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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: ENST00000332857
MT speed 1.28 s - this script 6.644332 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SPATA31A6polymorphism_automatic2.09832151654155e-14simple_aaeaffectedT643Msingle base exchangers574727392show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999979 (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) chr9:43626759G>AN/A show variant in all transcripts   IGV
HGNC symbol SPATA31A6
Ensembl transcript ID ENST00000332857
Genbank transcript ID NM_001145196
UniProt peptide Q5VVP1
alteration type single base exchange
alteration region CDS
DNA changes c.1928C>T
cDNA.1957C>T
g.3972C>T
AA changes T643M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS
643
frameshift no
known variant Reference ID: rs574727392
databasehomozygous (A/A)heterozygousallele carriers
1000G624319943
ExAC211132
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9790
-1.1120
(flanking)-1.8170
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 increased3979wt: 0.2342 / mu: 0.2374 (marginal change - not scored)wt: TGGCAGTCCTCCACGTCCACAGGTGAAAGCAGCAAGGAGGC
mu: TGGCAGTCCTCCATGTCCACAGGTGAAAGCAGCAAGGAGGC
 caca|GGTG
Acc increased3970wt: 0.32 / mu: 0.59wt: CCCAGTCCCTGGCAGTCCTCCACGTCCACAGGTGAAAGCAG
mu: CCCAGTCCCTGGCAGTCCTCCATGTCCACAGGTGAAAGCAG
 ctcc|ACGT
Acc increased3976wt: 0.43 / mu: 0.56wt: CCCTGGCAGTCCTCCACGTCCACAGGTGAAAGCAGCAAGGA
mu: CCCTGGCAGTCCTCCATGTCCACAGGTGAAAGCAGCAAGGA
 gtcc|ACAG
Acc marginally increased3980wt: 0.8981 / mu: 0.9526 (marginal change - not scored)wt: GGCAGTCCTCCACGTCCACAGGTGAAAGCAGCAAGGAGGCA
mu: GGCAGTCCTCCATGTCCACAGGTGAAAGCAGCAAGGAGGCA
 acag|GTGA
Donor marginally increased3977wt: 0.3113 / mu: 0.3196 (marginal change - not scored)wt: CGTCCACAGGTGAAA
mu: TGTCCACAGGTGAAA
 TCCA|cagg
Donor increased3975wt: 0.40 / mu: 0.52wt: CACGTCCACAGGTGA
mu: CATGTCCACAGGTGA
 CGTC|caca
distance from splice site 1620
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      643AKGKPSPWQSSTSTGESSKEAQKV
mutated  not conserved    643AKGKPSPWQSSMSTGESSKEAQK
Ptroglodytes  not conserved  ENSPTRG00000039979  647AKGKPSPWQSSMSTGESSKEAQK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000056223  389TLQ---ALGEHSNEGQK
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
13291336COMPBIASHis-rich.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4032 / 4032
position (AA) of stopcodon in wt / mu AA sequence 1344 / 1344
position of stopcodon in wt / mu cDNA 4061 / 4061
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 30 / 30
chromosome 9
strand -1
last intron/exon boundary 338
theoretical NMD boundary in CDS 258
length of CDS 4032
coding sequence (CDS) position 1928
cDNA position
(for ins/del: last normal base / first normal base)
1957
gDNA position
(for ins/del: last normal base / first normal base)
3972
chromosomal position
(for ins/del: last normal base / first normal base)
43626759
original gDNA sequence snippet CAGTCCCTGGCAGTCCTCCACGTCCACAGGTGAAAGCAGCA
altered gDNA sequence snippet CAGTCCCTGGCAGTCCTCCATGTCCACAGGTGAAAGCAGCA
original cDNA sequence snippet CAGTCCCTGGCAGTCCTCCACGTCCACAGGTGAAAGCAGCA
