Lab Journal - Task 8 (PAH)

Mutation dataset

For the generation of the mutation dataset the following five SNPs from the HGMD database were used (25th June 2013): <figtable id="mutds_hgmd">

Missense mutations (SNPs) from HGMD
Accession Number	Codon change	Sequence position	Amino acid change	Codon number	Disease	Reference
CM000542	CAG⇒CTG	59	Gln(Q)-Leu(L)	20	Hyperphenylalaninaemia	Hennermann (2000) Hum Mutat 15, 254
CM045080	GGT⇒AGT	307	Gly(G)-Ser(S)	103	Phenylketonuria	Lee (2004) J Hum Genet 49, 617
CM910286	GCC⇒GTC	776	Ala(A)-Val(V)	259	Phenylketonuria	Labrune (1991) Am J Hum Genet 48, 1115
CM010981	AAG⇒ACG	1022	Lys(K)-Thr(T)	341	Phenylketonuria	Tyfield (1997) Am J Hum Genet 60, 388
CM090791	CCA⇒CAA	1247	Pro(P)-Gln(Q)	416	Hyperphenylalaninaemia	Dobrowolski (2009) J Inherit Metab Dis 32, 10

...

</figtable>

Furthermore, the following five mutations from dbSNP were added (25th June 2013): <figtable id="mutds_dbSNP">

Missense mutations (SNPs) from dbSNP
Reference SNP	Codon change	Sequence position	Amino acid change	Codon number	Disease
rs199475569	CAC⇒AAC	190	His(H)-Asn(N)	64	?
rs199475681	AGA⇒ATA	368	Arg(R)-Ile(I)	123	?
rs62508752	ACA⇒CCA	796	Thr(T)-Ala(A)	266	Phenylketonuria
rs199475695	TTT⇒TCT	1175	Phe(F)-Ser(S)	392	?
rs199475696	ATT⇒ACT	1262	Ile(I)-Thr(T)	421	?

...

</figtable>

Analyze SNPs

PSSM

We created the PSSM matrix using the standard parameter of PsiBlast and five iterations. In the right matrix you can see, that for some of the ten residues the amino acid is not conserved as they have higher values for other amino acids. SNPs are marked in red.

Last position-specific scoring matrix computed, weighted observed percentages rounded down,
information per position, and relative weight of gapless real matches to pseudocounts
         A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V    A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V
 20 Q   -2  1  2  3 -4  2  2 -1  2 -3 -1  2 -2 -3 -3 -1 -1 -4 -3 -1    0  7 13 17  0 14 11  3  5  0  6 16  0  0  0  0  2  0  0  6 0.32 inf
 64 H   -5  2 -1 -3 -7  0  0 -6  9 -7 -6  2 -3 -2 -6 -2 -5 -6  1 -7    0 10  2  1  0  3  6  0 58  0  0 11  1  1  0  2  0  0  5  0 1.89 inf  
103 G    0  0  0  0  2  0  0 -1  1  0 -1  0  1  0  0  0  0 -2  1  0    5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  0  5  5 0.03 inf
123 R   -3  6 -1 -3 -3  0 -2 -3  0  0 -1  3 -1 -4 -3 -1  1 -4 -3 -3    1 49  1  0  1  3  0  1  2  7  4 16  1  0  0  2 10  0  0  0 0.72 inf
259 A    6 -2 -2 -3 -3 -1 -2 -1 -3 -2 -2 -2 -1 -4 -3  1 -2 -4 -2 -2   70  2  1  0  0  3  1  3  0  2  4  1  1  0  0  9  1  0  1  1 0.93 inf
266 T    3 -1 -1 -3 -3 -3 -3  0 -3 -3 -3  0 -3 -4 -3  0  5 -4  0 -2   29  3  1  0  0  0  0  6  0  0  1  6  0  0  0  5 43  0  3  1 0.70 inf
341 K   -2  4 -1 -2 -1  1  1 -3 -1 -3 -1  4 -1  0 -2 -1 -1 -1 -2 -2    0 28  0  0  2  2 10  0  0  0  8 39  1  7  0  1  1  1  0  1 0.44 inf 
392 F   -4 -5 -5 -5  0 -5 -5 -3 -3  3  2 -5  1  6 -5 -4 -3 -2  2  1    0  0  0  0  2  0  0  2  0 16 17  0  2 49  0  0  0  0  6  7 0.98 inf
416 P    0 -4  1 -3 -5 -3 -2 -3 -2 -2 -5 -2 -4 -1  7 -1 -3 -6 -4 -4    9  0  9  0  0  0  2  1  1  3  0  2  0  4 66  4  0  0  0  0 1.60 inf
421 I   -1 -4 -4 -4 -3 -1 -4 -1 -4  4  1 -3  0 -2 -4 -3 -2 -4 -3  4    5  0  0  0  0  4  0  6  0 32  9  0  1  0  0  0  0  0  0 41 0.62 inf

Mammalian Homologous Sequences

We used a normal BLAST search on the mammalian database of Uniprot and filter the results per hand for double entries. Althogether we found 21 homologues sequences (<xr id="IDs"/>). <figtable id="IDs">

UniProt-IDs
P00439	H2Q6R0	G3S964	G1R3M2	G7PJC2	F7HMW9	F7I717	F7BKF9
F6XY00	E2R366	G1T8B6	H2NIF5	M3YKN3	M9P0Q7	H0WTI6	M3W9R1
G3TIW0	G1LIM6	Q2KIH7	G1P4I7	P16331	M9P0Y5

UniProt IDs of the 22 mammalian homologues sequences of the PAH protein.

