Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000339615
Querying Taster for transcript #2: ENST00000438251
MT speed 3.16 s - this script 8.782269 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TTLL13Ppolymorphism_automatic0.000354637144848957simple_aaeaffectedT262Isingle base exchangers2063743show file
TTLL13Ppolymorphism_automatic0.000354637144848957simple_aaeaffectedT262Isingle base exchangers2063743show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999645362855151 (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) chr15:90800449C>TN/A show variant in all transcripts   IGV
HGNC symbol TTLL13P
Ensembl transcript ID ENST00000339615
Genbank transcript ID NM_001029964
UniProt peptide A6NNM8
alteration type single base exchange
alteration region CDS
DNA changes c.785C>T
cDNA.1075C>T
g.7688C>T
AA changes T262I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
262
frameshift no
known variant Reference ID: rs2063743
databasehomozygous (T/T)heterozygousallele carriers
1000G4968971393
ExAC80841659924683
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5481
3.1541
(flanking)2.0851
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 increased7690wt: 0.7952 / mu: 0.8522 (marginal change - not scored)wt: ACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCCGT
mu: ACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCCGT
 acat|ATGA
Acc marginally increased7688wt: 0.8831 / mu: 0.8834 (marginal change - not scored)wt: TGACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCC
mu: TGACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCC
 tcac|ATAT
Acc marginally increased7692wt: 0.9132 / mu: 0.9299 (marginal change - not scored)wt: CCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCCGTTT
mu: CCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCCGTTT
 atat|GAGG
Acc marginally increased7678wt: 0.7305 / mu: 0.7686 (marginal change - not scored)wt: TCACATCCTGTGACCCTCTCCGGATCTTCACATATGAGGAG
mu: TCACATCCTGTGACCCTCTCCGGATCTTCATATATGAGGAG
 ctcc|GGAT
Acc increased7679wt: 0.29 / mu: 0.39wt: CACATCCTGTGACCCTCTCCGGATCTTCACATATGAGGAGG
mu: CACATCCTGTGACCCTCTCCGGATCTTCATATATGAGGAGG
 tccg|GATC
Acc increased7694wt: 0.26 / mu: 0.43wt: TCTCCGGATCTTCACATATGAGGAGGGCCTAGCCCGTTTTG
mu: TCTCCGGATCTTCATATATGAGGAGGGCCTAGCCCGTTTTG
 atga|GGAG
Donor marginally increased7692wt: 0.9776 / mu: 0.9897 (marginal change - not scored)wt: ACATATGAGGAGGGC
mu: ATATATGAGGAGGGC
 ATAT|gagg
distance from splice site 65
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      262LITSCDPLRIFTYEEGLARFATTP
mutated  not conserved    262LITSCDPLRIFIYEEGLARFATT
Ptroglodytes  not conserved  ENSPTRG00000007451  262LITSCDPLRIFIYEEGLARFATT
Mmulatta  not conserved  ENSMMUG00000010181  267LITSCDPLRIFMYEEGLARFATT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000045467  262LITSCDPLRIFMYEEGLARFATM
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0039501  319LITSVDPLRIFVYNEGLARFATN
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
85430DOMAINTTL.lost
504528COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1380 / 1380
position (AA) of stopcodon in wt / mu AA sequence 460 / 460
position of stopcodon in wt / mu cDNA 1670 / 1670
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 291 / 291
chromosome 15
strand 1
last intron/exon boundary 1458
theoretical NMD boundary in CDS 1117
length of CDS 1380
coding sequence (CDS) position 785
cDNA position
(for ins/del: last normal base / first normal base)
1075
gDNA position
(for ins/del: last normal base / first normal base)
