This webpage was created as an assignment for an undergraduate course at Davidson College.


Coagulation Factor IX

a.k.a. Human Clotting Factor IX, Plasma Thromobplastin Component


The Protein

Coagulation Factor IX is an important protein in the process of hemostasis and normal blood clotting. Factor IX is plays an important intermediate role in the blood coagulation cascade. It is located within the blood plasma as a zymogen, an antecedent to enzymatic function, in its inactivated state. Factor IX is dependent on the presence of Vitamin K, and is activated to a serine protease by the function of Coagulation Factor XIa. Factor XIa cleaves the peptide bond associated with protein activation in Factor IX, leaving Factor IX with two exposed chains, a light chain and a heavy chain. These two chains are held together by several disulfide bonds that reinforce the structure of Factor IX's activated form. The structure of Factor IX closely resembles the structures of many other Vitamin K dependent plasma proteins, such as prothrombin, factor X and protein C. (Camerino et. al.) A depiction of activated Coagulation Factor IX is shown below.


Figure 1. The full structure of Coagulation Factor IX consists of 6 subunit chains. The chains are shown above coded in different colors. Arrows indicate the antiparallel beta-sheet secondary structure in each subunit. Red spheres depict the presence of one calcium ion in each subunit. This image can be found here - permission pending.


After being activated, Factor IX forms a complex with calcium ions, membrane phospholipids and Coagulation Factor VIII to activate Coagulation Factor X. The activation of Factor X then performs a similarly integral step in the blood coagulation cascade. (NCBI Locus Link) The ultimate result of phenotypically normal coagulation factors is the creation of platelets for normal blood clotting. When genetic mutation occurs in any of the major proteins in the blood coagulation cascade, there may be serious consequences. Hemophilia B, or Christmas Disease, is a sex-linked recessive disorder that results from genetic mutations within the gene that codes for Coagulation Factor IX.



The Gene


The identification of the gene or genes responsible for the coding of Coagulation Factor IX began in the 1950's. Even before then, hemophilia was known to be carried recessively, as an X-linked genetic disorder. However, nearly one-third of all cases of hemophilia occurred without any genetic history. Doctors, now knowing that hemophilia must be associated with the X chromosome, began exploring the genetics of its cause. An experiment in the early 1950's (Aggeler et. al.) found that the blood plasma from some hemophilia patients could be used to promote good clotting in other hemophilia patients. It was then hypothesized that hemophilia was not the result of a single gene, but that mutations in different genes could disrupt normal functioning of different proteins and consequently cause different forms of hemophilia.

With the advent of modern techniques in DNA sequencing, the exact locus of Coagulation Factor IX was found to exist in the Xq26-q27 region of the X chromosome. A depiction of Coagulation Factor IX's specific locus, Xq27.1-q27.2, can be found here or here.



In recent years, many blood clotting factors have been sequenced, including precursors, cofactors, etc. The knowledge of these sequences has aided in the discovery of new therapies to benefit those who suffer from hemophilia. Below are the amino acid sequences for Coagulation Factor IX in human, cow and house mouse stored at the National Center for Biotechnology Information:


1 mqrvnmimae spgliticll gyllsaectv fldhenanki lnrpkrynsg kleefvqgnl
61 erecmeekcs feearevfen terttefwkq yvdgdqcesn pclnggsckd dinsyecwcp
121 fgfegkncel dvtcnikngr ceqfcknsad nkvvcscteg yrlaenqksc epavpfpcgr
181 vsvsqtsklt raeavfpdvd yvnsteaeti ldnitqstqs fndftrvvgg edakpgqfpw
241 qvvlngkvda fcggsivnek wivtaahcve tgvkitvvag ehnieeteht eqkrnvirii
301 phhnynaain kynhdialle ldeplvlnsy vtpiciadke ytniflkfgs gyvsgwgrvf
361 hkgrsalvlq ylrvplvdra tclrstkfti ynnmfcagfh eggrdscqgd sggphvteve
421 gtsfltgiis wgeecamkgk ygiytkvsry vnwikektkl t


1 ynsgkleefv rgnlerecke ekcsfeeare vfentektte fwkqyvdgdq cesnpclngg
61 mckddinsye cwcqagfegt nceldatcsi kngrckqfck rdtdnkvvcs ctdgyrlaed
121 qkscepavpf pcgrvsvshi skkltraeti fsntnyenss eaeiiwdnvt qsnqsfdefs
181 rvvggedaer gqfpwqvllh geiaafcggs ivnekwvvta ahcikpgvki tvvagehnte
241 kpepteqkrn viraipyhsy nasinkyshd ialleldepl elnsyvtpic iadrdytnif
301 skfgygyvsg wgkvfnrgrs asilqylkvp lvdratclrs tkfsiyshmf cagyheggkd
361 scqgdsggph vtevegtsfl tgiiswgeec amkgkygiyt kvsryvnwik ektklt

House Mouse:

