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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000346144
Querying Taster for transcript #2: ENST00000215637
Querying Taster for transcript #3: ENST00000382683
MT speed 0 s - this script 3.789236 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MADCAM1polymorphism_automatic4.83002526863174e-12simple_aaeaffectedP300Hsingle base exchangers3745925show file
MADCAM1polymorphism_automatic1.16210215006518e-07without_aaeaffectedsingle base exchangers3745925show file
MADCAM1polymorphism_automatic1.16210215006518e-07without_aaeaffectedsingle base exchangers3745925show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999517 (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) chr19:501900C>AN/A show variant in all transcripts   IGV
HGNC symbol MADCAM1
Ensembl transcript ID ENST00000215637
Genbank transcript ID NM_130760
UniProt peptide Q13477
alteration type single base exchange
alteration region CDS
DNA changes c.899C>A
cDNA.945C>A
g.12725C>A
AA changes P300H Score: 77 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 300
frameshift no
known variant Reference ID: rs3745925
databasehomozygous (A/A)heterozygousallele carriers
1000G140808948
ExAC77371627935
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6320.001
-0.2430
(flanking)-2.0680
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 increased12727wt: 0.2743 / mu: 0.3304 (marginal change - not scored)wt: GGCCCACGCAGGGAG
mu: GGCACACGCAGGGAG		 CCCA|cgca
Donor increased12728wt: 0.21 / mu: 0.30wt: GCCCACGCAGGGAGA
mu: GCACACGCAGGGAGA		 CCAC|gcag
Donor increased12717wt: 0.49 / mu: 0.63wt: TCCCAGGCTGGGCCC
mu: TCCCAGGCTGGGCAC		 CCAG|gctg
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      300RTRRPEISQAGPTQGEVIPTGSSK
mutated  not conserved    300RTRRPEISQAGHTQGEVIPTGSS
Ptroglodytes  all identical  ENSPTRG00000010151  242RTHRPEISQAGPTQGEVIPTVSS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000020310  318ATYHKREAGAQAWLSVLPPGPMVEGWFQCRQDPGGQVTNLYVP
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 
19317TOPO_DOMExtracellular (Potential).lost
226317REGIONMucin-like.lost
318338TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
339382TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1149 / 1149
position (AA) of stopcodon in wt / mu AA sequence 383 / 383
position of stopcodon in wt / mu cDNA 1195 / 1195
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 47 / 47
chromosome 19
strand 1
last intron/exon boundary 975
theoretical NMD boundary in CDS 878
length of CDS 1149
coding sequence (CDS) position 899
cDNA position
(for ins/del: last normal base / first normal base)		 945
gDNA position
(for ins/del: last normal base / first normal base)		 12725
chromosomal position
(for ins/del: last normal base / first normal base)		 501900
original gDNA sequence snippet TGAGATCTCCCAGGCTGGGCCCACGCAGGGAGAAGTGATCC
altered gDNA sequence snippet TGAGATCTCCCAGGCTGGGCACACGCAGGGAGAAGTGATCC
original cDNA sequence snippet TGAGATCTCCCAGGCTGGGCCCACGCAGGGAGAAGTGATCC
altered cDNA sequence snippet TGAGATCTCCCAGGCTGGGCACACGCAGGGAGAAGTGATCC
wildtype AA sequence MDFGLALLLA GLLGLLLGQS LQVKPLQVEP PEPVVAVALG ASRQLTCRLA CADRGASVQW
RGLDTSLGAV QSDTGRSVLT VRNASLSAAG TRVCVGSCGG RTFQHTVQLL VYAFPDQLTV
SPAALVPGDP EVACTAHKVT PVDPNALSFS LLVGGQELEG AQALGPEVQE EEEEPQGDED
VLFRVTERWR LPPLGTPVPP ALYCQATMRL PGLELSHRQA IPVLHSPTSP EPPDTTSPES
PDTTSPESPD TTSQEPPDTT SPEPPDKTSP EPAPQQGSTH TPRSPGSTRT RRPEISQAGP
TQGEVIPTGS SKPAGDQLPA ALWTSSAVLG LLLLALPTYH LWKRCRHLAE DDTHPPASLR
