Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999649695 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990377)
  • known disease mutation: rs8416 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:101605538A>GN/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.4145A>G
cDNA.4258A>G
g.63050A>G
AA changes Q1382R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1382
frameshift no
known variant Reference ID: rs72558202
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8416 (pathogenic for Dubin-Johnson syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990377)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990377)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990377)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)6.0951
5.1021
(flanking)4.5121
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost63050sequence motif lost- wt: CCAG|gtga
 mu: CCGG.gtga
Donor marginally decreased63050wt: 0.9934 / mu: 0.9686 (marginal change - not scored)wt: CCCCCAGGTGAGCTC
mu: CCCCCGGGTGAGCTC		 CCCA|ggtg
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1382HDLREKLTIIPQDPILFSGSLRMN
mutated  all conserved    1382PRDPILFSGSLRM
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000023764  1381PQDPILFSGSLRM
Fcatus  all identical  ENSFCAG00000014380  1382QDPILFSGSLRM
Mmusculus  all identical  ENSMUSG00000025194  1380QDPILFSGNLRM
Ggallus  all identical  ENSGALG00000007395  1389HDLRQNLTIIPQDPVLFTGTLRM
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000014031  1396HDLRSRLTIIPQDPVLFSGTLRM
Dmelanogaster  all identical  FBgn0032456  1392HMLRSRLTIIPQDPVLFSGSLRI
Celegans  all identical  F57C12.5  1377EQLRSRLTIVPQDPVLFSGTMRM
Xtropicalis  all identical  ENSXETG00000003740  1383LTIIPQDPVLFSGNLRM
protein features
start (aa)end (aa)featuredetails 
12561545TOPO_DOMCytoplasmic (By similarity).lost
13001534DOMAINABC transporter 2.lost
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 4145
cDNA position
(for ins/del: last normal base / first normal base)		 4258
gDNA position
(for ins/del: last normal base / first normal base)		 63050
chromosomal position
(for ins/del: last normal base / first normal base)		 101605538
original gDNA sequence snippet GAAGCTGACCATCATCCCCCAGGTGAGCTCTAGAACTTACT
altered gDNA sequence snippet GAAGCTGACCATCATCCCCCGGGTGAGCTCTAGAACTTACT
original cDNA sequence snippet GAAGCTGACCATCATCCCCCAGGACCCCATCCTGTTCTCTG
altered cDNA sequence snippet GAAGCTGACCATCATCCCCCGGGACCCCATCCTGTTCTCTG
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 PVIRAFEHQQ RFLKHNEVRI DTNQKCVFSW
ITSNRWLAIR LELVGNLTVF FSALMMVIYR DTLSGDTVGF VLSNALNITQ TLNWLVRMTS
EIETNIVAVE RITEYTKVEN EAPWVTDKRP PPDWPSKGKI QFNNYQVRYR PELDLVLRGI
TCDIGSMEKI GVVGRTGAGK SSLTNCLFRI LEAAGGQIII DGVDIASIGL HDLREKLTII
PRDPILFSGS LRMNLDPFNN YSDEEIWKAL ELAHLKSFVA SLQLGLSHEV TEAGGNLSIG
QRQLLCLGRA LLRKSKILVL DEATAAVDLE TDNLIQTTIQ NEFAHCTVIT IAHRLHTIMD
SDKVMVLDNG KIIECGSPEE LLQIPGPFYF MAKEAGIENV NSTKF*
speed 1.06 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