Analysis of p.Met348Lys 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.
The mutant residue cannot be found in the alignment.
There is no gap in the alignment.
The wild-type residue M348 is highly conserved among the CFTR orthologs: 98% (49 / 50 CFTR orthologs)The variant M348K 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 348). 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.
Divergencies show the amino acids which have been selected in the evolution.
If you find your variant among them with a high occurrence, there are good chances that your variant will most likely either have a small impact or no impact at all on the CFTR function.
Please note that CYSMA does not consider splicing alterations.
Refer to the Help page for more details.
CYSMA's visualizing modules for Ortholog conservation:
⬇ Download the region alignment (50 residues, Fasta format)
⬇ Download the CFTR phylogenic tree
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Homo sapiens
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Pan troglodytes
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Pongo pygmaeus
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Gorilla gorilla
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Nomascus leucogenys
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Macaca mulatta
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Macaca nemestrina
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Macaca fascicularis
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Papio anubis
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Callithrix jacchus
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Chlorocebus aethiops
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Colobus guereza
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Ateles geoffroyi
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Plecturocebus moloch
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Saimiri boliviensis
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Aotus nancymaae
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Otolemur garnettii
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Microcebus murinus
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Vicugna pacos
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Sus scrofa
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Bos taurus
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Muntiacus reevesi
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Muntiacus muntjak
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Ovis aries
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Equus caballus
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Canis familiaris
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Loxodonta africana
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Mustela furo
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Oryctolagus cuniculus
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Atelerix albiventris
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Dasypus novemcinctus
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Rhinolophus ferrumequinum
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Cavia porcellus
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Monodelphis domestica
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Ornithorhynchus anatinus
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Didelphis virginiana
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G
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Trichosurus vulpecula
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Carollia perspicillata
P
Y
L
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N
E
G
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Mus musculus
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Rattus norvegicus
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Gallus gallus
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Taeniopygia guttata
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Xenopus tropicalis
P
H
L
L
L
D
G
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Xenopus laevis
P
H
L
L
L
D
G
I
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I
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Squalus acanthias
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Y
A
F
I
H
T
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L
R
R
I
F
T
T
I
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Y
N
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F
P
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A
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Danio rerio
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H
A
L
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I
N
L
R
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T
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Y
C
M
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L
P
G
S
I
Q
M
W
Y
D
T
M
R
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W
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I
E
E
Oryzias latipes
P
Q
A
L
T
H
G
I
I
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R
I
F
T
T
A
S
Y
C
I
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T
L
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L
P
G
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Y
D
T
L
A
L
I
E
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D
Takifugu rubripes
P
H
A
L
S
K
G
I
I
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R
R
I
F
T
T
A
S
Y
C
M
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M
T
L
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Q
L
P
G
S
I
Q
M
W
Y
D
T
L
A
L
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K
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D
Tetraodon nigroviridis
P
H
A
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S
K
G
I
I
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R
R
I
F
T
T
A
S
Y
C
M
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T
L
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Q
L
P
G
S
I
Q
M
W
Y
D
T
L
A
L
V
R
K
I
E
D
Caenorhabditis elegans
A
C
D
Y
F
D
E
I
L
T
T
R
V
F
A
S
S
A
L
F
N
S
V
R
L
P
F
A
L
F
L
P
L
G
L
L
F
G
R
E
L
F
S
T
S
R
R
I
D
L
Species color legend (basic classification):
Great apes | Other monkeys | Prosimians | Other mammals | Lizards | Birds | Amphibians | Fishes | Insects | Nematods | Tunicates | Echinoderms
Ortholog sequences have been selected from the Ensembl(1) and
NCBI websites. Alignment has been performed with
ClustalW(2), version 1.83 or 2.0.7.
Trees have been built using Phylogeny.fr(3), based on the alignments.
Software used is PhyML 3.0 aLRT with default parameters. Pictures of trees have been made using Phylip at Mobyle.
AAPI and AAPIR have been calculated thanks to Bioperl.
Domain conservation:
The domain MSD1 of CF Transmembrane conductance Regulator has been shown to interact with:
is the membrane-spanning domain 1, composed of six transmembrane helices (TM1-TM6). Four of the six TMs protrude into the cytosol to form the intracellular loops ICL1 (between TM2 and TM3) and ICL2 (between TM4 and TM5). ICL1 contacts NBD1 at the level of the ATP-binding site, while ICL2 binds in a groove located at the surface of NBD2.
MSD1: is the membrane-spanning domain 1, composed of six transmembrane helices (TM1-TM6). Four of the six TMs protrude into the cytosol to form the intracellular loops ICL1 (between TM2 and TM3) and ICL2 (between TM4 and TM5). ICL1 contacts NBD1 at the level of the ATP-binding site, while ICL2 binds in a groove located at the surface of NBD2.
MSD1 of CF Transmembrane conductance Regulator domain alignment including p.Met348 residue.