altered cDNA sequence snippet CAGTCCCTGGCAGTCCTCCATGTCCACAGGTGAAAGCAGCA
wildtype AA sequence MENLPFPLKL LSASSLNAPS STPWVLDIFL TLVFALGFFF LLLPYLSYFH CDDPPSPSPG
KRKCPVGRRR RPRGRMKNHS LRAGRECPRG LEETSDLLSQ LQSLLGPHLD KGDFGQLSGP
DPPGEVGERA PDGASQSSHE PMEDAAPILS PLASPDPQAK HPQDLASTPS PGPMTTSVSS
LSASQPPEPS LPLEHPSPEP PALFPHPPHT PDPLACSPPP PKGFTAPPLR DSTLITPSHC
DSVALPLGTV PQSLSPHEDL VASVPAISGL GGSNSHVSAS SRWQETARTS CAFNSSVQQD
PLSRHPPETC QMEAGSLFLL SSDGQNVVGI QVTETAKVNI WEEKENVGSF TNQMTPEKHL
NSLGNLAKSL DAEQDTTNPK PFWNMGENSK QLPGPQKCSD PRLLQESFWK NYSQLFWGLP
SLHSESLVAN AWVTDRSYTL QSPPFLFNEM SNVCPIQRET TMSPLLFQAQ PLSHRQPFIS
STPQFLPTPM AQAEAQAHLQ SSFPVLSPAF PSLIKNTGVA CPASQNKVQA LSLPETQHPE
WPLLRKQLEG RLALPSRVQK SQDVFSVSTP NLPQESLTSI LPENFPVSPE LRRQLEQHIK
KWIIQHWGNL GRIQESLDLM QLRDESPGTS QAKGKPSPWQ SSTSTGESSK EAQKVKFQLE
RDLCPHLGQI LGETPQNLSR DMKSFPRKVL GVTSEESERN LRKPLRSDSG SDLLRCTERT
HIENILKAHM GRNLGQTNEG LIPVRVRRSW LAVNQALPVS NTHVKTSNLA APKSGKACVN
TAQVLSFLEP CTQQGLGAHI VRFWAKHRWG LPLRVLKPIQ CFKLEKVSSL SLTQLAGPSS
ATCESGAGSE VEVDMFLRKP PMASLRKQVL TKASDHMPES LLASSPAWKQ FQRAPRGIPS
WNDHGPLKPP PAGQEGRWPS KPLTYSLTGS TQQSRSLGAQ SSKAGETREA VPQCRVPLET
CMLANLQATS EDVHGFEAPG TSKSSLHPRV SVSQDPRKLC LMEEVVSEFE PGMATKSETQ
PQVCAAVVLL PDGQASVVPH ASENLVSQVP QGHLQSMPTG NMRASQELHD LMAARRSKLV
QEEPRNPNCQ GSCKSQRPMF PPIHKSEKSR KPNLEKHEER LEGLRTPQLT PVRKTEDTHQ
DEGVQLLPSK KQPPSVSHFG ENIKQFFQWI FSKKKSKPAP VTAESQKTVK NRSCVYSSSA
EAQGLMTAVG QMLDKKMSLC HAHHASKVNQ HKQKFQAPVC GFPCNHRHLF YSEHGRILSY
AASSQQATLK SQGCPNRDRQ IRNQQPLKSV RCNNEQWGLR HPQILHPKKA VSPVSPPQHW
PKTSGASSHH HHCPRHCLLW EGI*
mutated AA sequence MENLPFPLKL LSASSLNAPS STPWVLDIFL TLVFALGFFF LLLPYLSYFH CDDPPSPSPG
KRKCPVGRRR RPRGRMKNHS LRAGRECPRG LEETSDLLSQ LQSLLGPHLD KGDFGQLSGP
DPPGEVGERA PDGASQSSHE PMEDAAPILS PLASPDPQAK HPQDLASTPS PGPMTTSVSS
LSASQPPEPS LPLEHPSPEP PALFPHPPHT PDPLACSPPP PKGFTAPPLR DSTLITPSHC
DSVALPLGTV PQSLSPHEDL VASVPAISGL GGSNSHVSAS SRWQETARTS CAFNSSVQQD
PLSRHPPETC QMEAGSLFLL SSDGQNVVGI QVTETAKVNI WEEKENVGSF TNQMTPEKHL
NSLGNLAKSL DAEQDTTNPK PFWNMGENSK QLPGPQKCSD PRLLQESFWK NYSQLFWGLP
SLHSESLVAN AWVTDRSYTL QSPPFLFNEM SNVCPIQRET TMSPLLFQAQ PLSHRQPFIS
STPQFLPTPM AQAEAQAHLQ SSFPVLSPAF PSLIKNTGVA CPASQNKVQA LSLPETQHPE
WPLLRKQLEG RLALPSRVQK SQDVFSVSTP NLPQESLTSI LPENFPVSPE LRRQLEQHIK
KWIIQHWGNL GRIQESLDLM QLRDESPGTS QAKGKPSPWQ SSMSTGESSK EAQKVKFQLE
RDLCPHLGQI LGETPQNLSR DMKSFPRKVL GVTSEESERN LRKPLRSDSG SDLLRCTERT
HIENILKAHM GRNLGQTNEG LIPVRVRRSW LAVNQALPVS NTHVKTSNLA APKSGKACVN
TAQVLSFLEP CTQQGLGAHI VRFWAKHRWG LPLRVLKPIQ CFKLEKVSSL SLTQLAGPSS
ATCESGAGSE VEVDMFLRKP PMASLRKQVL TKASDHMPES LLASSPAWKQ FQRAPRGIPS
WNDHGPLKPP PAGQEGRWPS KPLTYSLTGS TQQSRSLGAQ SSKAGETREA VPQCRVPLET
CMLANLQATS EDVHGFEAPG TSKSSLHPRV SVSQDPRKLC LMEEVVSEFE PGMATKSETQ
PQVCAAVVLL PDGQASVVPH ASENLVSQVP QGHLQSMPTG NMRASQELHD LMAARRSKLV
QEEPRNPNCQ GSCKSQRPMF PPIHKSEKSR KPNLEKHEER LEGLRTPQLT PVRKTEDTHQ
DEGVQLLPSK KQPPSVSHFG ENIKQFFQWI FSKKKSKPAP VTAESQKTVK NRSCVYSSSA
EAQGLMTAVG QMLDKKMSLC HAHHASKVNQ HKQKFQAPVC GFPCNHRHLF YSEHGRILSY
AASSQQATLK SQGCPNRDRQ IRNQQPLKSV RCNNEQWGLR HPQILHPKKA VSPVSPPQHW
PKTSGASSHH HHCPRHCLLW EGI*
speed 1.28 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