Ortholog conservation:

The wild-type residue I556 is highly conserved among the CFTR orthologs: 92% (46 / 50 CFTR orthologs)
The variant I556V has been found among the CFTR orthologs with a low frequency: 4% (2 / 50 CFTR orthologs)

*AAPI: Alignment Average Percentage Identity
**AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 556). 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:

The residue p.Ile556 belongs to the domain NBD1.

423

649

NBD1: is the nucleotide binding domain 1, also called the ATP-binding cassette (ABC). It contains the Walker A (P-loop) and Walker B motifs, the C-motif (also known as the signature sequence), the A-, D-, Q-, and H-loops.

	is the nucleotide binding domain 1, also called the ATP-binding cassette (ABC). It contains the Walker A (P-loop) and Walker B motifs, the C-motif (also known as the signature sequence), the A-, D-, Q-, and H-loops.

NBD1 of CF Transmembrane conductance Regulator domain alignment including p.Ile556 residue.

***AAPID: Alignment Average Percentage Identity of the Domain (positions are indicated).
^!AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 556). AAPIR appears in green if it is more than 10% compared to AAPID, in red if less than 10%.

The wild-type residue I556 belongs to the NBD1 domain and is conserved at 13.96% among the NBD1 homologs (556 / 3982 NBD1 homologs)
The variant I556V has been found among the NBD1 homologs with a very high frequency: 60.52% (2410 / 3982 NBD1 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 NBD1 domain conservation:

Display methods

Secondary structure analysis:

Residue p.Ile556 is predicted to belong to an α helice. Probability is 0.975.

Direct environment is as follow:

Q	R	A	R	I556	S	L	A	R

Observed frequencies in α helices:
I: 0.99
V: 0.88

Mutant residue is less observed in this type of structure.

Display methods

3D analysis:

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.

• Overall quality of the structure:
  
  

  PDB template	Sequence identity*	MolProbity bad rotamers	MolProbity Ramachandran outliers	MolProbity Ramachandran favored
  5UAK	99.8 %	18/1313 - 1.37 %	17/1478 - 1.15 %	1360/1478 - 92.2 %

  
  
  

• Click on the MolProbity logo for complete details on the structure quality
  
  
  
  

• This model is made of 37 α helices and of 20 β strands (and is mainly composed of helices (739 residues in helices against 102 in strands, for a total of 1480 amino acids)).
  
  
• 3D structures predicts I556 to be located in an α helice (which confirms PsiPred prediction) and V556 in an α helice.
  Moreover, the residue is located in the core of this α helice (which contains 14 residues).
  Helix interior propensities of wild-type and mutant residues are 1.3 and 1.03.
  A potential Side chain interaction of the type i,i+4 has been detected between wild-type residue and ARG560.
  This interaction presents an attracting energy of -0.22 kcal/mol.
  
  



CYSMA's modules to download the 3D structures:



Chech 3D coverage of CFTR models ⬇ Download the wild-type 3D structure (PDB format) ⬇ Download the mutant 3D model (PDB format)





CYSMA's 3D Automatic Annotation:





WARNING!
The experimental 3D structure used for our predictions is the complete human CFTR structure which have been solved at a 3.7 Å resolution using cryo-electron microscopy (PDB: 5UAK; Liu et al. 2017).
The overall resolution is fairly low so the CYSMA's 3D Automatic Annotation pipeline might have missed some important structural effects.




• Solvent accessibility: the wild-type I556 and the mutant I556V are predicted to be buried
  
  
• Hydrogen bond network:
  

  I556	V556
  none	none

  
  
  
• The mutant residue is predicted to form less hydrophobic interactions than the wild-type
  The wild-type residue ILE is buried and is likely to belong to a hydrophobic pocket or core. This hydrophobic core is maintained in the mutant residue VAL
  
  

  I556

  V556

  4.89 Å between ILE 556 CG1 and ILE 502 CB 4.46 Å between ILE 556 CD1 and ILE 502 CB 3.75 Å between ILE 556 CB and ILE 497 CD1 4.55 Å between ILE 556 CG1 and ILE 497 CD1 4.92 Å between ILE 556 CG2 and ILE 497 CG1 4.14 Å between ILE 556 CD1 and ILE 497 CD1 4.07 Å between ILE 556 CD1 and LEU 548 CD1 4.78 Å between ILE 556 CG2 and ILE 506 CG1 4.97 Å between ILE 556 CB and LEU 526 CD2 4.85 Å between ILE 556 CG1 and LEU 526 CG 4.70 Å between ILE 556 CD1 and LEU 526 CD2

  4.99 Å between VAL 556 CG1 and ILE 502 CB 4.94 Å between VAL 556 CG2 and ILE 502 CB 3.74 Å between VAL 556 CB and ILE 497 CD1 3.63 Å between VAL 556 CG1 and ILE 497 CD1 4.61 Å between VAL 556 CG2 and ILE 497 CD1 4.52 Å between VAL 556 CG1 and ILE 506 CG1 4.88 Å between VAL 556 CB and LEU 526 CD2 4.78 Å between VAL 556 CG2 and LEU 526 CG

  
  
  

For hydrophobic effects, the important point is the number of residues involved more than the number of interactions.