***AAPID: Alignment Average Percentage Identity of the Domain (positions are indicated). !AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 348). AAPIR appears in green if it is more than 10% compared to AAPID, in red if less than 10%.
Divergencies
Residues present in more than 10% of the sequences are highlighted in blue.
A - 8.16%
C - 0.47%
D - 3.03%
E - 5.13%
F - 6.29%
G - 7.46%
I - 1.86%
K - 5.83%
L - 5.83%
N - 2.10%
P - 1.86%
Q - 4.43%
R - 9.32%
S - 6.53%
T - 4.43%
V - 4.66%
W - 1.40%
Y - 0.70%
The wild-type residue M348 belongs to the MSD1 domain and is conserved at 12.82% among the MSD1 homologs (55 / 429 MSD1 homologs)
The variant M348K has been found among the MSD1 homologs with a notable frequency: 5.83% (25 / 429 MSD1 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 MSD1 domain conservation:
Sequence alignments for NBDs have all been extracted from Prosite(4). Sequence alignments for MSDs have been extracted using the PSI-BLAST web server.
Sequences alignments have been manually re-aligned using a structural alignment including the human CFTR and bacterian ABC transporters with know 3D structures (for MSDs and NBDs domains).
Predictions of secondary structures have been made with PsiPred(9)
, version 2.5, using Protein Multiple Sequences Alignments as input, in order to increase the accuracy of the prediction.
Amino acid frequencies have been calculated from a non redondant set defined by the RCSB.
The Help page will tell you more about it.
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.
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 M348 to be located in an α helice (which confirms PsiPred prediction) and K348 in an α helice. Moreover, the residue is located in the core of this α helice (which contains 43 residues). Helix interior propensities of wild-type and mutant residues are 1.34 and 1.11. A potential Side chain interaction of the type i,i-4 has been detected between mutant residue and ILE344. This
interaction presents an attracting energy of -0.22 kcal/mol.
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 residue M348 is predicted to be buried, while the mutant residue M348K is predicted to be exposed, what could destabilize the domain
The two residues have a different polarity, which could interfere with hydrogen-bonding capabilities
The two residues have different charge properties, which could interfere with ionic bonds or potential inter- or intra-molecular interactions
Hydrogen bond network:
M348
K348
none
none
The mutant residue is predicted to form less hydrophobic interactions than the wild-type
M348
K348
3.93 Å between MET 348 CE and TRP 1145 CZ2
none
For hydrophobic effects, the important point is the number of residues involved more than the number of interactions.
The mutant residue might introduce steric clashes
M348
K348
none
3.00 Å between LYS 348 CB and ALA 349 N
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.
JSmol Legends:
The residue at the position 348 is located in the center, labelled in yellow and surrounded by its neighboring residues (distance < 5 Å).
Van der Waals contacts with the residue 348 are represented by dotted lines.
Amino acids involved in H-bonds with the residue 348 are labelled in blue.
Amino acids involved in steric clashes with the residue 348 are labelled in red.
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.
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.
The variant M348K has been been described as Conflicting interpretations of pathogenicity - criteria provided, conflicting interpretations - (ClinVar for more details)
Click on the LOVD picture to check if a variant is described at position 348
Graphical display of the region at NCBI (including SNPs)
CYSMA Report:
Report for p.Met348Lys variant
CFTR orthologs conservation
The wild-type residue M348 is highly conserved among the CFTR orthologs: 98% (49 / 50 CFTR orthologs)The variant M348K has never been found among the CFTR orthologs
MSD1 homologs conservation
The wild-type residue M348 belongs to the MSD1 domain and is conserved at 12.82% among the MSD1 homologs (55 / 429 MSD1 homologs)
The variant M348K has been found among the MSD1 homologs with a notable frequency: 5.83% (25 / 429 MSD1 homologs)
Structural effects
Solvent accessibility: the wild-type residue M348 is predicted to be buried, while the mutant residue M348K is predicted to be exposed, which could destabilize the domain
The two residues have a different polarity, which could interfere with hydrogen-bonding capabilities
The two residues have different charge properties, which could interfere with ionic bonds or potential inter- or intra-molecular interactions
The mutant residue is predicted to form less hydrophobic interactions than the wild-type
The mutant residue might introduce steric clashes
Allele frequency
The variant M348V in gnomAD (123,136 exomes): 3.98e-06 The variant M348K in gnomAD (123,136 exomes): 1.35e-04 ; variant M348K in gnomAD (15,496 genomes): 6.37e-05
Clinical significance
The variant M348K has been been described as Conflicting interpretations of pathogenicity - criteria provided, conflicting interpretations - (ClinVar for more details)
CFTR-France
The variant M348K might correspond to: NM_000492.3:c.1043T>A, which is reported to be unclassified (CFTR-France for more details)
Additional resources
SIFT prediction: variant M348K is predicted to be damaging (score: 0)
PPH2 prediction: variant M348K is predicted to be damaging (score: 0.996)
