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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: ENST00000367412
MT speed 0 s - this script 3.185983 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
F13Bdisease_causing_automatic0.999997193527731simple_aaeaffected0C450Fsingle base exchangers121913075show file

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997193527731 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM930203)
  • known disease mutation: rs16519 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:197024850C>AN/A show variant in all transcripts   IGV
HGNC symbol F13B
Ensembl transcript ID ENST00000367412
Genbank transcript ID NM_001994
UniProt peptide P05160
alteration type single base exchange
alteration region CDS
DNA changes c.1349G>T
cDNA.1393G>T
g.11548G>T
AA changes C450F Score: 205 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 450
frameshift no
known variant Reference ID: rs121913075
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16519 (pathogenic for Factor XIII, b subunit, deficiency of) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM930203)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930203)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930203)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4441
3.7121
(flanking)3.1091
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 increased11548wt: 0.2371 / mu: 0.2578 (marginal change - not scored)wt: ATGGTCATCCCCACCTGTTTGCTTGGGTAAGAAAGAGAACA
mu: ATGGTCATCCCCACCTGTTTTCTTGGGTAAGAAAGAGAACA		 tttg|CTTG
Acc increased11552wt: 0.39 / mu: 0.92wt: TCATCCCCACCTGTTTGCTTGGGTAAGAAAGAGAACACATG
mu: TCATCCCCACCTGTTTTCTTGGGTAAGAAAGAGAACACATG		 cttg|GGTA
Acc increased11557wt: 0.43 / mu: 0.80wt: CCCACCTGTTTGCTTGGGTAAGAAAGAGAACACATGGAATG
mu: CCCACCTGTTTTCTTGGGTAAGAAAGAGAACACATGGAATG		 gtaa|GAAA
Acc marginally increased11551wt: 0.9390 / mu: 0.9548 (marginal change - not scored)wt: GTCATCCCCACCTGTTTGCTTGGGTAAGAAAGAGAACACAT
mu: GTCATCCCCACCTGTTTTCTTGGGTAAGAAAGAGAACACAT		 gctt|GGGT
Donor marginally increased11552wt: 0.9730 / mu: 0.9909 (marginal change - not scored)wt: TGCTTGGGTAAGAAA
mu: TTCTTGGGTAAGAAA		 CTTG|ggta
Acc gained115500.69mu: GGTCATCCCCACCTGTTTTCTTGGGTAAGAAAGAGAACACA ttct|TGGG
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      450CEQGKWSSPPVCLEPCTVNVDYMN
mutated  not conserved    450CEQGKWSSPPVFLEPCTVNVDYM
Ptroglodytes  all identical  ENSPTRG00000001806  450CEQGKWSSPPVCLEPCTVNVDYM
Mmulatta  all identical  ENSMMUG00000000244  450CEQGKWSSPPVCLEPCTVNVDYM
Fcatus  not conserved  ENSFCAG00000005019  428XXXXXXXXXXPCTINVDYM
Mmusculus  all identical  ENSMUSG00000026368  451CEQGAWSSPPVCLEPCTIDVDHM
Ggallus  all identical  ENSGALG00000002369  450CKRGNWTERPTCLDPCILNVTEM
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000092786  299CQDAEWTGKIYCLKPCSVTLDTM
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000031728  454CLTDGWSSQPECHQISEPCTVSVDQM
protein features
start (aa)end (aa)featuredetails 
394452DOMAINSushi 7.lost
450450DISULFIDBy similarity.lost
453516DOMAINSushi 8.might get lost (downstream of altered splice site)
454454DISULFIDBy similarity.might get lost (downstream of altered splice site)
486486DISULFIDBy similarity.might get lost (downstream of altered splice site)
505505DISULFIDBy similarity.might get lost (downstream of altered splice site)
515515DISULFIDBy similarity.might get lost (downstream of altered splice site)
