershey-3, Homburg-2, Homburg-3, Kawaguchi-1, Ledyard, Leogan, New Albany, Osaka-1, Schwarzach-1, Stony Brook-1, Torino-1, Zurich-1, and Milano … (more)
Fibrinogen Metz has also been called fibrinogen Bergamo-1, Hershey-2, Hershey-3, Homburg-2, Homburg-3, Kawaguchi-1, Ledyard, Leogan, New Albany, Osaka-1, Schwarzach-1, Stony Brook-1, Torino-1, Zurich-1, and Milano XII digenic. Fibrinogen Metz is an arg16-to-cys (R16C) substitution in the fibrinogen alpha chain (Henschen et al., 1981). See also Southan et al. (1982), Henschen et al. (1983), Reber et al. (1985), Miyashita et al. (1985), and Miyata et al. (1987). Galanakis et al. (1989) stated that 52 dysfibrinogens had been structurally characterized and that most were single amino acid substitutions with a high frequency of substitutions at arg positions A-alpha-16, A-alpha-19, B-beta-14, and gamma-275. Galanakis et al. (1989) described an R16C substitution in fibrinogen Stony Brook and described the functional characteristics of the variant. According to Galanakis (1993), this mutation has been identified in 15 unrelated families. In 2 of these, an arg16-to-his (R16H; 134820.0004) mutation was detected by both DNA and protein sequencing. Lee et al. (1991) found the R16C variant, which they called fibrinogen Ledyard, in a 10-year-old boy with a history of mild bleeding whose father had the same defect and a history of bleeding after surgery. Both patients were heterozygous. Bolliger-Stucki et al. (2001) described an anomalous fibrinogen called Milano XII in an asymptomatic Italian woman, and demonstrated that its basis was double heterozygosity for the R16C mutation in exon 2 of the FGA gene, and a G165R mutation in the FGG gene (134850.0018). The woman's condition was discovered when routine coagulation test results showed a prolonged thrombin time. Fibrinogen levels in functional assays were considerably lower than levels in immunologic assays. Bolliger-Stucki et al. (2001) concluded that the FGA mutation was mainly responsible for the coagulation abnormalities, whereas the change in the FGG gene was responsible for a conformational change in the D3 fragment. The R16C mutation of the FGA gene is a common cause of dysfibrinogenemia (616004) and is associated with both bleeding and thrombosis. Flood et al. (2006) proposed to understand the mechanism of the thrombotic phenotype. They studied a young patient with dysfibrinogenemia (fibrinogen Hershey III) who was found to be heterozygous for the R16C mutation. Functional assays were performed on purified fibrinogen to characterize clot formation and lysis with plasmin and trypsin. Consistent with previous results, clot formation was diminished, but unexpectedly, fibrinolysis was also delayed. When clot lysis was assayed with trypsin substituted for plasminogen, a significant delay was also observed, indicating that defective binding to plasminogen could not explain the fibrinolytic resistance. The results suggested that the defective fibrinolysis is due to increased proteolytic resistance, most likely reflecting changes in clot structure. Flood et al. (2006) stated that the R16C mutation is the most common fibrinogen mutation in humans. Although about 30% of the reported cases of the R16C mutation in humans are associated with hemorrhage, some 15% of reported cases are associated with thrombosis (Hanss and Biot, 2001). (less)
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Pathogenic
(Jan 04, 2024)
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no assertion criteria provided
Method: clinical testing
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FGA-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004729647.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
The FGA c.103C>T variant is predicted to result in the amino acid substitution p.Arg35Cys. This variant is also described using legacy nomenclature as p.Arg16Cys, has … (more)
The FGA c.103C>T variant is predicted to result in the amino acid substitution p.Arg35Cys. This variant is also described using legacy nomenclature as p.Arg16Cys, has been reported to be causative for autosomal dominant dysfibrinogenemia in several families (Miesbach et al. 2010. PubMed ID: 19923982; Galanakis et al. 1993. PubMed ID: 8457654; Jiang et al. 2012. PubMed ID: 22967385). Other missense variants affecting amino acid residue p.Arg35 have also been reported in many patients with dysfibrinogenemia suggesting p.Arg35 is important for proper FGA protein function (see p.Arg35Ser Miesbach et al. 2010. PubMed ID: 19923982; p.Arg35His Soya et al. 2012. PubMed ID: 22880226; p.Ser35Pro Shapiro et al. 2013. PubMed ID: 23061815). This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD. This variant is interpreted as pathogenic. (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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Clinical and molecular characterization of Iranian patients with congenital fibrinogen disorders. | Mohsenian S | Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis | 2021 | PMID: 34275736 |
Resolving Differential Diagnostic Problems in von Willebrand Disease, in Fibrinogen Disorders, in Prekallikrein Deficiency and in Hereditary Hemorrhagic Telangiectasia by Next-Generation Sequencing. | Gindele R | Life (Basel, Switzerland) | 2021 | PMID: 33807613 |
