Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000288235
Querying Taster for transcript #2: ENST00000307144
MT speed 0 s - this script 3.127457 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
LDHAL6Bpolymorphism_automatic7.57949258911594e-13simple_aaeaffectedV14Msingle base exchangers3809530show file
MYO1Epolymorphism_automatic1.16380113589498e-05without_aaeaffectedsingle base exchangers3809530show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999242 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:59499179G>AN/A show variant in all transcripts   IGV
HGNC symbol LDHAL6B
Ensembl transcript ID ENST00000307144
Genbank transcript ID NM_033195
UniProt peptide Q9BYZ2
alteration type single base exchange
alteration region CDS
DNA changes c.40G>A
cDNA.138G>A
g.138G>A
AA changes V14M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 14
frameshift no
known variant Reference ID: rs3809530
databasehomozygous (A/A)heterozygousallele carriers
1000G47110751546
ExAC80141673924753
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0280.004
1.2460.004
(flanking)-0.2710.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased130wt: 0.7001 / mu: 0.7244 (marginal change - not scored)wt: GGCCAGCCAGAGAGT
mu: GGCCAGCCAGAGAAT		 CCAG|ccag
Donor increased133wt: 0.67 / mu: 0.99wt: CAGCCAGAGAGTGAG
mu: CAGCCAGAGAATGAG		 GCCA|gaga
distance from splice site 138
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      14WTVPVVRASQRVSSVGANFLCLGM
mutated  all conserved    14WTVPVVRASQRMSSVGANFLCLG
Ptroglodytes  all identical  ENSPTRG00000007125  14WTVPVVRASQRVSSVGANFPCLG
Mmulatta  all identical  ENSMMUG00000012934  14WTVPLVRASQRVSSVGANFLCLK
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no alignment  ENSGALG00000006300  n/a
Trubripes  no alignment  ENSTRUG00000010800  n/a
Drerio  no alignment  ENSDARG00000040856  n/a
Dmelanogaster  no alignment  FBgn0001258  n/a
Celegans  no alignment  F13D12.2  n/a
Xtropicalis  no alignment  ENSXETG00000013957  n/a
protein features
start (aa)end (aa)featuredetails 
101106NP_BINDNAD (By similarity).might get lost (downstream of altered splice site)
148148BINDINGNAD (By similarity).might get lost (downstream of altered splice site)
155155BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
187187BINDINGNAD or substrate (By similarity).might get lost (downstream of altered splice site)
218218BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
242242ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
297297BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1146 / 1146
position (AA) of stopcodon in wt / mu AA sequence 382 / 382
position of stopcodon in wt / mu cDNA 1244 / 1244
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 99 / 99
chromosome 15
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1146
coding sequence (CDS) position 40
cDNA position
(for ins/del: last normal base / first normal base)		 138
gDNA position
(for ins/del: last normal base / first normal base)		 138
chromosomal position
(for ins/del: last normal base / first normal base)		 59499179
original gDNA sequence snippet TTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAAT
altered gDNA sequence snippet TTGTGCGGGCCAGCCAGAGAATGAGCTCGGTGGGAGCGAAT
original cDNA sequence snippet TTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAAT
altered cDNA sequence snippet TTGTGCGGGCCAGCCAGAGAATGAGCTCGGTGGGAGCGAAT
wildtype AA sequence MSWTVPVVRA SQRVSSVGAN FLCLGMALCP RQATRIPLNG TWLFTPVSKM ATVKSELIER
FTSEKPVHHS KVSIIGTGSV GMACAISILL KGLSDELALV DLDEDKLKGE TMDLQHGSPF
TKMPNIVCSK DYFVTANSNL VIITAGARQE KGETRLNLVQ RNVAIFKLMI SSIVQYSPHC
KLIIVSNPVD ILTYVAWKLS AFPKNRIIGS GCNLDTARFR FLIGQKLGIH SESCHGWILG
EHGDSSVPVW SGVNIAGVPL KDLNSDIGTD KDPEQWKNVH KEVTATAYEI IKMKGYTSWA
IGLSVADLTE SILKNLRRIH PVSTIIKGLY GIDEEVFLSI PCILGENGIT NLIKIKLTPE
EEAHLKKSAK TLWEIQNKLK L*
mutated AA sequence MSWTVPVVRA SQRMSSVGAN FLCLGMALCP RQATRIPLNG TWLFTPVSKM ATVKSELIER
FTSEKPVHHS KVSIIGTGSV GMACAISILL KGLSDELALV DLDEDKLKGE TMDLQHGSPF
TKMPNIVCSK DYFVTANSNL VIITAGARQE KGETRLNLVQ RNVAIFKLMI SSIVQYSPHC
KLIIVSNPVD ILTYVAWKLS AFPKNRIIGS GCNLDTARFR FLIGQKLGIH SESCHGWILG