522580DOMAINSushi 9.might get lost (downstream of altered splice site)
524524DISULFIDBy similarity.might get lost (downstream of altered splice site)
545545CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
553553DISULFIDBy similarity.might get lost (downstream of altered splice site)
567567DISULFIDBy similarity.might get lost (downstream of altered splice site)
578578DISULFIDBy similarity.might get lost (downstream of altered splice site)
581647DOMAINSushi 10.might get lost (downstream of altered splice site)
582582DISULFIDBy similarity.might get lost (downstream of altered splice site)
616616DISULFIDBy similarity.might get lost (downstream of altered splice site)
617619MOTIFCell attachment site.might get lost (downstream of altered splice site)
636636DISULFIDBy similarity.might get lost (downstream of altered splice site)
646646DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1986 / 1986
position (AA) of stopcodon in wt / mu AA sequence 662 / 662
position of stopcodon in wt / mu cDNA 2030 / 2030
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 45 / 45
chromosome 1
strand -1
last intron/exon boundary 1997
theoretical NMD boundary in CDS 1902
length of CDS 1986
coding sequence (CDS) position 1349
cDNA position
(for ins/del: last normal base / first normal base)		 1393
gDNA position
(for ins/del: last normal base / first normal base)		 11548
chromosomal position
(for ins/del: last normal base / first normal base)		 197024850
original gDNA sequence snippet ATGGTCATCCCCACCTGTTTGCTTGGGTAAGAAAGAGAACA
altered gDNA sequence snippet ATGGTCATCCCCACCTGTTTTCTTGGGTAAGAAAGAGAACA
original cDNA sequence snippet ATGGTCATCCCCACCTGTTTGCTTGGAACCATGTACTGTTA
altered cDNA sequence snippet ATGGTCATCCCCACCTGTTTTCTTGGAACCATGTACTGTTA
wildtype AA sequence MRLKNLTFII ILIISGELYA EEKPCGFPHV ENGRIAQYYY TFKSFYFPMS IDKKLSFFCL
AGYTTESGRQ EEQTTCTTEG WSPEPRCFKK CTKPDLSNGY ISDVKLLYKI QENMRYGCAS
GYKTTGGKDE EVVQCLSDGW SSQPTCRKEH ETCLAPELYN GNYSTTQKTF KVKDKVQYEC
ATGYYTAGGK KTEEVECLTY GWSLTPKCTK LKCSSLRLIE NGYFHPVKQT YEEGDVVQFF
CHENYYLSGS DLIQCYNFGW YPESPVCEGR RNRCPPPPLP INSKIQTHST TYRHGEIVHI
ECELNFEIHG SAEIRCEDGK WTEPPKCIEG QEKVACEEPP FIENGAANLH SKIYYNGDKV
TYACKSGYLL HGSNEITCNR GKWTLPPECV ENNENCKHPP VVMNGAVADG ILASYATGSS
VEYRCNEYYL LRGSKISRCE QGKWSSPPVC LEPCTVNVDY MNRNNIEMKW KYEGKVLHGD
LIDFVCKQGY DLSPLTPLSE LSVQCNRGEV KYPLCTRKES KGMCTSPPLI KHGVIISSTV
DTYENGSSVE YRCFDHHFLE GSREAYCLDG MWTTPPLCLE PCTLSFTEME KNNLLLKWDF
DNRPHILHGE YIEFICRGDT YPAELYITGS ILRMQCDRGQ LKYPRCIPRQ STLSYQEPLR
T*
mutated AA sequence MRLKNLTFII ILIISGELYA EEKPCGFPHV ENGRIAQYYY TFKSFYFPMS IDKKLSFFCL
AGYTTESGRQ EEQTTCTTEG WSPEPRCFKK CTKPDLSNGY ISDVKLLYKI QENMRYGCAS
GYKTTGGKDE EVVQCLSDGW SSQPTCRKEH ETCLAPELYN GNYSTTQKTF KVKDKVQYEC
ATGYYTAGGK KTEEVECLTY GWSLTPKCTK LKCSSLRLIE NGYFHPVKQT YEEGDVVQFF
CHENYYLSGS DLIQCYNFGW YPESPVCEGR RNRCPPPPLP INSKIQTHST TYRHGEIVHI
ECELNFEIHG SAEIRCEDGK WTEPPKCIEG QEKVACEEPP FIENGAANLH SKIYYNGDKV
TYACKSGYLL HGSNEITCNR GKWTLPPECV ENNENCKHPP VVMNGAVADG ILASYATGSS
VEYRCNEYYL LRGSKISRCE QGKWSSPPVF LEPCTVNVDY MNRNNIEMKW KYEGKVLHGD
LIDFVCKQGY DLSPLTPLSE LSVQCNRGEV KYPLCTRKES KGMCTSPPLI KHGVIISSTV
DTYENGSSVE YRCFDHHFLE GSREAYCLDG MWTTPPLCLE PCTLSFTEME KNNLLLKWDF
DNRPHILHGE YIEFICRGDT YPAELYITGS ILRMQCDRGQ LKYPRCIPRQ STLSYQEPLR
T*
speed 1.07 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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