Difference between revisions of "Task 5: Mapping point mutations"

From Bioinformatikpedia
(→‎Alignment with the reference sequence used in HGMD)
(→‎SNPdb)
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=== SNPdb ===
  
=== SNPdb ===
−
==== Reference Sequence ====
 +
==== Methodology ====
  +
−
==== SNPs ====
  
  +
==== Results ====
  +
  +
We could find the following silent mutations in dbSNP:
  +
  +
{| border="1"
  +
|-
  +
! Identifier
  +
! AA-Position
  +
! Reference Triplet
  +
! Mutated Triplet
  +
! Reference Allele
  +
! Mutated Allele
  +
! Frame
  +
! Reference Residue
  +
! Mutated Residue
  +
|-
  +
| rs117308669
  +
| 65
  +
| GAA
  +
| GAG
  +
| A
  +
| G
  +
| 3
  +
| E
  +
| E
  +
|-
  +
| rs75065106
  +
| 257
  +
| CTG
  +
| TTG
  +
| C
  +
| T
  +
| 1
  +
| L
  +
| L
  +
|-
  +
| rs62651567
  +
| 322
  +
| ACA
  +
| ACG
  +
| A
  +
| G
  +
| 3
  +
| T
  +
| T
  +
|-
  +
| rs62508648
  +
| 366
  +
| CTG
  +
| CTA
  +
| G
  +
| A
  +
| 3
  +
| L
  +
| L
  +
|-
  +
| rs61747292
  +
| 320
  +
| CTC
  +
| CTT
  +
| C
  +
| T
  +
| 3
  +
| L
  +
| L
  +
|-
  +
| rs59326968
  +
| 425
  +
| AAT
  +
| AAC
  +
| T
  +
| C
  +
| 3
  +
| N
  +
| N
  +
|-
  +
| rs17852374
  +
| 35
  +
| TCA
  +
| TCG
  +
| A
  +
| G
  +
| 3
  +
| S
  +
| S
  +
|-
  +
| rs1801152
  +
| 413
  +
| TAC
  +
| TAT
  +
| C
  +
| T
  +
| 3
  +
| Y
  +
| Y
  +
|-
  +
| rs1801151
  +
| 399
  +
| AGG
  +
| CGG
  +
| A
  +
| C
  +
| 1
  +
| R
  +
| R
  +
|-
  +
| rs1801150
  +
| 398
  +
| GTA
  +
| GTT
  +
| A
  +
| T
  +
| 3
  +
| V
  +
| V
  +
|-
  +
| rs1801147
  +
| 202
  +
| TGC
  +
| TGT
  +
| C
  +
| T
  +
| 3
  +
| C
  +
| C
  +
|-
  +
| rs1801146
  +
| 136
  +
| AGC
  +
| AGT
  +
| C
  +
| T
  +
| 3
  +
| S
  +
| S
  +
|-
  +
| rs1801145
  +
| 9
  +
| GGC
  +
| GGG
  +
| C
  +
| G
  +
| 3
  +
| G
  +
| G
  +
|-
  +
| rs1126758
  +
| 231
  +
| CAG
  +
| CAG
  +
| A
  +
| G
  +
| 3
  +
| Q
  +
| Q
  +
|-
  +
| rs1042503
  +
| 244
  +
| GTG
  +
| GTA
  +
| G
  +
| A
  +
| 3
  +
| V
  +
| V
  +
|-
  +
| rs772897
  +
| 384
  +
| CTG
  +
| CTC
  +
| G
  +
| C
  +
| 3
  +
| L
  +
| L
  +
|}
   
 
== Comparing the annotation of HGMD and SNPdb ==
  
== Comparing the annotation of HGMD and SNPdb ==

Revision as of 19:09, 16 June 2011

Task description

A detailed task description can be found here: Mapping point mutations

SNP databases

HGMD

  • HGMD
  • Searched for PAH
  • 429 Missense/Nonsense mutations known by HGMD Professional

There are several mutation types known for PAH:

  • Missense/nonsense
  • Splicing
  • Regulatory
  • Small deletions
  • Small insertions
  • Small indels
  • Gross deletions
  • Gross insertions/duplications
  • Complex rearrangements

One additional category of mutation is known, but is not recorded for PAH

  • Repeat variations

Reference Sequence

The reference sequence is given by the accession number NM_000277.1, whose entry contains the following amino acid sequence:

MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEEN DVNLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDI GATVHELSRDKKKDTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQ FADIAYNYRHGQPIPRVEYMEEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCG FHEDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPM YTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLC KQGDSIKAYGAGLLSSFGELQYCLSEKPKLLPLELEKTAIQNYTVTEFQPLYYVAESF NDAKEKVRNFAATIPRPFSVRYDPYTQRIEVLDNTQQLKILADSINSEIGILCSALQK IK

SNPs

SNPdb

Methodology

Results

We could find the following silent mutations in dbSNP:

Identifier AA-Position Reference Triplet Mutated Triplet Reference Allele Mutated Allele Frame Reference Residue Mutated Residue
rs117308669 65 GAA GAG A G 3 E E
rs75065106 257 CTG TTG C T 1 L L
rs62651567 322 ACA ACG A G 3 T T
rs62508648 366 CTG CTA G A 3 L L
rs61747292 320 CTC CTT C T 3 L L
rs59326968 425 AAT AAC T C 3 N N
rs17852374 35 TCA TCG A G 3 S S
rs1801152 413 TAC TAT C T 3 Y Y
rs1801151 399 AGG CGG A C 1 R R
rs1801150 398 GTA GTT A T 3 V V
rs1801147 202 TGC TGT C T 3 C C
rs1801146 136 AGC AGT C T 3 S S
rs1801145 9 GGC GGG C G 3 G G
rs1126758 231 CAG CAG A G 3 Q Q
rs1042503 244 GTG GTA G A 3 V V
rs772897 384 CTG CTC G C 3 L L

Comparing the annotation of HGMD and SNPdb

Alignment of the reference sequences

We decided to use the sequence of PAH of Uniprot (see UniProt).

  • MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV
    NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
    FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM
    EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF
    RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
    QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE
    KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR
    IEVLDNTQQLKILADSINSEIGILCSALQKIK

Alignment with the reference sequence used in HGMD

The resulting alignment shows a 100% identity without any gaps. Therefore it is a "self-alignment".

Alignment with the reference sequence used in SNPdb

Mapping

Discussion

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