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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: ENST00000264870
MT speed 0 s - this script 2.934619 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
F13A1disease_causing0.999999678055778simple_aaeaffectedR261Hsingle base exchangers121913071show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999678055778      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM043488)
  • known disease mutation at this position (HGMD CM990522)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:6248561C>TN/A show variant in all transcripts   IGV
HGNC symbol F13A1
Ensembl transcript ID ENST00000264870
Genbank transcript ID NM_000129
UniProt peptide P00488
alteration type single base exchange
alteration region CDS
DNA changes c.782G>A
cDNA.1048G>A
g.72686G>A
AA changes R261H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 261
frameshift no
known variant Reference ID: rs121913071
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation at this position, please check HGMD for details (HGMD ID CM990522)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990522)
known disease mutation at this position, please check HGMD for details (HGMD ID CM043488)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990522)
known disease mutation at this position, please check HGMD for details (HGMD ID CM043488)
known disease mutation at this position, please check HGMD for details (HGMD ID CM043488)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990522)
known disease mutation at this position, please check HGMD for details (HGMD ID CM043488)
known disease mutation at this position, please check HGMD for details (HGMD ID CM043488)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990522)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2850.641
3.1380.997
(flanking)2.6381
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 increased72682wt: 0.9650 / mu: 0.9965 (marginal change - not scored)wt: AAGTCAGCCGTGTGG
mu: AAGTCAGCCATGTGG		 GTCA|gccg
Donor marginally increased72678wt: 0.8461 / mu: 0.8481 (marginal change - not scored)wt: ATCAAAGTCAGCCGT
mu: ATCAAAGTCAGCCAT		 CAAA|gtca
Donor increased72687wt: 0.58 / mu: 0.84wt: AGCCGTGTGGGGTCT
mu: AGCCATGTGGGGTCT		 CCGT|gtgg
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      261LSGRGNPIKVSRVGSAMVNAKDDE
mutated  not conserved    261LSGRGNPIKVSHVGSAMVNAKDD
Ptroglodytes  all identical  ENSPTRG00000017694  261LSGRGNPIKVSRVGSAMVNAKDD
Mmulatta  all identical  ENSMMUG00000001248  261LSGRGNPIKVSRVGSAMVNAKDD
Fcatus  all identical  ENSFCAG00000015505  261GRGNPIKVSRVGSAMVNAKDD
Mmusculus  all identical  ENSMUSG00000039109  261LSGRGNPIKVSRVGSAMVNAKDD
Ggallus  all identical  ENSGALG00000012802  268LSGRGNPIKICRVASAMINSKDD
Trubripes  all identical  ENSTRUG00000018071  279ITNRGDPIKVTRKASAMLNSRDD
Drerio  all identical  ENSDARG00000036893  278LSNRGDVVKVTRVASAMLNSRDD
Dmelanogaster  all identical  FBgn0031975  275PAYRGDPVRVARALSALVNSVDD
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
256267HELIXlost
270272STRANDmight get lost (downstream of altered splice site)
274278STRANDmight get lost (downstream of altered splice site)
290292HELIXmight get lost (downstream of altered splice site)
297306HELIXmight get lost (downstream of altered splice site)
310313STRANDmight get lost (downstream of altered splice site)
315315ACT_SITEmight get lost (downstream of altered splice site)
315329HELIXmight get lost (downstream of altered splice site)
333341STRANDmight get lost (downstream of altered splice site)
350355STRANDmight get lost (downstream of altered splice site)
357359STRANDmight get lost (downstream of altered splice site)
363365TURNmight get lost (downstream of altered splice site)
371381STRANDmight get lost (downstream of altered splice site)
374374ACT_SITEmight get lost (downstream of altered splice site)
384386STRANDmight get lost (downstream of altered splice site)
392402STRANDmight get lost (downstream of altered splice site)
397397ACT_SITEmight get lost (downstream of altered splice site)
404414STRANDmight get lost (downstream of altered splice site)
415420HELIXmight get lost (downstream of altered splice site)
425428STRANDmight get lost (downstream of altered splice site)
429437HELIXmight get lost (downstream of altered splice site)
437437METALCalcium.might get lost (downstream of altered splice site)
439439METALCalcium.might get lost (downstream of altered splice site)
439445STRANDmight get lost (downstream of altered splice site)
447449TURNmight get lost (downstream of altered splice site)
