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Analysis of p.Leu1480Pro variant, CFTR gene, CF Transmembrane conductance Regulator protein (1480 residues)


Data provided and calculated by CYSMA must be considered as predictions.
They are meant for educational purposes only and are provided with NO WARRANTY with respect to their biological reliability.



  • Allele frequency:

    variant L1480P gnomAD (123,136 exomes): 3.99e-06


  • Ortholog conservation: Help


    Number of sequences AAPI* AAPIR** Number of divergencies Number of mutant P1480 Number of gaps Conservation of L1480 Conservation - gap
    50 80.72% 69.77% 1
    show divergencies
    0
    details
    1
    details
    96.00% (48 / 50) 97.96% (48 / 49)


    The wild-type residue L1480 is highly conserved among the CFTR orthologs: 96% (48 / 50 CFTR orthologs)
    The variant L1480P has never been found among the CFTR orthologs

    *AAPI: Alignment Average Percentage Identity
    **AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 1480). AAPIR appears in green if it is more than 10% compared to AAPI, in red if less than 10%.
    Click here for more details on the alignment.


    CYSMA's visualizing modules for Ortholog conservation:





    ⬇ Download the region alignment (50 residues, Fasta format)
    ⬇ Download the CFTR phylogenic tree



    Display methods


  • Domain conservation: Help

    The domain C-ter of CF Transmembrane conductance Regulator has been shown to interact with:



    The residue p.Leu1480 (C-ter) seems to play a key role in the CFTR function:

    p.Leu1480 belongs to the PDZ-binding motif.


    The residue p.Leu1480 belongs to the domain C-ter.

    1444
    1480


    C-ter: C-terminal region








    C-ter of CF Transmembrane conductance Regulator domain alignment including p.Leu1480 residue.



    Number of sequences AAPID***
    (from aa 1444 to aa 1480)
    AAPIR! Number of divergencies Number of mutant Number of gaps Conservation of L1480 Conservation - gap
    22 62.20% 78.63% 0
    show divergencies
    0 1 95.45% (21 / 22) 100.00% (21 / 21)



    ***AAPID: Alignment Average Percentage Identity of the Domain (positions are indicated).
    !AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 1480). AAPIR appears in green if it is more than 10% compared to AAPID, in red if less than 10%.

    The wild-type residue L1480 is conserved at 95.45% among the C-ter domain homologs

    Divergencies show the amino acids which have been selected in the evolution. Residues present in more than 10% of the sequences are highlighted in blue.
    Please note that CYSMA does not consider splicing alterations.
    Refer to the Help page for more details.



    CYSMA's visualizing modules for C-ter domain conservation:





    Display methods


  • Refer to the Help page for more details.


  • Secondary structure analysis: Help


    Residue p.Leu1480 is predicted to belong to a loop. Probability is 0.981.

    Direct environment is as follow:

    VQDTRL1480
    HHHCCC


    Display methods











  • 3D analysis: Help


    Models provided and analysed by CYSMA must be considered as predictions, therefore be careful when interpreting the results. All efforts have been made to build structures of quality, however, they are provided with NO WARRANTY as to their accuracy with the real biological molecules studied.

    Wild type and predicted mutant structures have been compared. You will find the results below.


  • Clinical significance:

    The variant L1480P has not been reported in ClinVar


  • Patients data: CFTR-France

  • Variant L1480P might correspond to:


    Variant details from CFTR-France:
    Name NM_000492.3:c.4439T>C
    Protein name NP_000483.3:p.(Leu1480Pro)
    Genomic name chr7:g.117307158T>C
    Class unclassified


    Patients carrying this variant in CFTR-France:
    Total number of patients 1
    CFTR-RD1
    • Other  1

    (CFTR-France for more details)




  • Additional resources:



  • References


    CYSMA has completed its calculations; Execution time: 12 wallclock secs ( 8.45 usr 0.04 sys + 3.58 cusr 0.06 csys = 12.13 CPU)