EHGDSSVPVW SGVNIAGVPL KDLNSDIGTD KDPEQWKNVH KEVTATAYEI IKMKGYTSWA
IGLSVADLTE SILKNLRRIH PVSTIIKGLY GIDEEVFLSI PCILGENGIT NLIKIKLTPE
EEAHLKKSAK TLWEIQNKLK L*
speed 0.86 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999988361988641 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:59499179G>AN/A show variant in all transcripts   IGV
HGNC symbol MYO1E
Ensembl transcript ID ENST00000288235
Genbank transcript ID NM_004998
UniProt peptide Q12965
alteration type single base exchange
alteration region intron
DNA changes g.165921C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3809530
databasehomozygous (A/A)heterozygousallele carriers
1000G47110751546
ExAC80141673924753
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0280.004
1.2460.004
(flanking)-0.2710.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased165927wt: 0.7272 / mu: 0.7719 (marginal change - not scored)wt: TCCCACCGAGCTCACTCTCTGGCTGGCCCGCACAACAGGCA
mu: TCCCACCGAGCTCATTCTCTGGCTGGCCCGCACAACAGGCA		 tctg|GCTG
Acc marginally increased165926wt: 0.8700 / mu: 0.9225 (marginal change - not scored)wt: CTCCCACCGAGCTCACTCTCTGGCTGGCCCGCACAACAGGC
mu: CTCCCACCGAGCTCATTCTCTGGCTGGCCCGCACAACAGGC		 ctct|GGCT
Acc increased165931wt: 0.33 / mu: 0.61wt: ACCGAGCTCACTCTCTGGCTGGCCCGCACAACAGGCACAGT
mu: ACCGAGCTCATTCTCTGGCTGGCCCGCACAACAGGCACAGT		 gctg|GCCC
Acc increased165928wt: 0.51 / mu: 0.58wt: CCCACCGAGCTCACTCTCTGGCTGGCCCGCACAACAGGCAC
mu: CCCACCGAGCTCATTCTCTGGCTGGCCCGCACAACAGGCAC		 ctgg|CTGG
Donor marginally increased165915wt: 0.4343 / mu: 0.4381 (marginal change - not scored)wt: CACCGAGCTCACTCT
mu: CACCGAGCTCATTCT		 CCGA|gctc
distance from splice site 1495
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
1679DOMAINMyosin head-like.might get lost (downstream of altered splice site)
581591REGIONActin-binding (Potential).might get lost (downstream of altered splice site)
695724DOMAINIQ.might get lost (downstream of altered splice site)
889892CONFLICTWSAG -> GVQGA (in Ref. 1; AAA62667).might get lost (downstream of altered splice site)
980980MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
984984CONFLICTN -> I (in Ref. 1; AAA62667).might get lost (downstream of altered splice site)
10511108DOMAINSH3.might get lost (downstream of altered splice site)
10971097CONFLICTQ -> P (in Ref. 1; AAA62667).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 401 / 401
chromosome 15
strand -1
last intron/exon boundary 3651
theoretical NMD boundary in CDS 3200
length of CDS 3327
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 165921
chromosomal position
(for ins/del: last normal base / first normal base)		 59499179
original gDNA sequence snippet ATTCGCTCCCACCGAGCTCACTCTCTGGCTGGCCCGCACAA
altered gDNA sequence snippet ATTCGCTCCCACCGAGCTCATTCTCTGGCTGGCCCGCACAA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGSKGVYQYH WQSHNVKHSG VDDMVLLSKI TENSIVENLK KRYMDDYIFT YIGSVLISVN
PFKQMPYFGE KEIEMYQGAA QYENPPHIYA LADNMYRNMI IDRENQCVII SGESGAGKTV
AAKYIMSYIS RVSGGGTKVQ HVKDIILQSN PLLEAFGNAK TVRNNNSSRF GKYFEIQFSP
GGEPDGGKIS NFLLEKSRVV MRNPGERSFH IFYQLIEGAS AEQKHSLGIT SMDYYYYLSL
SGSYKVDDID DRREFQETLH AMNVIGIFAE EQTLVLQIVA GILHLGNISF KEVGNYAAVE
SEEFLAFPAY LLGINQDRLK EKLTSRQMDS KWGGKSESIH VTLNVEQACY TRDALAKALH
ARVFDFLVDS INKAMEKDHE EYNIGVLDIY GFEIFQKNGF EQFCINFVNE KLQQIFIELT
LKAEQEEYVQ EGIRWTPIEY FNNKIVCDLI ENKVNPPGIM SILDDVCATM HAVGEGADQT
LLQKLQMQIG SHEHFNSWNQ GFIIHHYAGK VSYDMDGFCE RNRDVLFMDL IELMQSSELP
FIKSLFPENL QADKKGRPTT AGSKIKKQAN DLVSTLMKCT PHYIRCIKPN ETKKPRDWEE
SRVKHQVEYL GLKENIRVRR AGYAYRRIFQ KFLQRYAILT KATWPSWQGE EKQGVLHLLQ
SVNMDSDQFQ LGRSKVFIKA PESLFLLEEM RERKYDGYAR VIQKSWRKFV ARKKYVQMRE
EASDLLLNKK ERRRNSINRN FIGDYIGMEE HPELQQFVGK REKIDFADTV TKYDRRFKGV
KRDLLLTPKC LYLIGREKVK QGPDKGLVKE VLKRKIEIER ILSVSLSTMQ DDIFILHEQE
YDSLLESVFK TEFLSLLAKR YEEKTQKQLP LKFSNTLELK LKKENWGPWS AGGSRQVQFH
QGFGDLAVLK PSNKVLQVSI GPGLPKNSRP TRRNTTQNTG YSSGTQNANY PVRAAPPPPG
YHQNGVIRNQ YVPYPHAPGS QRSNQKSLYT SMARPPLPRQ QSTSSDRVSQ TPESLDFLKV
PDQGAAGVRR QTTSRPPPAG GRPKPQPKPK PQVPQCKALY AYDAQDTDEL SFNANDIIDI
IKEDPSGWWT GRLRGKQGLF PNNYVTKI*
mutated AA sequence N/A
speed 0.28 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

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