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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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000370449
MT speed 0 s - this script 4.451956 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCC2disease_causing_automatic0.999999999492503simple_aaeaffected0I1173Fsingle base exchangers72558201show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999999999492503 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014972)
  • known disease mutation: rs8418 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:101595950A>TN/A show variant in all transcripts   IGV
HGNC symbol ABCC2
Ensembl transcript ID ENST00000370449
Genbank transcript ID NM_000392
UniProt peptide Q92887
alteration type single base exchange
alteration region CDS
DNA changes c.3517A>T
cDNA.3630A>T
g.53462A>T
AA changes I1173F Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
1173
frameshift no
known variant Reference ID: rs72558201
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs8418 (pathogenic for Dubin-Johnson syndrome|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014972)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014972)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014972)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2010.955
3.4461
(flanking)5.1451
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased53467wt: 0.33 / mu: 0.90wt: TCAGGTTTGCCAGTTATCCGTGCCTTTGAGCACCAGCAGCG
mu: TCAGGTTTGCCAGTTTTCCGTGCCTTTGAGCACCAGCAGCG
 ccgt|GCCT
Acc increased53458wt: 0.43 / mu: 0.56wt: GAGACCGTATCAGGTTTGCCAGTTATCCGTGCCTTTGAGCA
mu: GAGACCGTATCAGGTTTGCCAGTTTTCCGTGCCTTTGAGCA
 gcca|GTTA
Acc increased53469wt: 0.37 / mu: 0.88wt: AGGTTTGCCAGTTATCCGTGCCTTTGAGCACCAGCAGCGAT
mu: AGGTTTGCCAGTTTTCCGTGCCTTTGAGCACCAGCAGCGAT
 gtgc|CTTT
Acc increased53471wt: 0.30 / mu: 0.84wt: GTTTGCCAGTTATCCGTGCCTTTGAGCACCAGCAGCGATTT
mu: GTTTGCCAGTTTTCCGTGCCTTTGAGCACCAGCAGCGATTT
 gcct|TTGA
Acc gained534730.57mu: TTGCCAGTTTTCCGTGCCTTTGAGCACCAGCAGCGATTTCT cttt|GAGC
distance from splice site 98
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1173HFSETVSGLPVIRAFEHQQRFLKH
mutated  not conserved    1173HFSETVSGLPVFRAFEHQQRFLK
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000023764  1172HFSETVSGLPVIRAFEHQQRFLK
Fcatus  all identical  ENSFCAG00000014380  1173HFSETVSGLSVIRAFEHQQRFLK
Mmusculus  all identical  ENSMUSG00000025194  1171HFSETVSGLPVIRAFEHQQRFLA
Ggallus  all identical  ENSGALG00000007395  1180HFGETVSGLSVIRAYGHQQR
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000014031  1187HFGETVSGLSVIRAYGHQDRFLK
Dmelanogaster  all identical  FBgn0032456  1182HFSETVTGASTIRAYNVGDRFIE
Celegans  all identical  F57C12.5  1169HFQESIQGASSIRAYGVVDKFIR
Xtropicalis  all identical  ENSXETG00000003740  1174HFGETVSGLSVIRAYGHQDRFLQ
protein features
start (aa)end (aa)featuredetails 