LLPQVSAWAG LRGTGQVGIS PS*
mutated AA sequence MDFGLALLLA GLLGLLLGQS LQVKPLQVEP PEPVVAVALG ASRQLTCRLA CADRGASVQW
RGLDTSLGAV QSDTGRSVLT VRNASLSAAG TRVCVGSCGG RTFQHTVQLL VYAFPDQLTV
SPAALVPGDP EVACTAHKVT PVDPNALSFS LLVGGQELEG AQALGPEVQE EEEEPQGDED
VLFRVTERWR LPPLGTPVPP ALYCQATMRL PGLELSHRQA IPVLHSPTSP EPPDTTSPES
PDTTSPESPD TTSQEPPDTT SPEPPDKTSP EPAPQQGSTH TPRSPGSTRT RRPEISQAGH
TQGEVIPTGS SKPAGDQLPA ALWTSSAVLG LLLLALPTYH LWKRCRHLAE DDTHPPASLR
LLPQVSAWAG LRGTGQVGIS PS*
speed 0.84 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: without_aae, prob: 0.999999883789785 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr19:501900C>AN/A show variant in all transcripts   IGV
HGNC symbol MADCAM1
Ensembl transcript ID ENST00000346144
Genbank transcript ID NM_130762
UniProt peptide Q13477
alteration type single base exchange
alteration region intron
DNA changes g.12725C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3745925
databasehomozygous (A/A)heterozygousallele carriers
1000G140808948
ExAC77371627935
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6320.001
-0.2430
(flanking)-2.0680
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 increased12727wt: 0.2743 / mu: 0.3304 (marginal change - not scored)wt: GGCCCACGCAGGGAG
mu: GGCACACGCAGGGAG		 CCCA|cgca
Donor increased12728wt: 0.21 / mu: 0.30wt: GCCCACGCAGGGAGA
mu: GCACACGCAGGGAGA		 CCAC|gcag
Donor increased12717wt: 0.49 / mu: 0.63wt: TCCCAGGCTGGGCCC
mu: TCCCAGGCTGGGCAC		 CCAG|gctg
distance from splice site 2845
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
19317TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
113231DOMAINIg-like 2.might get lost (downstream of altered splice site)
213223STRANDmight get lost (downstream of altered splice site)
226317REGIONMucin-like.might get lost (downstream of altered splice site)
228231REPEAT1; truncated.might get lost (downstream of altered splice site)
228271REGION5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.might get lost (downstream of altered splice site)
232239REPEAT2.might get lost (downstream of altered splice site)
240240CONFLICTS -> P (in Ref. 2; AAB02194 and 3; AAC51354).might get lost (downstream of altered splice site)
240247REPEAT3.might get lost (downstream of altered splice site)
242242CONFLICTD -> N (in Ref. 2; AAB02194 and 3; AAC51354).might get lost (downstream of altered splice site)
248255REPEAT4.might get lost (downstream of altered splice site)
254254CONFLICTQ -> P (in Ref. 1; AAC13661).might get lost (downstream of altered splice site)
256263REPEAT5.might get lost (downstream of altered splice site)
264271REPEAT6.might get lost (downstream of altered splice site)
318338TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
339382TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 47 / 47
chromosome 19
strand 1
last intron/exon boundary 714
theoretical NMD boundary in CDS 617
length of CDS 888
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 12725
chromosomal position
(for ins/del: last normal base / first normal base)		 501900
original gDNA sequence snippet TGAGATCTCCCAGGCTGGGCCCACGCAGGGAGAAGTGATCC
altered gDNA sequence snippet TGAGATCTCCCAGGCTGGGCACACGCAGGGAGAAGTGATCC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDFGLALLLA GLLGLLLGQS LQVKPLQVEP PEPVVAVALG ASRQLTCRLA CADRGASVQW
RGLDTSLGAV QSDTGRSVLT VRNASLSAAG TRVCVGSCGG RTFQHTVQLL VYAFPDQLTV
SPAALVPGDP EVACTAHKVT PVDPNALSFS LLVGGQELEG AQALGPEVQE EEEEPQGDED
VLFRVTERWR LPPLGTPVPP ALYCQATMRL PGLELSHRQA IPASKPAGDQ LPAALWTSSA