1 maespaliti fllgyllste cavfldrena tkiltrpkry nsgkleefvr gnlereciee
61 rcsfeearev fentekttef wkqyvdgdqc esnpclnggi ckddissyec wcqvgfegrn
121 celdatcnik ngrckqfckn spdnkvicsc tegyqlaedq ksceptvpfp cgrasisyss
181 kkitraetvf snmdyenste avfiqdditd gailnnvtes seslndftrv vggenakpgq
241 ipwqvilnge ieafcggaii nekwivtaah clkpgdkiev vageynidkk edteqrrnvi
301 rtiphhqyna tinkyshdia lleldkplil nsyvtpicva nreytniflk fgsgyvsgwg
361 kvfnkgrqas ilqylrvplv dratclrstt ftiynnmfca gyreggkdsc egdsggphvt
421 evegtsfltg iiswgeecam kgkygiytkv sryvnwikek tklt

Mutation in Human Coagulation Factor IX (Hemophilia B, Christmas Disease)

Genetic mutation (either missense, substitution or deletion) in genes coding for coagulation factors cause hemophilia - deficient blood-clotting capability, spontaneous bleeding at joints and tissues and extended bleeding after injury. Although it was originally thought to be one disease, hemophilia exists in two distinct forms. The two forms, hemophilia A and hemophilia B, although indistinguishable in symptom, are different diseases that result from mutations at different genetic loci. Hemophilia B effects roughly 1 in 30,000 males, an occurrence much lower than that of hemophilia A. Hemophilia patients are classified by the seriousness of their symptoms: mild, moderate or severe. Approximately 60% of hemophilia patients suffer from severe hemophilia. (Massimini 182)

Unlike the gene for Coagulation Factor VIII, which exists in length at many loci on the X Chromosome, the gene for Factor IX is fairly concise and localized. Therefore, deletions involving large portions of the gene are a less common cause of hemophilia B than hemophilia A. Over 100 allelic variants of hemophilia B have been discovered in patients, each resulting from a unique base or amino acid substitution, deletion or missense in the Xq27.1-q27.2 region of the large arm of the X chromosome. One of the earliest mutated forms of Coagulation Factor IX was found to be a single-base mutation (from G to A) at nucleotide 6 in the 5' UT region, later termed the Leyden-specific region. Consequently, this first of many mutated forms of Factor IX has been termed Factor IX Leyden. (Hirowasa et. al.) Interestingly, this form of hemophilia is temporary. Normal production levels of fully functional Factor IX begin at puberty. However, many children still suffer from the disease. Good things are going on to improve the situation here. Many other forms of mutated Factor IX have been discovered and are listed here at OMIM.

Gene Therapy:

With the recent advances in molecular research techniques, there has been renewed hope for those suffering from hemophilia. Prior to the discovery of the gene for Coagulation Factor IX (and Coagulation Factor VIII), therapies were limited to injections of pooled plasma from normal individuals. These consistent blood transfusions are inefficient and facilitate the spreading of disease such as hepatitis and HIV. Biotechnology has produced methods for subcloning Coagulation Factor IX into transgenic non-human species and introducing these harvested plasmids to effected individuals. In 1990, researchers produced a functional Factor IX protein from rabbits that was indistinguishable from human Factor IX. (Armentano et. al.) Harvesting of large quantities of Coagulation Factor IX from transgenic species has prospered as a way to treat sufferers of hemophilia B.


1. Aggeler, P. M.; White, S. G.; Glendening, M. B.; Page, E. W.; Leake, T. B.; Bates, G. :
Plasma thromboplastin component (PTC) deficiency: a new disease resembling hemophilia. Proc. Soc. Exp. Biol. Med. 79: 692-694, 1952.

2. Armentano, D.; Thompson, A. R.; Darlington, G.; Woo, S. L. C. :
Expression of human factor IX in rabbit hepatocytes by retrovirus-mediated gene transfer: potential for gene therapy of hemophilia B. Proc. Nat. Acad. Sci. 87: 6141-6145, 1990.

3. Camerino, G et. al. Regional Localization on the Human X Chromosome and Polymorphism of the Coagulation Factor IX Gene (Hemophilia B Locus). Proceedings of the National Academy of Sciences of the United States of America, Volume 81, Issue 2, 498-502, 1984.

4. Hirowasa, Shinsaku et. al. Structural and Functional Basis of the Development Regulation of Human Coagulation Factor IX gene: Factor IX Leyden. Proceedings of the National Academy of Sciences of the United States of America, Volume 87, Issue 12, 4421-4425, 1990.

5. Kay, Mary A. et. al. Gene Therapy for the Hemophilias. Proceedings of the National Academy of Sciences of the United States of America, Volume 96, Issue 18, 9973-9975, 1999.

6. Locus Link Report: F9 - Coagulation Factor IX. 2003. March 13, 2003. < >

7. Massimini, Kathy, ed. Genetic Disorders Sourcebook, Second Edition, Overview of Bleeding Disorders, Omnigraphics: Detroit, 181-261, 2000.

8. NCBI - National Center for Biotechnology Information Online. 1996-2003, Johns Hopkins University. March 13, 2003. <>

9. OMIM - Online Mendelian Inheritance in Man: Hemophilia B. Last edited 2002. March 13, 2003. <>

10. Vehar, Gordon A. Production of Recombinant Coagulation Proteins. Annals of the New York Academy of Sciences, Volume 509. The New York Academy of Sciences: New York, 82, 1987.

Biology At Davidson

Molecular Biology At Davidson

© Copyright 2003 Department of Biology, Davidson College, Davidson, NC 28036

Send comments, questions, and suggestions to: Charles Wood