7688
chromosomal position
(for ins/del: last normal base / first normal base)
90800449
original gDNA sequence snippet TGACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCC
altered gDNA sequence snippet TGACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCC
original cDNA sequence snippet TGACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCC
altered cDNA sequence snippet TGACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCC
wildtype AA sequence MEPSTCRTME SEEDYVEEKE SEKCVKEGVT NPSNSSQQAL LKADYKALKN GVPSPIMATK
IPKKVIAPVD TGDLEAGRRK RRRKRRSLAI NLTNCKYESV RRAAQMCGLK EVGEDEEWTL
YWTDCAVSLE RVMDMKRFQK INHFPGMTEI CRKDLLARNL NRMYKLYPSE YNIFPRTWCL
PADYGDFQSY GRQRKARTYI CKPDSGCQGR GIFITRNPRE IKPGEHMICQ QYISKPLLID
GFKFDMRVYV LITSCDPLRI FTYEEGLARF ATTPYMEPSH NNLDNVCMHL TNYAINKHNE
NFVRDGAVGS KRKLSTLNIW LQEHSYNPGE LWGDIEDIII KTIISAHSVL RHNYRTCFPQ
YLNGGTCACF EILGFDILLD HKLKPWLLEV NHSPSFTTDS CLDQEVKDAL LCDAMTLVNL
RGCDKRKVME EDKRRVKERL FQCYRQPRES RCARCLACV*
mutated AA sequence MEPSTCRTME SEEDYVEEKE SEKCVKEGVT NPSNSSQQAL LKADYKALKN GVPSPIMATK
IPKKVIAPVD TGDLEAGRRK RRRKRRSLAI NLTNCKYESV RRAAQMCGLK EVGEDEEWTL
YWTDCAVSLE RVMDMKRFQK INHFPGMTEI CRKDLLARNL NRMYKLYPSE YNIFPRTWCL
PADYGDFQSY GRQRKARTYI CKPDSGCQGR GIFITRNPRE IKPGEHMICQ QYISKPLLID
GFKFDMRVYV LITSCDPLRI FIYEEGLARF ATTPYMEPSH NNLDNVCMHL TNYAINKHNE
NFVRDGAVGS KRKLSTLNIW LQEHSYNPGE LWGDIEDIII KTIISAHSVL RHNYRTCFPQ
YLNGGTCACF EILGFDILLD HKLKPWLLEV NHSPSFTTDS CLDQEVKDAL LCDAMTLVNL
RGCDKRKVME EDKRRVKERL FQCYRQPRES RCARCLACV*
speed 1.57 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: simple_aae, prob: 0.999645362855151 (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) chr15:90800449C>TN/A show variant in all transcripts   IGV
HGNC symbol TTLL13P
Ensembl transcript ID ENST00000438251
Genbank transcript ID N/A
UniProt peptide A6NNM8
alteration type single base exchange
alteration region CDS
DNA changes c.785C>T
cDNA.1075C>T
g.7688C>T
AA changes T262I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
262
frameshift no
known variant Reference ID: rs2063743
databasehomozygous (T/T)heterozygousallele carriers
1000G4968971393
ExAC80841659924683
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5481
3.1541
(flanking)2.0851
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 increased7690wt: 0.7952 / mu: 0.8522 (marginal change - not scored)wt: ACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCCGT
mu: ACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCCGT
 acat|ATGA
Acc marginally increased7688wt: 0.8831 / mu: 0.8834 (marginal change - not scored)wt: TGACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCC
mu: TGACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCC
 tcac|ATAT
Acc marginally increased7692wt: 0.9132 / mu: 0.9299 (marginal change - not scored)wt: CCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCCGTTT
mu: CCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCCGTTT
 atat|GAGG
Acc marginally increased7678wt: 0.7305 / mu: 0.7686 (marginal change - not scored)wt: TCACATCCTGTGACCCTCTCCGGATCTTCACATATGAGGAG
mu: TCACATCCTGTGACCCTCTCCGGATCTTCATATATGAGGAG
 ctcc|GGAT
Acc increased7679wt: 0.29 / mu: 0.39wt: CACATCCTGTGACCCTCTCCGGATCTTCACATATGAGGAGG
mu: CACATCCTGTGACCCTCTCCGGATCTTCATATATGAGGAGG
 tccg|GATC
Acc increased7694wt: 0.26 / mu: 0.43wt: TCTCCGGATCTTCACATATGAGGAGGGCCTAGCCCGTTTTG
mu: TCTCCGGATCTTCATATATGAGGAGGGCCTAGCCCGTTTTG
 atga|GGAG
Donor marginally increased7692wt: 0.9776 / mu: 0.9897 (marginal change - not scored)wt: ACATATGAGGAGGGC