9791264DOMAINABC transmembrane type-1 2.lost
11411211TOPO_DOMCytoplasmic (By similarity).lost
12121232TRANSMEMHelical; Name=16; (By similarity).might get lost (downstream of altered splice site)
12331234TOPO_DOMExtracellular (By similarity).might get lost (downstream of altered splice site)
12351255TRANSMEMHelical; Name=17; (By similarity).might get lost (downstream of altered splice site)
12541254MUTAGENW->F: Fails to transport methotrexate and leukotriene C4. Does not affect estradiol glucuronide transport.might get lost (downstream of altered splice site)
12541254MUTAGENW->A,C: Fails to transport methotrexate, leukotriene C4 and estradiol glucuronide.might get lost (downstream of altered splice site)
12541254MUTAGENW->Y: Fails to transport methotrexate; reduces leukotriene C4 transport. Does not affect estradiol glucuronide transport.might get lost (downstream of altered splice site)
12561545TOPO_DOMCytoplasmic (By similarity).might get lost (downstream of altered splice site)
13001534DOMAINABC transporter 2.might get lost (downstream of altered splice site)
13341341NP_BINDATP 2 (Potential).might get lost (downstream of altered splice site)
14301430CONFLICTV -> G (in Ref. 5; CAB45309).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4638 / 4638
position (AA) of stopcodon in wt / mu AA sequence 1546 / 1546
position of stopcodon in wt / mu cDNA 4751 / 4751
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 114 / 114
chromosome 10
strand 1
last intron/exon boundary 4622
theoretical NMD boundary in CDS 4458
length of CDS 4638
coding sequence (CDS) position 3517
cDNA position
(for ins/del: last normal base / first normal base)
3630
gDNA position
(for ins/del: last normal base / first normal base)
53462
chromosomal position
(for ins/del: last normal base / first normal base)
101595950
original gDNA sequence snippet CCGTATCAGGTTTGCCAGTTATCCGTGCCTTTGAGCACCAG
altered gDNA sequence snippet CCGTATCAGGTTTGCCAGTTTTCCGTGCCTTTGAGCACCAG
original cDNA sequence snippet CCGTATCAGGTTTGCCAGTTATCCGTGCCTTTGAGCACCAG
altered cDNA sequence snippet CCGTATCAGGTTTGCCAGTTTTCCGTGCCTTTGAGCACCAG
wildtype AA sequence MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGYL WLLAPWQLLH VYKSRTKRSS
TTKLYLAKQV FVGFLLILAA IELALVLTED SGQATVPAVR YTNPSLYLGT WLLVLLIQYS
RQWCVQKNSW FLSLFWILSI LCGTFQFQTL IRTLLQGDNS NLAYSCLFFI SYGFQILILI
FSAFSENNES SNNPSSIASF LSSITYSWYD SIILKGYKRP LTLEDVWEVD EEMKTKTLVS
KFETHMKREL QKARRALQRR QEKSSQQNSG ARLPGLNKNQ SQSQDALVLE DVEKKKKKSG
TKKDVPKSWL MKALFKTFYM VLLKSFLLKL VNDIFTFVSP QLLKLLISFA SDRDTYLWIG
YLCAILLFTA ALIQSFCLQC YFQLCFKLGV KVRTAIMASV YKKALTLSNL ARKEYTVGET
VNLMSVDAQK LMDVTNFMHM LWSSVLQIVL SIFFLWRELG PSVLAGVGVM VLVIPINAIL
STKSKTIQVK NMKNKDKRLK IMNEILSGIK ILKYFAWEPS FRDQVQNLRK KELKNLLAFS
QLQCVVIFVF QLTPVLVSVV TFSVYVLVDS NNILDAQKAF TSITLFNILR FPLSMLPMMI
SSMLQASVST ERLEKYLGGD DLDTSAIRHD CNFDKAMQFS EASFTWEHDS EATVRDVNLD