451457STRANDmight get lost (downstream of altered splice site)
464468STRANDmight get lost (downstream of altered splice site)
470473STRANDmight get lost (downstream of altered splice site)
475477STRANDmight get lost (downstream of altered splice site)
479482HELIXmight get lost (downstream of altered splice site)
486486METALCalcium.might get lost (downstream of altered splice site)
489499HELIXmight get lost (downstream of altered splice site)
491491METALCalcium.might get lost (downstream of altered splice site)
500502TURNmight get lost (downstream of altered splice site)
519525STRANDmight get lost (downstream of altered splice site)
534542STRANDmight get lost (downstream of altered splice site)
544546STRANDmight get lost (downstream of altered splice site)
548559STRANDmight get lost (downstream of altered splice site)
565578STRANDmight get lost (downstream of altered splice site)
582590STRANDmight get lost (downstream of altered splice site)
592595HELIXmight get lost (downstream of altered splice site)
596598TURNmight get lost (downstream of altered splice site)
604613STRANDmight get lost (downstream of altered splice site)
614614CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
614616TURNmight get lost (downstream of altered splice site)
619627STRANDmight get lost (downstream of altered splice site)
634639STRANDmight get lost (downstream of altered splice site)
647654STRANDmight get lost (downstream of altered splice site)
657659STRANDmight get lost (downstream of altered splice site)
661670STRANDmight get lost (downstream of altered splice site)
671673TURNmight get lost (downstream of altered splice site)
674684STRANDmight get lost (downstream of altered splice site)
689696STRANDmight get lost (downstream of altered splice site)
702711STRANDmight get lost (downstream of altered splice site)
718727STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2199 / 2199
position (AA) of stopcodon in wt / mu AA sequence 733 / 733
position of stopcodon in wt / mu cDNA 2465 / 2465
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 267 / 267
chromosome 6
strand -1
last intron/exon boundary 2312
theoretical NMD boundary in CDS 1995
length of CDS 2199
coding sequence (CDS) position 782
cDNA position
(for ins/del: last normal base / first normal base)		 1048
gDNA position
(for ins/del: last normal base / first normal base)		 72686
chromosomal position
(for ins/del: last normal base / first normal base)		 6248561
original gDNA sequence snippet GAATCCCATCAAAGTCAGCCGTGTGGGGTCTGCAATGGTAA
altered gDNA sequence snippet GAATCCCATCAAAGTCAGCCATGTGGGGTCTGCAATGGTAA
original cDNA sequence snippet GAATCCCATCAAAGTCAGCCGTGTGGGGTCTGCAATGGTGA
altered cDNA sequence snippet GAATCCCATCAAAGTCAGCCATGTGGGGTCTGCAATGGTGA
wildtype AA sequence MSETSRTAFG GRRAVPPNNS NAAEDDLPTV ELQGVVPRGV NLQEFLNVTS VHLFKERWDT
NKVDHHTDKY ENNKLIVRRG QSFYVQIDFS RPYDPRRDLF RVEYVIGRYP QENKGTYIPV
PIVSELQSGK WGAKIVMRED RSVRLSIQSS PKCIVGKFRM YVAVWTPYGV LRTSRNPETD
TYILFNPWCE DDAVYLDNEK EREEYVLNDI GVIFYGEVND IKTRSWSYGQ FEDGILDTCL
YVMDRAQMDL SGRGNPIKVS RVGSAMVNAK DDEGVLVGSW DNIYAYGVPP SAWTGSVDIL
LEYRSSENPV RYGQCWVFAG VFNTFLRCLG IPARIVTNYF SAHDNDANLQ MDIFLEEDGN
VNSKLTKDSV WNYHCWNEAW MTRPDLPVGF GGWQAVDSTP QENSDGMYRC GPASVQAIKH
GHVCFQFDAP FVFAEVNSDL IYITAKKDGT HVVENVDATH IGKLIVTKQI GGDGMMDITD
TYKFQEGQEE ERLALETALM YGAKKPLNTE GVMKSRSNVD MDFEVENAVL GKDFKLSITF
RNNSHNRYTI TAYLSANITF YTGVPKAEFK KETFDVTLEP LSFKKEAVLI QAGEYMGQLL
EQASLHFFVT ARINETRDVL AKQKSTVLTI PEIIIKVRGT QVVGSDMTVT VEFTNPLKET
LRNVWVHLDG PGVTRPMKKM FREIRPNSTV QWEEVCRPWV SGHRKLIASM SSDSLRHVYG
ELDVQIQRRP SM*
mutated AA sequence MSETSRTAFG GRRAVPPNNS NAAEDDLPTV ELQGVVPRGV NLQEFLNVTS VHLFKERWDT
NKVDHHTDKY ENNKLIVRRG QSFYVQIDFS RPYDPRRDLF RVEYVIGRYP QENKGTYIPV
PIVSELQSGK WGAKIVMRED RSVRLSIQSS PKCIVGKFRM YVAVWTPYGV LRTSRNPETD
TYILFNPWCE DDAVYLDNEK EREEYVLNDI GVIFYGEVND IKTRSWSYGQ FEDGILDTCL
YVMDRAQMDL SGRGNPIKVS HVGSAMVNAK DDEGVLVGSW DNIYAYGVPP SAWTGSVDIL
LEYRSSENPV RYGQCWVFAG VFNTFLRCLG IPARIVTNYF SAHDNDANLQ MDIFLEEDGN
VNSKLTKDSV WNYHCWNEAW MTRPDLPVGF GGWQAVDSTP QENSDGMYRC GPASVQAIKH
GHVCFQFDAP FVFAEVNSDL IYITAKKDGT HVVENVDATH IGKLIVTKQI GGDGMMDITD
TYKFQEGQEE ERLALETALM YGAKKPLNTE GVMKSRSNVD MDFEVENAVL GKDFKLSITF
RNNSHNRYTI TAYLSANITF YTGVPKAEFK KETFDVTLEP LSFKKEAVLI QAGEYMGQLL
EQASLHFFVT ARINETRDVL AKQKSTVLTI PEIIIKVRGT QVVGSDMTVT VEFTNPLKET
LRNVWVHLDG PGVTRPMKKM FREIRPNSTV QWEEVCRPWV SGHRKLIASM SSDSLRHVYG
ELDVQIQRRP SM*
speed 0.87 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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