mu: ATATATGAGGAGGGC
 ATAT|gagg
distance from splice site 65
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      262LITSCDPLRIFTYEEGLARFATTP
mutated  not conserved    262LITSCDPLRIFIYEEGLARFATT
Ptroglodytes  not conserved  ENSPTRG00000007451  262LITSCDPLRIFIYEEGLARFATT
Mmulatta  not conserved  ENSMMUG00000010181  267LITSCDPLRIFMYEEGLARFATT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000045467  262LITSCDPLRIFMYEEGLARFATM
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0039501  319LITSVDPLRIFVYNEGLARFATN
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
85430DOMAINTTL.lost
504528COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2448 / 2448
position (AA) of stopcodon in wt / mu AA sequence 816 / 816
position of stopcodon in wt / mu cDNA 2738 / 2738
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 291 / 291
chromosome 15
strand 1
last intron/exon boundary 2491
theoretical NMD boundary in CDS 2150
length of CDS 2448
coding sequence (CDS) position 785
cDNA position
(for ins/del: last normal base / first normal base)
1075
gDNA position
(for ins/del: last normal base / first normal base)
7688
chromosomal position
(for ins/del: last normal base / first normal base)
90800449
original gDNA sequence snippet TGACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCC
altered gDNA sequence snippet TGACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCC
original cDNA sequence snippet TGACCCTCTCCGGATCTTCACATATGAGGAGGGCCTAGCCC
altered cDNA sequence snippet TGACCCTCTCCGGATCTTCATATATGAGGAGGGCCTAGCCC
wildtype AA sequence MEPSTCRTME SEEDYVEEKE SEKCVKEGVT NPSNSSQQAL LKADYKALKN GVPSPIMATK
IPKKVIAPVD TGDLEAGRRK RRRKRRSLAI NLTNCKYESV RRAAQMCGLK EVGEDEEWTL
YWTDCAVSLE RVMDMKRFQK INHFPGMTEI CRKDLLARNL NRMYKLYPSE YNIFPRTWCL
PADYGDFQSY GRQRKARTYI CKPDSGCQGR GIFITRNPRE IKPGEHMICQ QYISKPLLID
GFKFDMRVYV LITSCDPLRI FTYEEGLARF ATTPYMEPSH NNLDNVCMHL TNYAINKHNE
NFVRDGAVGS KRKLSTLNIW LQEHSYNPGE LWGDIEDIII KTIISAHSVL RHNYRTCFPQ
YLNGGTCACF EILGFDILLD HKLKPWLLEV NHSPSFTTDS CLDQEVKDAL LCDAMTLVNL
RGCDKRKVME EDKRRVKERL FQCYRQPRES RKEKTESSHV AMLDQERYED SHLGKYRRIY
PGPDTEKYAR FFKHNGSLFQ ETAASKAREE CARQQLEEIR LKQEQQETSG TKRQKARDQN
QGESAGEKSR PRAGLQSLST HLAYRNRNWE KELLPGQLDT MRPQEIVEEE ELERMKALLQ
RETLIRSLGI VEQLTRLQHP GPQGQKKLHE SRDRLGSQEL KSMSLVLLVL LRGAATEQGA
PHFLHPVLPH ESIPRILGAL PSMNAAIPHV PRYHLQPKNF NWTGEPAAIN SCSLSMKKAG
RCYFSSARIR LTSQGQASRR LEAINRVLAG SVPPTLTPKQ GYFLQPERVA SDSWTECTLP
SMVNSEHRAA KVPLCPASAP MLQRSRALLN INQFR*
mutated AA sequence MEPSTCRTME SEEDYVEEKE SEKCVKEGVT NPSNSSQQAL LKADYKALKN GVPSPIMATK
IPKKVIAPVD TGDLEAGRRK RRRKRRSLAI NLTNCKYESV RRAAQMCGLK EVGEDEEWTL
YWTDCAVSLE RVMDMKRFQK INHFPGMTEI CRKDLLARNL NRMYKLYPSE YNIFPRTWCL
PADYGDFQSY GRQRKARTYI CKPDSGCQGR GIFITRNPRE IKPGEHMICQ QYISKPLLID
GFKFDMRVYV LITSCDPLRI FIYEEGLARF ATTPYMEPSH NNLDNVCMHL TNYAINKHNE
NFVRDGAVGS KRKLSTLNIW LQEHSYNPGE LWGDIEDIII KTIISAHSVL RHNYRTCFPQ
YLNGGTCACF EILGFDILLD HKLKPWLLEV NHSPSFTTDS CLDQEVKDAL LCDAMTLVNL
RGCDKRKVME EDKRRVKERL FQCYRQPRES RKEKTESSHV AMLDQERYED SHLGKYRRIY
PGPDTEKYAR FFKHNGSLFQ ETAASKAREE CARQQLEEIR LKQEQQETSG TKRQKARDQN
QGESAGEKSR PRAGLQSLST HLAYRNRNWE KELLPGQLDT MRPQEIVEEE ELERMKALLQ
RETLIRSLGI VEQLTRLQHP GPQGQKKLHE SRDRLGSQEL KSMSLVLLVL LRGAATEQGA
PHFLHPVLPH ESIPRILGAL PSMNAAIPHV PRYHLQPKNF NWTGEPAAIN SCSLSMKKAG
RCYFSSARIR LTSQGQASRR LEAINRVLAG SVPPTLTPKQ GYFLQPERVA SDSWTECTLP
SMVNSEHRAA KVPLCPASAP MLQRSRALLN INQFR*
speed 1.59 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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