ClinVar Genomic variation as it relates to human health
NM_000133.4(F9):c.881G>A (p.Arg294Gln)
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_000133.4(F9):c.881G>A (p.Arg294Gln)
Variation ID: 10602 Accession: VCV000010602.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: Xq27.1 X: 139561566 (GRCh38) [ NCBI UCSC ] X: 138643725 (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 Apr 4, 2013 Oct 8, 2024 Mar 27, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000133.4:c.881G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000124.1:p.Arg294Gln missense NM_001313913.2:c.767G>A NP_001300842.1:p.Arg256Gln missense NC_000023.11:g.139561566G>A NC_000023.10:g.138643725G>A NG_007994.1:g.35831G>A LRG_556:g.35831G>A LRG_556t1:c.881G>A LRG_556p1:p.Arg294Gln P00740:p.Arg294Gln - Protein change
- R294Q, R256Q
- Other names
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F9, ARG248GLN
R248Q
- Canonical SPDI
- NC_000023.11:139561565: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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Trans-Omics for Precision Medicine (TOPMed) 0.00003
- 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
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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F9 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
582 | 767 |
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
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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 (7) |
criteria provided, multiple submitters, no conflicts
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Jul 1, 2023 | RCV000011348.17 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 17, 2023 | RCV000814168.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Feb 1, 2019 | RCV000851909.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 27, 2024 | RCV004724733.1 |
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
(Feb 01, 2019)
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criteria provided, single submitter
Method: research
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Hereditary factor VIII deficiency disease
Affected status: yes
Allele origin:
unknown
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NIHR Bioresource Rare Diseases, University of Cambridge
Study: ThromboGenomics
Accession: SCV000899974.1 First in ClinVar: Sep 29, 2019 Last updated: Sep 29, 2019 |
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Pathogenic
(Jul 01, 2023)
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criteria provided, single submitter
Method: research
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Hereditary factor IX deficiency disease
Affected status: yes
Allele origin:
germline
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Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand
Accession: SCV004123083.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
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Pathogenic
(Sep 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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Thrombophilia, X-linked, due to factor 9 defect
Hereditary factor IX deficiency disease
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: SCV000954569.4
First in ClinVar: Aug 14, 2019 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 294 of the F9 protein (p.Arg294Gln). … (more)
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 294 of the F9 protein (p.Arg294Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hemophilia B (PMID: 2472424, 19699296, 22544209, 32155688; Invitae). This variant is also known as p.Arg248Gln. ClinVar contains an entry for this variant (Variation ID: 10602). 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 F9 protein function. Experimental studies have shown that this missense change affects F9 function (PMID: 29993188). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Hereditary factor IX deficiency disease
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV002073155.1
First in ClinVar: Feb 04, 2022 Last updated: Feb 04, 2022 |
Comment:
The missense variant p.R294Q in F9 (NM_000133.4 has been reported previously in affected patients with hemophilia B (Chavali et al, 2009; Yu et al, 2012). … (more)
The missense variant p.R294Q in F9 (NM_000133.4 has been reported previously in affected patients with hemophilia B (Chavali et al, 2009; Yu et al, 2012). The p.R294Q variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. Experimental studies have shown that this missense change impairs intracellular trafficking of factor IX (Pignani et al, 2018). It has been submitted to ClinVar as Pathogenic. For these reasons, this variant has been classified as Pathogenic (less)
Clinical Features:
Reduced factor IX activity (present)
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Pathogenic
(Mar 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary factor IX deficiency disease
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV003922517.1
First in ClinVar: May 13, 2023 Last updated: May 13, 2023 |
Comment:
