Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000381801
Querying Taster for transcript #2: ENST00000540661
MT speed 0 s - this script 3.285784 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MTMR6polymorphism_automatic0.926773761419505simple_aaeaffectedI319Vsingle base exchangers7995033show file
MTMR6polymorphism_automatic0.975324148570712simple_aaeaffectedI319Vsingle base exchangers7995033show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0732262385804955 (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) chr13:25831888T>CN/A show variant in all transcripts   IGV
HGNC symbol MTMR6
Ensembl transcript ID ENST00000381801
Genbank transcript ID NM_004685
UniProt peptide Q9Y217
alteration type single base exchange
alteration region CDS
DNA changes c.955A>G
cDNA.1717A>G
g.30260A>G
AA changes I319V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 319
frameshift no
known variant Reference ID: rs7995033
databasehomozygous (C/C)heterozygousallele carriers
1000G7669331699
ExAC32111-31455656
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.9511
0.5150.999
(flanking)0.3470.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased30268wt: 0.30 / mu: 0.41wt: ATGGATGCTGCAATCTTCTTGGCCAAAGTAATACTTTATCT
mu: ATGGATGCTGCAGTCTTCTTGGCCAAAGTAATACTTTATCT		 cttg|GCCA
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      319LRHIKAVMDAAIFLAKAITVENAS
mutated  all conserved    319LRHIKAVMDAAVFLAKAITVENA
Ptroglodytes  all identical  ENSPTRG00000005718  319LRHIKAVMDAAIFLAKAITVENA
Mmulatta  all identical  ENSMMUG00000018419  319LRHIKAVMDAAIFLAKAITVENA
Fcatus  no alignment  ENSFCAG00000010195  n/a
Mmusculus  all identical  ENSMUSG00000021987  319LRHIKAVLDAAIFLAKAIVVENA
Ggallus  all conserved  ENSGALG00000017112  319LRHIKAVLDAAVFLVKAIAVESA
Trubripes  all conserved  ENSTRUG00000001228  324LRHIKAVVDNLDLVFCSKAVTGEGA
Drerio  all identical  ENSDARG00000016794  320LRHIKAIMDAAIFLAKAVSVEGA
Dmelanogaster  not conserved  FBgn0028497  390LKHIRSILDTSSFIANAVD-KGV
Celegans  all conserved  F53A2.8  425LKHVRSVVECSLFLAESIS-RGT
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
124499DOMAINMyotubularin phosphatase.lost
307326HELIXlost
332334STRANDmight get lost (downstream of altered splice site)
333333CONFLICTL -> S (in Ref. 2; AAL01037 and 7; AAC78841).might get lost (downstream of altered splice site)
336336ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
336338TURNmight get lost (downstream of altered splice site)
336342REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
339341STRANDmight get lost (downstream of altered splice site)
342354HELIXmight get lost (downstream of altered splice site)
357359HELIXmight get lost (downstream of altered splice site)
361371HELIXmight get lost (downstream of altered splice site)
368368CONFLICTI -> T (in Ref. 3; BAG37162).might get lost (downstream of altered splice site)
372376TURNmight get lost (downstream of altered splice site)
379383HELIXmight get lost (downstream of altered splice site)
382382BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
385387STRANDmight get lost (downstream of altered splice site)
