Sequence-based mutation analysis

SNP's

Because the HFE-Gen has no annotated functional site, we can just adress the biochemical changes for each SNP. A change in functionality or stability can not described.
To compare the biochemical properties of the amino acid's, we used the very convenient function of wolfram alpha.

Mutation	Position	Database	Blosum62	PAM1	Pam250	Physicochemical changes
S/C	65	HGMD/dbSNP	-1	5	3	There is no change in size and charge, just the polarity changes .
I/T	105	HGMD/dbSNP	-1	11	6	An OH-group is replaced by an ethyl-group which leads so a small change in size and a large change in hydrophobicity.
Q/H	127	HGMD/dbSNP	0	20	7	Because of the aromatic ring, the flexibility is reduced with a histidine at this position. The polarity and hydrophobicity remain the same.
C/Y,S	282	HGMD/dbSNP	-2/-1	3/11	3/7	In both cases, the hydrophobicity is changed. Cysteine is a nonpolar whereas Serine and Tyrosine are polar amino acids.
R/M	330	HGMD	-1	1	1
A/V	176	HGMD	0	13	9
R/S	6	HGMD	-1	11	6
T/I	217	dbSNP	-1	7	4
M/T	35	dbSNP	-1	6	5
R/M	58	dbSNP	-1	1	1

A change in polarity is just important for residues at the surface of the protein, because with a change in polarity, the hydrophobicity changes and so the water solubility decreases.

SIFT

The prediction of SIFT is marked with a low confidence warning because, the sequences used for the prediction were not diverse enough.

• Server: http://sift.jcvi.org/www/SIFT_seq_submit2.html

Mutation	Position	Prediction	Score	Cause disease
S/C	65	AFFECT PROTEIN FUNCTION	0.00	yes
I/T	105	AFFECT PROTEIN FUNCTION	0.00	yes
Q/H	127	TOLERATED	0.16	yes
C/Y,S	282	AFFECT PROTEIN FUNCTION	0.00	yes
R/M	330	TOLERATED	0.06	yes
A/V	176	AFFECT PROTEIN FUNCTION	0.01	yes
R/S	6	AFFECT PROTEIN FUNCTION	0.01	yes
T/I	217	TOLERATED	1.00
M/T	35	TOLERATED	1.00
R/M	58	AFFECT PROTEIN FUNCTION	0.00

The complete prediction for each position and amino acid can be found here

We got three warning messages form SIFT for which we have no explanation at this time.

WARNING: Original amino acid H at position 31 is not allowed by the prediction. 
WARNING: Original amino acid S at position 45 is not allowed by the prediction. 
WARNING: Original amino acid Y at position 230 is not allowed by the prediction.

PolyPhen-2

• Server: http://genetics.bwh.harvard.edu/pph2/

Mutation	Position	Prediction	Score	Cause disease
S/C	65	PROBABLY DAMAGING	0.997	yes
I/T	105	PROBABLY DAMAGING	0.998	yes
Q/H	127	BENIGN	0.002	yes
C/Y,S	282	PROBABLY DAMAGING	1.000/0.997	yes
R/M	330	PROBABLY DAMAGING	0.948	yes
A/V	176	PROBABLY DAMAGING	0.998	yes
R/S	6	PROBABLY DAMAGING	0.738	yes
T/I	217	BENIGN	0.195
M/T	35	PROBABLY DAMAGING	0.989
R/M	58	PROBABLY DAMAGING	0.998