Variant summary: F9 c.881G>A (p.Arg294Gln) results in a conservative amino acid change located in the Serine proteases, trypsin domain (IPR001254) of the encoded protein sequence. … (more)
Variant summary: F9 c.881G>A (p.Arg294Gln) results in a conservative amino acid change located in the Serine proteases, trypsin domain (IPR001254) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 179083 control chromosomes (gnomAD). c.881G>A has been reported in the literature in multiple individuals affected with Factor IX Deficiency (Hemophilia B) (Chen_1989, Chavali_2009, Onay_2003), including de novo occurrences. These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four ClinVar submitters (evaluation after 2014) cite this variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Hereditary factor IX deficiency disease
Affected status: yes
Allele origin:
unknown
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3billion
Accession: SCV004013531.1
First in ClinVar: Jul 22, 2023 Last updated: Jul 22, 2023 |
Comment:
The variant is not observed in the gnomAD v2.1.1 dataset. The variant is located in a mutational hot spot and/or well-established functional domain in which … (more)
The variant is not observed in the gnomAD v2.1.1 dataset. The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.58; 3Cnet: 0.73). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000010602 / PMID: 2472424). A different missense change at the same codon (p.Arg294Gly) has been reported to be associated with F9 related disorder (PMID: 7937052). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Abnormality of the coagulation cascade (present) , Oral bleeding (present)
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Pathogenic
(Mar 27, 2024)
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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: SCV005332589.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
Published functional studies demonstrate a damaging effect (PMID: 29993188); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this … (more)
Published functional studies demonstrate a damaging effect (PMID: 29993188); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31064749, 22639855, 1346975, 32155688, 32224444, 22544209, 19699296, 2472424, 12588353, 29993188) (less)
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Pathogenic
(Mar 01, 1992)
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no assertion criteria provided
Method: literature only
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HEMOPHILIA B
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000031580.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
This variant has been called factor IX Seattle-4 and factor IX Dreihacken. See Chen et al. (1989). In a patient with hemophilia B (306900), Ludwig … (more)
This variant has been called factor IX Seattle-4 and factor IX Dreihacken. See Chen et al. (1989). In a patient with hemophilia B (306900), Ludwig et al. (1992) identified a G-to-A transition at nucleotide 30864 of the F9 gene, resulting in replacement of arg248 by gln in the mature factor IX protein. (less)
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Pathogenic
(Jun 01, 2019)
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no assertion criteria provided
Method: clinical testing
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Hereditary factor IX deficiency disease
Affected status: yes
Allele origin:
germline
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Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico
Accession: SCV001424892.1
First in ClinVar: Nov 19, 2020 Last updated: Nov 19, 2020 |
Number of individuals with the variant: 1
Sex: female
Ethnicity/Population group: Causasians
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Pathogenic
(Aug 01, 2021)
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no assertion criteria provided
Method: clinical testing
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Hemophilia B
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV002083708.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
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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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Molecular characterization of hemophilia B patients in Colombia. | Parrado Jara YA | Molecular genetics & genomic medicine | 2020 | PMID: 32155688 |
Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders. | Downes K | Blood | 2019 | PMID: 31064749 |
The chaperone-like sodium phenylbutyrate improves factor IX intracellular trafficking and activity impaired by the frequent p.R294Q mutation. | Pignani S | Journal of thrombosis and haemostasis : JTH | 2018 | PMID: 29993188 |
Assessment of the F9 genotype-specific FIX inhibitor risks and characterisation of 10 novel severe F9 defects in the first molecular series of Argentinian patients with haemophilia B. | Radic CP | Thrombosis and haemostasis | 2013 | PMID: 23093250 |
Spectrum of F9 mutations in Chinese haemophilia B patients: identification of 20 novel mutations. | Yu T | Pathology | 2012 | PMID: 22544209 |
