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Question

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Domain

Conserved?

Similar Chemical side chain?

Likely to be pathogenic?

C18R

Ins P46

Q59L

Pro63fsdelC

D76N

P95Q

A140T

E178G

R197H

V220D

CLUSTAL O(1.2.1) multiple sequence alignment (use as a guide to answer the question)

zebrafish_PDX1        MNREEHYYPPNHLYKDSCAFQRHPNEDYSQNPPPCLYMRQAH-------SVYASPLGAQD
house_mouse_PDX1      MNSEEQYYAATQLYKDPCAFQRGPVPEFSANPPACLYMGRQPPPP--PPPQFTSSLGSLE
Norway_rat_PDX1       MNSEEQYYAATQLYKDPCAFQRGPVPEFSANPPACLYMGRQPPPP--PTPQFAGSLGTLE
cattle_PDX1           MNREEQYYAATQLYKDPCAFQRGPAPDFSASPPACLYMGRQPPPPPPPPPPFPGALGALE
dog_PDX1              MNSEEQFYAATQLYKDPCAFQRGPAPEFSASPPACLYMGRQPPPP---PPPFPGTLGALE
Human_PDX1            MNGEEQYYAATQLYKDPCAFQRGPAPEFSASPPACLYMGRQPPPP--PPHPFPGALGALE
Rhesus_PDX1           MNGEEQYYAATQLYKDPCAFQRGPAPEFSASPPACLYMGRQPPPP--PPPQFPGALGALE
                     ** **::* .:**** ***** * ::* .** **** :           : . **: :

zebrafish_PDX1        QPNLTDITSYNMSS--RDDLAGPHLHLPQTSQ--TSLQSLGGYGDSL--DLCGDRNRYHL
house_mouse_PDX1      QGSPPDISPYEVPPLASDDPAGAHLHHHLPAQLGLAHPPPGPFPNGTEPGGLEEPNRVQL
Norway_rat_PDX1       QGSPPDISPYEVPPLA-DDPAGAHLHHHLPAQLGLAHPPPGPFPNGTETGGLEEPSRVHL
cattle_PDX1           QGSPPDISPYEVPPLA-DDPAMAHLHHHLPAQLALAHPPAGPFQDGADPGALEEPGSVQL
dog_PDX1              QGSPPDISPYEVPPLA-DDSAVAHLHHHLPAQLALPHPPAGPFPEGAEPAALEEPSRVQL
Human_PDX1            QGSPPDISPYEVPPLA-DDPAVAHLHHHLPAQLALPHPPAGPFPEGAEPGVLEEPNRVQL
Rhesus_PDX1           QGSPPDISPYEVPPLA-DDPAVAHLHHHLPAQLALPHPPSGPFPEGAEPGVLEEPNRVQL
                     * . **: *::     ** * ***    :*        * : :.       :    :*

zebrafish_PDX1        PFPWMKSTKSHTHAWKGQWTG-PYMVEAEENKRTRTAYTRAQLLELEKEFLFNKYISRPR
house_mouse_PDX1      PFPWMKSTKA--HAWKGQWAGGAYTAEPEENKRTRTAYTRAQLLELEKEFLFNKYISRPR
Norway_rat_PDX1       PFPWMKSTKA--HAWKSQWAGGAYAAEPEENKRTRTAYTRAQLLELEKEFLFNKYISRPR
cattle_PDX1           PFPWMKSTKA--HAWKGQWAGGAYAAEPEENKRTRTAYTRAQLLELEKEFLFNKYISRPR
dog_PDX1              PFPWMKSTKA--HAWKGQWAGGAYVAEPEENKRTRTAYTRAQLLELEKEFLFNKYISRPR
Human_PDX1            PFPWMKSTKA--HAWKGQWAGGAYAAEPEENKRTRTAYTRAQLLELEKEFLFNKYISRPR
Rhesus_PDX1           PFPWMKSTKA--HAWKGQWAGGAYAAEPEENKRTRTAYTRAQLLELEKEFLFNKYISRPR
                     *********: ****.**:* * .* ********************************

zebrafish_PDX1        RVELALTLSLTERHIKIWFQNRRMKWKKEEDKRRARGV--------DPEQDSSITSGDLK
house_mouse_PDX1      RVELAVMLNLTERHIKIWFQNRRMKWKKEEDKKRSSGTPSGGGGGEEPEQDCAVTSGEE-
Norway_rat_PDX1       RVELAVMLNLTERHIKIWFQNRRMKWKKEEDKKRSSGTTSGGGGGEEPEQDCAVTSGEE-
cattle_PDX1           RVELAVMLNLTERHIKIWFQNRRMKWKKEEDKKRSCGPPAAGGGDAEPEQDCAVTSGEE-
dog_PDX1              RVELAVMLNLTERHIKIWFQNRRMKWKKEEDKKRSCGTAPGGVADAEPEQDCAVSSGEE-
Human_PDX1            RVELAVMLNLTERHIKIWFQNRRMKWKKEEDKKRGGGTAVGGGGVAEPEQDCAVTSGEE-
Rhesus_PDX1           RVELAVMLNLTERHIKIWFQNRRMKWKKEEDKKRGGGTAVGGGGVAEPEQDCAVTSGEE-
                     *****: *.***********************:*. *         :****.:::**:

zebrafish_PDX1        DESCVGTATLAGPPSP-----LHPHAPSVQQDS------------------------
house_mouse_PDX1      --------LLAVPPLPPPGGAVPPGVPAAVREGLLPSGLSVSPQPSSIAPLRPQEPR
Norway_rat_PDX1       --------LLALPKPPPPGGVVPSGVPAAAREGRLPSGLSASPQPSSIAPLRPQEPR
cattle_PDX1           --------LLALPPPPPPGGAVPPAGPSAAREGRLPPGLSASPQPSSVAPLRPQESR
dog_PDX1              --------LLALPPALPPGGAVPPAVPAAAREGRLPPGLSASPQPSSVAPVRPQEPR
Human_PDX1            --------LLALPPPPPPGGAVPPAAPVAAREGRLPPGLSASPQPSSVAPRRPQEPR
Rhesus_PDX1           --------LL--PPPPPPGGAVPPAAPVAAREGRLPPGLSASPQPSSVAPRRPQEPR
                              * *        :    * . ::.      

Domain

Conserved?

Similar Chemical side chain?

Likely to be pathogenic?

C18R

Ins P46

Q59L

Pro63fsdelC

D76N

P95Q

A140T

E178G

R197H

V220D

Below is a list of protein mutations discovered in humans. Missense mutations are given as 'Normal amino acid--position within protein--Mutated amino acid'. For example, C18R means that a cysteine at position 18 in the human PDX1 protein is mutated to arginine. Frameshift mutations are denoted by 'fs'. For example, Pro63fsdelC means that a cytosine DNA base is which normally is found in the codon for proline 63. Using your sequence alignment as a guide and your knowledge about the functional of PDX1, predict whether each of these mutations are likely to be pathogenic or nonpathogenic and explain why. In your answer, reference the chemical nature of the amino acids in question, as well as the conservation and functional domains of the protein.

Explanation / Answer

These mutations may not cause disease because the mutation from cysteine to arginine is a gene disorder called point mutation. Here normal cysteine amnot acid is coded by UGU or UGC and arginine is coded by CGU or CGC or CGA or CGG. here the mutation in one letter 'U' replaced by 'C'.

The next mutation deletion is basically chromosomal deletion. The chemical nature of arginine basic and cysteine is neutral and it's a sulphur containing amino acid.

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