390392HELIXmight get lost (downstream of altered splice site)
396410HELIXmight get lost (downstream of altered splice site)
412414TURNmight get lost (downstream of altered splice site)
419429HELIXmight get lost (downstream of altered splice site)
430430CONFLICTH -> D (in Ref. 3; BAG52676).might get lost (downstream of altered splice site)
430432TURNmight get lost (downstream of altered splice site)
439441STRANDmight get lost (downstream of altered splice site)
442442CONFLICTQ -> P (in Ref. 2; AAL01037 and 7; AAC78841).might get lost (downstream of altered splice site)
442447HELIXmight get lost (downstream of altered splice site)
450453HELIXmight get lost (downstream of altered splice site)
458461HELIXmight get lost (downstream of altered splice site)
465468HELIXmight get lost (downstream of altered splice site)
488491STRANDmight get lost (downstream of altered splice site)
496502HELIXmight get lost (downstream of altered splice site)
561561MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
589589MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1866 / 1866
position (AA) of stopcodon in wt / mu AA sequence 622 / 622
position of stopcodon in wt / mu cDNA 2628 / 2628
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 763 / 763
chromosome 13
strand -1
last intron/exon boundary 2368
theoretical NMD boundary in CDS 1555
length of CDS 1866
coding sequence (CDS) position 955
cDNA position
(for ins/del: last normal base / first normal base)		 1717
gDNA position
(for ins/del: last normal base / first normal base)		 30260
chromosomal position
(for ins/del: last normal base / first normal base)		 25831888
original gDNA sequence snippet AAGCTGTTATGGATGCTGCAATCTTCTTGGCCAAAGTAATA
altered gDNA sequence snippet AAGCTGTTATGGATGCTGCAGTCTTCTTGGCCAAAGTAATA
original cDNA sequence snippet AAGCTGTTATGGATGCTGCAATCTTCTTGGCCAAAGCAATA
altered cDNA sequence snippet AAGCTGTTATGGATGCTGCAGTCTTCTTGGCCAAAGCAATA
wildtype AA sequence MEHIRTTKVE QVKLLDRFST SNKSLTGTLY LTATHLLFID SHQKETWILH HHIASVEKLA
LTTSGCPLVI QCKNFRTVHF IVPRERDCHD IYNSLLQLSK QAKYEDLYAF SYNPKQNDSE
RLQGWQLIDL AEEYKRMGVP NSHWQLSDAN RDYKICETYP RELYVPRIAS KPIIVGSSKF
RSKGRFPVLS YYHQDKEAAI CRCSQPLSGF SARCLEDEHL LQAISKANPV NRYMYVMDTR
PKLNAMANRA AGKGYENEDN YSNIRFQFVG IENIHVMRSS LQKLLEVNGT KGLSVNDFYS
GLESSGWLRH IKAVMDAAIF LAKAITVENA SVLVHCSDGW DRTSQVCSLG SLLLDSYYRT
IKGFMVLIEK DWISFGHKFS ERCGQLDGDP KEVSPVFTQF LECVWHLTEQ FPQAFEFSEA
FLLQIHEHIH SCQFGNFLGN CQKEREELKL KEKTYSLWPF LLEDQKKYLN PLYSSESHRF
TVLEPNTVSF NFKFWRNMYH QFDRTLHPRQ SVFNIIMNMN EQNKQLEKDI KDLESKIKQR
KNKQTDGILT KELLHSVHPE SPNLKTSLCF KEQTLLPVND ALRTIEGSSP ADNRYSEYAE
EFSKSEPAVV SLEYGVARMT C*
mutated AA sequence MEHIRTTKVE QVKLLDRFST SNKSLTGTLY LTATHLLFID SHQKETWILH HHIASVEKLA
LTTSGCPLVI QCKNFRTVHF IVPRERDCHD IYNSLLQLSK QAKYEDLYAF SYNPKQNDSE
RLQGWQLIDL AEEYKRMGVP NSHWQLSDAN RDYKICETYP RELYVPRIAS KPIIVGSSKF
RSKGRFPVLS YYHQDKEAAI CRCSQPLSGF SARCLEDEHL LQAISKANPV NRYMYVMDTR
PKLNAMANRA AGKGYENEDN YSNIRFQFVG IENIHVMRSS LQKLLEVNGT KGLSVNDFYS
GLESSGWLRH IKAVMDAAVF LAKAITVENA SVLVHCSDGW DRTSQVCSLG SLLLDSYYRT
IKGFMVLIEK DWISFGHKFS ERCGQLDGDP KEVSPVFTQF LECVWHLTEQ FPQAFEFSEA
