Task 8 (MSUD)

Results

Lab journal

SIFT

The following table shows the prediction of mutation effects by SIFT. 6 out of 10 mutations are predicted to affect protein function.

mutation	prediction	score	median sequence conservation	sequences represented at position
P38H	tolerated	0.16	3.16	17
M82L	tolerated	0.56	3.03	43
T151M	tolerated	0.05	3.03	46
A222T	affect protein function	0.04	3.03	46
C264W	affect protein function	0.00	3.03	46
R265W	affect protein function	0.00	3.03	46
R314Q	affect protein function	0.01	3.03	46
R346H	affect protein function	0.00	3.03	46
I361V	tolerated	0.12	3.03	46
Y413H	affect protein function	0.00	3.03	46

Polyphen2

The prediction resuls of Polyphen2 are shown in the following table. 7 out of 10 mutations are predicted to be probably damaging (at least for the trained set HumDiv). For the mutation T151M, this does not agree with the results of SIFT. But for this mutations the Polyphen scores are also the lowest of all mutations that are predicted to be damaging. So Polyphen sees an uncertainty for this mutation too, if it is damaging.

	HumDiv				HumVar
mutation	prediction	score	sensitivity	specificity	prediction	score	sensitivity	specificity
P38H	benign	0.118	0.93	0.96	benign	0.042	0.93	0.62
M82L	benign	0.002	0.99	0.30	benign	0.006	0.97	0.45
T151M	probably damaging	0.963	0.78	0.95	possibly damaging	0.622	0.80	0.85
A222T	probably damaging	1.000	0.00	1.00	probably damaging	0.943	0.65	0.91
C264W	probably damaging	0.989	0.72	0.97	possibly damaging	0.887	0.71	0.89
R265W	probably damaging	1.000	0.00	1.00	probably damaging	1.000	0.00	1.00
R314Q	probably damaging	1.000	0.00	1.00	probably damaging	0.998	0.18	0.98
R346H	probably damaging	1.000	0.00	1.00	probably damaging	0.993	0.47	0.96
I361V	benign	0.386	0.90	0.89	possibly damaging	0.610	0.80	0.83
Y413H	probably damaging	1.000	0.00	1.0	probably damaging	0.999	0.09	0.99