F8 and F9 mutations in US haemophilia patients: correlation with history of inhibitor and race/ethnicity. | Miller CH | Haemophilia : the official journal of the World Federation of Hemophilia | 2012 | PMID: 22103590 |
Hemophilia B is a quasi-quantitative condition with certain mutations showing phenotypic plasticity. | Chavali S | Genomics | 2009 | PMID: 19699296 |
Insight into molecular changes of the FIX protein in a series of Italian patients with haemophilia B. | Bicocchi MP | Haemophilia : the official journal of the World Federation of Hemophilia | 2006 | PMID: 16643212 |
Molecular genotyping of the Italian cohort of patients with hemophilia B. | Belvini D | Haematologica | 2005 | PMID: 15921378 |
Mutation analysis in F9 gene of 17 families with haemophilia B from Iran. | Enayat MS | Haemophilia : the official journal of the World Federation of Hemophilia | 2004 | PMID: 15569175 |
Molecular pathology of haemophilia B in Turkish patients: identification of a large deletion and 33 independent point mutations. | Onay UV | British journal of haematology | 2003 | PMID: 12588353 |
Haemophilia B mutations in Sweden: a population-based study of mutational heterogeneity. | Ljung R | British journal of haematology | 2001 | PMID: 11328285 |
Factor IX gene sequencing by a simple and sensitive 15-hour procedure for haemophilia B diagnosis: identification of two novel mutations. | Vidal F | British journal of haematology | 2000 | PMID: 11122099 |
Fast and efficient mutation detection method using multiplex PCR and cycle sequencing--application to haemophilia B. | Costa JM | Thrombosis and haemostasis | 2000 | PMID: 10739381 |
Molecular analysis of hemophilia B in Poland: 12 novel mutations of the factor IX gene. | Wulff K | Acta biochimica Polonica | 1999 | PMID: 10698280 |
Factor IX gene analysis in 70 unrelated patients with haemophilia B: description of 13 new mutations. | Attali O | Thrombosis and haemostasis | 1999 | PMID: 10595634 |
Identification of twenty-one new mutations in the factor IX gene by SSCP analysis. | Montejo JM | Human mutation | 1999 | PMID: 10094553 |
Consequences of factor IX mutations in 26 families with haemophilia B. | Weinmann AF | British journal of haematology | 1998 | PMID: 9450791 |
Mutations associated with hemophilia B in Turkish patients. | Cağlayan SH | Human mutation | 1997 | PMID: 9222764 |
Molecular epidemiology of factor IX germline mutations in Mexican Hispanics: pattern of mutation and potential founder effects. | Thorland EC | Thrombosis and haemostasis | 1995 | PMID: 8772212 |
Twenty-five novel mutations of the factor IX gene in haemophilia B. | Wulff K | Human mutation | 1995 | PMID: 8680410 |
Detection of ten new mutations by screening the gene encoding factor IX of Danish hemophilia B patients. | Nielsen LR | Thrombosis and haemostasis | 1995 | PMID: 7482402 |
First report on UK database of haemophilia B mutations and pedigrees. UK Haemophilia Centres. | Saad S | Thrombosis and haemostasis | 1994 | PMID: 8091381 |
Haemophilia B: database of point mutations and short additions and deletions, fifth edition, 1994. | Giannelli F | Nucleic acids research | 1994 | PMID: 7937052 |
Hemophilia B carrier determination based on family-specific mutation detection by DNA single-strand conformation analysis. | Poon MC | The Journal of laboratory and clinical medicine | 1993 | PMID: 8320491 |
The pattern of spontaneous germ-line mutation: relative rates of mutation at or near CpG dinucleotides in the factor IX gene. | Bottema CD | Human genetics | 1993 | PMID: 8314564 |
Single-strand conformation polymorphism (SSCP) analysis of the molecular pathology of hemophilia B. | David D | Human mutation | 1993 | PMID: 8257988 |
Twenty-four novel hemophilia B mutations revealed by rapid scanning of the whole factor IX gene in a French population sample. | Ghanem N | European journal of human genetics : EJHG | 1993 | PMID: 8055323 |
Hemophilia B caused by five different nondeletion mutations in the protease domain of factor IX. | Ludwig M | Blood | 1992 | PMID: 1346975 |
Missense mutations and evolutionary conservation of amino acids: evidence that many of the amino acids in factor IX function as "spacer" elements. | Bottema CD | American journal of human genetics | 1991 | PMID: 1680287 |
Mutations causing hemophilia B: direct estimate of the underlying rates of spontaneous germ-line transitions, transversions, and deletions in a human gene. | Koeberl DD | American journal of human genetics | 1990 | PMID: 2198809 |
Factor IXPortland: a nonsense mutation (CGA to TGA) resulting in hemophilia B. | Chen SH | American journal of human genetics | 1989 | PMID: 2929599 |
Three point mutations in the factor IX genes of five hemophilia B patients. Identification strategy using localization by altered epitopes in their hemophilic proteins. | Chen SH | The Journal of clinical investigation | 1989 | PMID: 2472424 |
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Text-mined citations for rs137852249 ...
HelpRecord last updated Oct 27, 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.