FLLQIHEHIH SCQFGNFLGN CQKEREELKL KEKTYSLWPF LLEDQKKYLN PLYSSESHRF
TVLEPNTVSF NFKFWRNMYH QFDRTLHPRQ SVFNIIMNMN EQNKQLEKDI KDLESKIKQR
KNKQTDGILT KELLHSVHPE SPNLKTSLCF KEQTLLPVND ALRTIEGSSP ADNRYSEYAE
EFSKSEPAVV SLEYGVARMT C*
speed 1.16 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0246758514292884 (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) chr13:25831888T>CN/A show variant in all transcripts   IGV
HGNC symbol MTMR6
Ensembl transcript ID ENST00000540661
Genbank transcript ID N/A
UniProt peptide Q9Y217
alteration type single base exchange
alteration region CDS
DNA changes c.955A>G
cDNA.1274A>G
g.30260A>G
AA changes I319V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 319
frameshift no
known variant Reference ID: rs7995033
databasehomozygous (C/C)heterozygousallele carriers
1000G7669331699
ExAC32111-31455656
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.9511
0.5150.999
(flanking)0.3470.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased30268wt: 0.30 / mu: 0.41wt: ATGGATGCTGCAATCTTCTTGGCCAAAGTAATACTTTATCT
mu: ATGGATGCTGCAGTCTTCTTGGCCAAAGTAATACTTTATCT		 cttg|GCCA
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      319LRHIKAVMDAAIFLAKAITVENAS
mutated  all conserved    319LRHIKAVMDAAVFLAKAITVENA
Ptroglodytes  all identical  ENSPTRG00000005718  319LRHIKAVMDAAIFLAKAITVENA
Mmulatta  all identical  ENSMMUG00000018419  319LRHIKAVMDAAIFLAKAITVENA
Fcatus  all identical  ENSFCAG00000010195  319LRHIKAVMDAAIFLAKAITVESA
Mmusculus  all identical  ENSMUSG00000021987  319LRHIKAVLDAAIFLAKAIVVENA
Ggallus  all conserved  ENSGALG00000017112  319LRHIKAVLDAAVFLVKAIAVESA
Trubripes  all conserved  ENSTRUG00000001228  324LRHIKAVVDNLDLVFCSKAVTGEGA
Drerio  all identical  ENSDARG00000016794  320LRHIKAIMDAAIFLAKAVSVEGA
Dmelanogaster  not conserved  FBgn0028497  390LKHIRSILDTSSFIANAVD-KGV
Celegans  all conserved  F53A2.8  425LKHVRSVVECSLFLAESIS-RGT
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
124499DOMAINMyotubularin phosphatase.lost
307326HELIXlost
332334STRANDmight get lost (downstream of altered splice site)
333333CONFLICTL -> S (in Ref. 2; AAL01037 and 7; AAC78841).might get lost (downstream of altered splice site)
336336ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
336338TURNmight get lost (downstream of altered splice site)
336342REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
339341STRANDmight get lost (downstream of altered splice site)
342354HELIXmight get lost (downstream of altered splice site)
357359HELIXmight get lost (downstream of altered splice site)
361371HELIXmight get lost (downstream of altered splice site)
368368CONFLICTI -> T (in Ref. 3; BAG37162).might get lost (downstream of altered splice site)
372376TURNmight get lost (downstream of altered splice site)
379383HELIXmight get lost (downstream of altered splice site)
382382BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
385387STRANDmight get lost (downstream of altered splice site)
390392HELIXmight get lost (downstream of altered splice site)
396410HELIXmight get lost (downstream of altered splice site)
412414TURNmight get lost (downstream of altered splice site)