Familial Multiple Coagulation Factor Deficiencies (FMCFDs) in a Large Cohort of Patients-A Single-Center Experience in Genetic Diagnosis. | Preisler B | Journal of clinical medicine | 2021 | PMID: 33477601 |
Identification and characterization of novel mutations in Chinese patients with congenital fibrinogen disorders. | Zhou P | Blood cells, molecules & diseases | 2021 | PMID: 32877852 |
Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling. | Klykov O | Proceedings of the National Academy of Sciences of the United States of America | 2020 | PMID: 31924745 |
Identification and characterization of novel mutations implicated in congenital fibrinogen disorders. | Smith N | Research and practice in thrombosis and haemostasis | 2018 | PMID: 30349899 |
Mutational Epidemiology of Congenital Fibrinogen Disorders. | Casini A | Thrombosis and haemostasis | 2018 | PMID: 30332696 |
Fibrin Formation, Structure and Properties. | Weisel JW | Sub-cellular biochemistry | 2017 | PMID: 28101869 |
Hepatic Fibrinogen Storage Disease in a Patient with Hypofibrinogenemia: Report of a Case with a Missense Mutation of the FGA Gene. | Lee MJ | Seminars in liver disease | 2015 | PMID: 26676819 |
[Genotype and function analyses of four inherited dysfibrinogenemia pedigree caused by Arg16 amino acid substitution in fibrinogen Aα chain]. | Jiang LL | Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi | 2012 | PMID: 22967385 |
Inherited dysfibrinogenemia: clinical phenotypes associated with five different fibrinogen structure defects. | Miesbach W | Blood coagulation & fibrinolysis : an international journal in haemostasis and thrombosis | 2010 | PMID: 19923982 |
The fibrinogen Aalpha R16C mutation results in fibrinolytic resistance. | Flood VH | British journal of haematology | 2006 | PMID: 16846481 |
Recombinant fibrinogen, gamma275Arg-->Cys, exhibits formation of disulfide bond with cysteine and severely impaired D:D interactions. | Ishikawa S | Journal of thrombosis and haemostasis : JTH | 2004 | PMID: 15009465 |
A database for human fibrinogen variants. | Hanss M | Annals of the New York Academy of Sciences | 2001 | PMID: 11460527 |
Fibrinogen Milano XII: a dysfunctional variant containing 2 amino acid substitutions, Aalpha R16C and gamma G165R. | Bolliger-Stucki B | Blood | 2001 | PMID: 11435303 |
Unusual A alpha 16Arg-->Cys dysfibrinogenaemic family: absence of normal A alpha-chains in fibrinogen from two of four heterozygous siblings. | Galanakis D | Blood coagulation & fibrinolysis : an international journal in haemostasis and thrombosis | 1993 | PMID: 8457654 |
Inherited dysfibrinogenemia: emerging abnormal structure associations with pathologic and nonpathologic dysfunctions. | Galanakis DK | Seminars in thrombosis and hemostasis | 1993 | PMID: 8140431 |
Fibrinogen Ledyard (A alpha Arg16----Cys): biochemical and physiologic characterization. | Lee MH | Blood | 1991 | PMID: 1912564 |
Fibrinogen Stony Brook, a heterozygous A alpha 16Arg----Cys dysfibrinogenemia. Evaluation of diminished platelet aggregation support and of enhanced inhibition of fibrin assembly. | Galanakis DK | The Journal of clinical investigation | 1989 | PMID: 2738154 |
Fibrinogens Kawaguchi and Osaka: an amino acid substitution of A alpha arginine-16 to cysteine which forms an extra interchain disulfide bridge between the two A alpha chains. | Miyata T | Journal of biochemistry | 1987 | PMID: 3667568 |
Fibrinogen Bergamo I (A alpha 16Arg----Cys): susceptibility towards thrombin following aminoethylation, methylation or carboxamidomethylation of cysteine residues. | Reber P | Thrombosis and haemostasis | 1985 | PMID: 4082078 |
Novel structure elucidation strategy for genetically abnormal fibrinogens with incomplete fibrinopeptide release as applied to fibrinogen Schwarzach. | Henschen A | Hoppe-Seyler's Zeitschrift fur physiologische Chemie | 1983 | PMID: 6667926 |
Galanakis, D. K., Henschen, A., Keeling, M., Kehl, M., Dismore, R., Peerschke, E. I. Fibrinogen Louisville: an A-alpha-16-arg-to-his defect that forms no hybrid molecules in heterozygous individuals and inhibits aggregation of normal fibrin monomers. Ann. N.Y. Acad. Sci. 408: 644-648, 1983. | - | - | - | - |
Henschen, A., Southan, C., Soria, J., Soria, C., Samama, M. Structure abnormality of fibrinogen Metz and its relation to the clotting defect. (Abstract) Thromb. Haemost. 45: 103-only, 1981. | - | - | - | - |
Miyashita, C., Schwamborn, J., von Blohn, G., Wenzel, E., Hellstern, P. Preliminary report concerning two new cases of congenital dysfibrinogenemia (Homburg II and Homburg III). In: Henschen, A., Hessel, B., McDonagh, J., Saldeen, T. (eds.) Fibrinogen--Structural Variants and Interactions. Berlin: Walter de Gruyter (pub.) 237-246, 1985. | - | - | - | - |
Southan, C., Henschen, A., Lottspeich, F. The search for molecular defects in abnormal fibrinogens. In: Henschen, A., Graeff, H., Lottspeich, F. (eds.) Fibrinogen--Recent Biochemical and Medical Aspects. Berlin: W. de Gruyter (pub.) 153-166, 1982. | - | - | - | - |
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Text-mined citations for rs121909606 ...
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.