IMAGQLVAVI GPVGSGKSSL ISAMLGEMEN VHGHITIKGT TAYVPQQSWI QNGTIKDNIL
FGTEFNEKRY QQVLEACALL PDLEMLPGGD LAEIGEKGIN LSGGQKQRIS LARATYQNLD
IYLLDDPLSA VDAHVGKHIF NKVLGPNGLL KGKTRLLVTH SMHFLPQVDE IVVLGNGTIV
EKGSYSALLA KKGEFAKNLK TFLRHTGPEE EATVHDGSEE EDDDYGLISS VEEIPEDAAS
ITMRRENSFR RTLSRSSRSN GRHLKSLRNS LKTRNVNSLK EDEELVKGQK LIKKEFIETG
KVKFSIYLEY LQAIGLFSIF FIILAFVMNS VAFIGSNLWL SAWTSDSKIF NSTDYPASQR
DMRVGVYGAL GLAQGIFVFI AHFWSAFGFV HASNILHKQL LNNILRAPMR FFDTTPTGRI
VNRFAGDIST VDDTLPQSLR SWITCFLGII STLVMICMAT PVFTIIVIPL GIIYVSVQMF
YVSTSRQLRR LDSVTRSPIY SHFSETVSGL PVIRAFEHQQ RFLKHNEVRI DTNQKCVFSW
ITSNRWLAIR LELVGNLTVF FSALMMVIYR DTLSGDTVGF VLSNALNITQ TLNWLVRMTS
EIETNIVAVE RITEYTKVEN EAPWVTDKRP PPDWPSKGKI QFNNYQVRYR PELDLVLRGI
TCDIGSMEKI GVVGRTGAGK SSLTNCLFRI LEAAGGQIII DGVDIASIGL HDLREKLTII
PQDPILFSGS LRMNLDPFNN YSDEEIWKAL ELAHLKSFVA SLQLGLSHEV TEAGGNLSIG
QRQLLCLGRA LLRKSKILVL DEATAAVDLE TDNLIQTTIQ NEFAHCTVIT IAHRLHTIMD
SDKVMVLDNG KIIECGSPEE LLQIPGPFYF MAKEAGIENV NSTKF*
mutated AA sequence MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGYL WLLAPWQLLH VYKSRTKRSS
TTKLYLAKQV FVGFLLILAA IELALVLTED SGQATVPAVR YTNPSLYLGT WLLVLLIQYS
RQWCVQKNSW FLSLFWILSI LCGTFQFQTL IRTLLQGDNS NLAYSCLFFI SYGFQILILI
FSAFSENNES SNNPSSIASF LSSITYSWYD SIILKGYKRP LTLEDVWEVD EEMKTKTLVS
KFETHMKREL QKARRALQRR QEKSSQQNSG ARLPGLNKNQ SQSQDALVLE DVEKKKKKSG
TKKDVPKSWL MKALFKTFYM VLLKSFLLKL VNDIFTFVSP QLLKLLISFA SDRDTYLWIG
YLCAILLFTA ALIQSFCLQC YFQLCFKLGV KVRTAIMASV YKKALTLSNL ARKEYTVGET
VNLMSVDAQK LMDVTNFMHM LWSSVLQIVL SIFFLWRELG PSVLAGVGVM VLVIPINAIL
STKSKTIQVK NMKNKDKRLK IMNEILSGIK ILKYFAWEPS FRDQVQNLRK KELKNLLAFS
QLQCVVIFVF QLTPVLVSVV TFSVYVLVDS NNILDAQKAF TSITLFNILR FPLSMLPMMI
SSMLQASVST ERLEKYLGGD DLDTSAIRHD CNFDKAMQFS EASFTWEHDS EATVRDVNLD
IMAGQLVAVI GPVGSGKSSL ISAMLGEMEN VHGHITIKGT TAYVPQQSWI QNGTIKDNIL
FGTEFNEKRY QQVLEACALL PDLEMLPGGD LAEIGEKGIN LSGGQKQRIS LARATYQNLD
IYLLDDPLSA VDAHVGKHIF NKVLGPNGLL KGKTRLLVTH SMHFLPQVDE IVVLGNGTIV
EKGSYSALLA KKGEFAKNLK TFLRHTGPEE EATVHDGSEE EDDDYGLISS VEEIPEDAAS
ITMRRENSFR RTLSRSSRSN GRHLKSLRNS LKTRNVNSLK EDEELVKGQK LIKKEFIETG
KVKFSIYLEY LQAIGLFSIF FIILAFVMNS VAFIGSNLWL SAWTSDSKIF NSTDYPASQR
DMRVGVYGAL GLAQGIFVFI AHFWSAFGFV HASNILHKQL LNNILRAPMR FFDTTPTGRI
VNRFAGDIST VDDTLPQSLR SWITCFLGII STLVMICMAT PVFTIIVIPL GIIYVSVQMF
YVSTSRQLRR LDSVTRSPIY SHFSETVSGL PVFRAFEHQQ RFLKHNEVRI DTNQKCVFSW
ITSNRWLAIR LELVGNLTVF FSALMMVIYR DTLSGDTVGF VLSNALNITQ TLNWLVRMTS
EIETNIVAVE RITEYTKVEN EAPWVTDKRP PPDWPSKGKI QFNNYQVRYR PELDLVLRGI
TCDIGSMEKI GVVGRTGAGK SSLTNCLFRI LEAAGGQIII DGVDIASIGL HDLREKLTII
PQDPILFSGS LRMNLDPFNN YSDEEIWKAL ELAHLKSFVA SLQLGLSHEV TEAGGNLSIG
QRQLLCLGRA LLRKSKILVL DEATAAVDLE TDNLIQTTIQ NEFAHCTVIT IAHRLHTIMD
SDKVMVLDNG KIIECGSPEE LLQIPGPFYF MAKEAGIENV NSTKF*
speed 1.30 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
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Problems