• The mutant residue is not predicted to introduce steric clashes
  

  I556	V556
  none	none

  
  
  

CYSMA's 3D visualizing module:



• If you want to investigate further the structures, you can use the JSmol applets of the wild-type (left) and mutant (right) structures.
  
  Click on the JSmol applets' link to hide it.
  You have a full access to Jmol commands with a simple right click on one applet.
  
  
  
  
  

  I556 (wild-type)	V556 (mutant)

  
                Slab       Spin on/off       Show measurements       Change background       Sharper/Faster                    

  
  JSmol Legends:
  The residue at the position 556 is located in the center, labelled in yellow and surrounded by its neighboring residues (distance < 5 Å).
  Van der Waals contacts with the residue 556 are represented by dotted lines.
  Amino acids involved in H-bonds with the residue 556 are labelled in blue.
  Amino acids involved in steric clashes with the residue 556 are labelled in red.

  
  Display JSmol complete legends

  The overall structure of the complete human CFTR is represented in ribbon diagrams (click on the Reset button to visualize the overall CFTR structure).
  The membrane-spanning domain MSD1 is represented in blue and MSD2 in light blue.The nucleotide-binding domain NBD1 is represented in orange, NBD2 in light salmon.The lasso domain is shown in red and the R domain in green.

  Display Molecular Modelling methods

  The 3D structures used in CYSMA are models based on the CFTR experimental 3D structure in the channel-closed conformation (PDB: 5UAK; resolution: 3.9 Å).
  In the wild-type model, the (missing) loops and the (missing) R domain were built de novo using the software Modeller. For the variant models, the point mutation (homology modelling) are made on the fly with Modeller (more). Each structure has been assessed with MolProbity⁽¹⁹⁾. Msms⁽²⁰⁾ is used to calculate solvent accessibility, and STRIDE⁽²¹⁾ (plus stride2pdb) for secondary structure assignment.
  Secondary structure analyses in 3D models uses side chain interaction energies reviewed in ⁽²³⁾, as well as amino-acids propensities for N-caps, N1-N3, helix middle, C3-C1 and C-caps extracted from ⁽²⁴⁾(PDB values).
  Structural properties are calculated using an in-house developped program based for the USMA's 3D Automatic Annotation pipeline.

  Refer to the Help page for more details.

• Functional studies for c.1666A>G (I556V):
  
  

  Reference	PMID	Splicing	mRNA level	Maturation	Localization	Channel fonction (Cl-)	Bicarbonate
  Lee et al, 2003	12952861			✓		✓	✓




« ✓ » indicates the type of analysis performed and not the results




• SIFT prediction: variant I556V is predicted to be tolerated (score: 0.52)


• PPH2 prediction: variant I556V is predicted to be benign (score: 0.334)


• UNIPROT annotations
  

  The variation is not reported in Uniprot.

• Click on the LOVD picture to check if a variant is described at position 556    
  
  
  
  



• Graphical display of the region at NCBI (including SNPs)



• CYSMA Report:

  
  

  Report for p.Ile556Val variant

  CFTR orthologs conservation	The wild-type residue I556 is highly conserved among the CFTR orthologs: 92% (46 / 50 CFTR orthologs) The variant I556V has been found among the CFTR orthologs with a low frequency: 4% (2 / 50 CFTR orthologs)
  NBD1 homologs conservation	The wild-type residue I556 belongs to the NBD1 domain and is conserved at 13.96% among the NBD1 homologs (556 / 3982 NBD1 homologs) The variant I556V has been found among the NBD1 homologs with a very high frequency: 60.52% (2410 / 3982 NBD1 homologs)
  Structural effects	The wild-type residue I556 seems to play a key role in the CFTR function. I556 is involved in the CFTR folding Solvent accessibility: the wild-type I556 and the mutant I556V are predicted to be buried The mutant residue is predicted to form less hydrophobic interactions than the wild-type The wild-type residue ILE is buried and is likely to belong to a hydrophobic pocket or core. This hydrophobic core is maintained in the mutant residue VAL The mutant residue is not predicted to introduce steric clashes
  Allele frequency	The variant I556V in gnomAD (123,136 exomes): 3.51e-03 ; variant I556V in gnomAD (15,496 genomes): 2.23e-03
  Clinical significance	The variant I556V has been been described as Conflicting interpretations of pathogenicity - criteria provided, conflicting interpretations - (ClinVar for more details)
  CFTR-France	The variant I556V might correspond to: NM_000492.3:c.1666A>G, which is reported to be disease-causing ( CFTR-France for more details)
  Additional resources	SIFT prediction: variant I556V is predicted to be tolerated (score: 0.52) PPH2 prediction: variant I556V is predicted to be benign (score: 0.334)