</figtable>

SIFT

• A259V

Substitution at pos 20 from Q to L is predicted to be TOLERATED with a score of 0.16.
   Median sequence conservation: 3.20
   Sequences represented at this position:42

• R123I

Substitution at pos 64 from H to N is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.01
   Sequences represented at this position:77

• Q20L

Substitution at pos 103 from G to S is predicted to be TOLERATED with a score of 0.90.
   Median sequence conservation: 3.02
   Sequences represented at this position:72

• G103S

Substitution at pos 123 from R to I is predicted to be TOLERATED with a score of 0.05.
   Median sequence conservation: 3.01
   Sequences represented at this position:76

• H64N

Substitution at pos 259 from A to V is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.01
   Sequences represented at this position:77

• I421T

Substitution at pos 266 from T to A is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.01
   Sequences represented at this position:77

• K341T

Substitution at pos 341 from K to T is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.01
   Sequences represented at this position:77

• F392S

Substitution at pos 392 from F to S is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.01
   Sequences represented at this position:77

• P416Q

Substitution at pos 416 from P to Q is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.00
   Sequences represented at this position:74

• T266A

Substitution at pos 421 from I to T is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.00
   Sequences represented at this position:74

PolyPhen2

• A259V

HumDiv
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
HumVar
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)

• R123I

HumDiv
This mutation is predicted to be possibly damaging with a score of 0.807 (sensitivity: 0.84; specificity: 0.93)
HumVar
This mutation is predicted to be possibly damaging with a score of 0.582 (sensitivity: 0.81; specificity: 0.83)

• Q20L

HumDiv
This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)
HumVar
This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)

• G103S

HumDiv
This mutation is predicted to be benign with a score of 0.003 (sensitivity: 0.98; specificity: 0.44)
HumVar
This mutation is predicted to be benign with a score of 0.006 (sensitivity: 0.97; specificity: 0.45)

• H64N

HumDiv
This mutation is predicted to be probably damaging with a score of 0.993 (sensitivity: 0.70; specificity: 0.97)
HumVar
This mutation is predicted to be probably damaging with a score of 0.962 (sensitivity: 0.62; specificity: 0.92)

• I421T

HumDiv
This mutation is predicted to be possibly damaging with a score of 0.667 (sensitivity: 0.86; specificity: 0.91)
HumVar
This mutation is predicted to be probably damaging with a score of 0.913 (sensitivity: 0.69; specificity: 0.90)

• K341T

HumDiv
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
HumVar
This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.36; specificity: 0.97)

• F392S

HumDiv
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
HumVar
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)

• P416Q

HumDiv
This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.55; specificity: 0.98)
HumVar
This mutation is predicted to be probably damaging with a score of 0.985 (sensitivity: 0.55; specificity: 0.94)

• T266A

HumDiv
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
HumVar
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)

SNAP

• A259V
• R123I
• Q20L
• G103S
• H64N
• I421T
• K341T
• F392S
• P416Q
• T266A

MutationTaster

Gene: ENSG00000171759
Transcript: ENST00000553106
For affected protein features only those are reported that are annotated as "lost" and not as "might get lost".

• A259V - C776T

Prediction: disease causing, Model: simple_aae, prob: ~1 (classification due to ClinVar)
Summary: 
•	amino acid sequence changed
•	known disease mutation at this position (HGMD CM910286)
•	known disease mutation: rs118203921 (pathogenic)
•	protein features (might be) affected (HELIX: 251-259, lost)
splice sites: Acc marginally increased

• R123I - G368T

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	listed as SNP
•	protein features (might be) affected
•	splice site changes (Acc increased)

• Q20L - A59T

Prediction: disease causing, Model: simple_aae, prob: ~0.95
Summary
•	amino acid sequence changed
•	known disease mutation at this position (HGMD CM000542)
•	protein features (might be) affected
•	splice site changes (Donor lost, acc marginally increased)

• G103S - G307A

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	known disease mutation at this position (HGMD CM045080)
•	protein features (might be) affected (Domain ACT: lost)
•	splice site changes (Donor gained)

• H64N - C190A

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	known disease mutation at this position (HGMD CD993066)
•	protein features (might be) affected (Domain ACT: lost)

• I421T - T1262C

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	listed as SNP
•	protein features (might be) affected (STRAND: 420-424, lost)

• K341T - A1022C

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	known disease mutation at this position (HGMD CM010980)
•	known disease mutation at this position (HGMD CM010981)
•	protein features (might be) affected (STRAND: 339-342, lost)

• F392S - T1175C

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	listed as SNP
•	protein features (might be) affected (HELIX: 392-403, lost)
•	splice site changes (Donor increased)

• P416Q - C1247A

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	known disease mutation at this position (HGMD CM090791)
•	protein features (might be) affected (TURN: 416-419, lost)
•	splice site changes (Acc marginally increased, donor increased, donor gained)

• T266A - A796C

Prediction: disease causing, Model: simple_aae, prob: ~1
Summary
•	amino acid sequence changed
•	listed as SNP
•	protein features (might be) affected 
•	splice site changes (Acc increased, acc gained, donor increased)