419429HELIXmight get lost (downstream of altered splice site)
430430CONFLICTH -> D (in Ref. 3; BAG52676).might get lost (downstream of altered splice site)
430432TURNmight get lost (downstream of altered splice site)
439441STRANDmight get lost (downstream of altered splice site)
442442CONFLICTQ -> P (in Ref. 2; AAL01037 and 7; AAC78841).might get lost (downstream of altered splice site)
442447HELIXmight get lost (downstream of altered splice site)
450453HELIXmight get lost (downstream of altered splice site)
458461HELIXmight get lost (downstream of altered splice site)
465468HELIXmight get lost (downstream of altered splice site)
488491STRANDmight get lost (downstream of altered splice site)
496502HELIXmight get lost (downstream of altered splice site)
561561MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
589589MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1647 / 1647
position (AA) of stopcodon in wt / mu AA sequence 549 / 549
position of stopcodon in wt / mu cDNA 1966 / 1966
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 320 / 320
chromosome 13
strand -1
last intron/exon boundary 1925
theoretical NMD boundary in CDS 1555
length of CDS 1647
coding sequence (CDS) position 955
cDNA position
(for ins/del: last normal base / first normal base)		 1274
gDNA position
(for ins/del: last normal base / first normal base)		 30260
chromosomal position
(for ins/del: last normal base / first normal base)		 25831888
original gDNA sequence snippet AAGCTGTTATGGATGCTGCAATCTTCTTGGCCAAAGTAATA
altered gDNA sequence snippet AAGCTGTTATGGATGCTGCAGTCTTCTTGGCCAAAGTAATA
original cDNA sequence snippet AAGCTGTTATGGATGCTGCAATCTTCTTGGCCAAAGCAATA
altered cDNA sequence snippet AAGCTGTTATGGATGCTGCAGTCTTCTTGGCCAAAGCAATA
wildtype AA sequence MEHIRTTKVE QVKLLDRFST SNKSLTGTLY LTATHLLFID SHQKETWILH HHIASVEKLA
LTTSGCPLVI QCKNFRTVHF IVPRERDCHD IYNSLLQLSK QAKYEDLYAF SYNPKQNDSE
RLQGWQLIDL AEEYKRMGVP NSHWQLSDAN RDYKICETYP RELYVPRIAS KPIIVGSSKF
RSKGRFPVLS YYHQDKEAAI CRCSQPLSGF SARCLEDEHL LQAISKANPV NRYMYVMDTR
PKLNAMANRA AGKGYENEDN YSNIRFQFVG IENIHVMRSS LQKLLEVNGT KGLSVNDFYS
GLESSGWLRH IKAVMDAAIF LAKAITVENA SVLVHCSDGW DRTSQVCSLG SLLLDSYYRT
IKGFMVLIEK DWISFGHKFS ERCGQLDGDP KEVSPVFTQF LECVWHLTEQ FPQAFEFSEA
FLLQIHEHIH SCQFGNFLGN CQKEREELKL KEKTYSLWPF LLEDQKKYLN PLYSSESHRF
TVLEPNTVSF NFKFWRNMYH QFDRTLHPRQ SVFNIIMNMN EQNKQLEKDI KDLESLTSYS
SFKIIVGQ*
mutated AA sequence MEHIRTTKVE QVKLLDRFST SNKSLTGTLY LTATHLLFID SHQKETWILH HHIASVEKLA
LTTSGCPLVI QCKNFRTVHF IVPRERDCHD IYNSLLQLSK QAKYEDLYAF SYNPKQNDSE
RLQGWQLIDL AEEYKRMGVP NSHWQLSDAN RDYKICETYP RELYVPRIAS KPIIVGSSKF
RSKGRFPVLS YYHQDKEAAI CRCSQPLSGF SARCLEDEHL LQAISKANPV NRYMYVMDTR
PKLNAMANRA AGKGYENEDN YSNIRFQFVG IENIHVMRSS LQKLLEVNGT KGLSVNDFYS
GLESSGWLRH IKAVMDAAVF LAKAITVENA SVLVHCSDGW DRTSQVCSLG SLLLDSYYRT
IKGFMVLIEK DWISFGHKFS ERCGQLDGDP KEVSPVFTQF LECVWHLTEQ FPQAFEFSEA
FLLQIHEHIH SCQFGNFLGN CQKEREELKL KEKTYSLWPF LLEDQKKYLN PLYSSESHRF
TVLEPNTVSF NFKFWRNMYH QFDRTLHPRQ SVFNIIMNMN EQNKQLEKDI KDLESLTSYS
SFKIIVGQ*
speed 0.14 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
back to results table

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