VLGLLLLALP TYHLWKRCRH LAEDDTHPPA SLRLLPQVSA WAGLRGTGQV GISPS*
mutated AA sequence N/A
speed 0.86 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: without_aae, prob: 0.999999883789785 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr19:501900C>AN/A show variant in all transcripts   IGV
HGNC symbol MADCAM1
Ensembl transcript ID ENST00000382683
Genbank transcript ID N/A
UniProt peptide Q13477
alteration type single base exchange
alteration region intron
DNA changes g.12725C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3745925
databasehomozygous (A/A)heterozygousallele carriers
1000G140808948
ExAC77371627935
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6320.001
-0.2430
(flanking)-2.0680
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 increased12727wt: 0.2743 / mu: 0.3304 (marginal change - not scored)wt: GGCCCACGCAGGGAG
mu: GGCACACGCAGGGAG		 CCCA|cgca
Donor increased12728wt: 0.21 / mu: 0.30wt: GCCCACGCAGGGAGA
mu: GCACACGCAGGGAGA		 CCAC|gcag
Donor increased12717wt: 0.49 / mu: 0.63wt: TCCCAGGCTGGGCCC
mu: TCCCAGGCTGGGCAC		 CCAG|gctg
distance from splice site 2845
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
19317TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
113231DOMAINIg-like 2.might get lost (downstream of altered splice site)
131140STRANDmight get lost (downstream of altered splice site)
134134DISULFIDmight get lost (downstream of altered splice site)
144146TURNmight get lost (downstream of altered splice site)
147153STRANDmight get lost (downstream of altered splice site)
167170STRANDmight get lost (downstream of altered splice site)
175177STRANDmight get lost (downstream of altered splice site)
183190STRANDmight get lost (downstream of altered splice site)
200210STRANDmight get lost (downstream of altered splice site)
204204DISULFIDmight get lost (downstream of altered splice site)
213223STRANDmight get lost (downstream of altered splice site)
226317REGIONMucin-like.might get lost (downstream of altered splice site)
228231REPEAT1; truncated.might get lost (downstream of altered splice site)
228271REGION5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.might get lost (downstream of altered splice site)
232239REPEAT2.might get lost (downstream of altered splice site)
240240CONFLICTS -> P (in Ref. 2; AAB02194 and 3; AAC51354).might get lost (downstream of altered splice site)
240247REPEAT3.might get lost (downstream of altered splice site)
242242CONFLICTD -> N (in Ref. 2; AAB02194 and 3; AAC51354).might get lost (downstream of altered splice site)
248255REPEAT4.might get lost (downstream of altered splice site)
254254CONFLICTQ -> P (in Ref. 1; AAC13661).might get lost (downstream of altered splice site)
256263REPEAT5.might get lost (downstream of altered splice site)
264271REPEAT6.might get lost (downstream of altered splice site)
318338TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
339382TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 1 / 1
chromosome 19
strand 1
last intron/exon boundary 383
theoretical NMD boundary in CDS 332
length of CDS 603
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 12725
chromosomal position
(for ins/del: last normal base / first normal base)		 501900
original gDNA sequence snippet TGAGATCTCCCAGGCTGGGCCCACGCAGGGAGAAGTGATCC
altered gDNA sequence snippet TGAGATCTCCCAGGCTGGGCACACGCAGGGAGAAGTGATCC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDFGLALLLA GLLGLLLAFP DQLTVSPAAL VPGDPEVACT AHKVTPVDPN ALSFSLLVGG
QELEGAQALG PEVQEEEEEP QGDEDVLFRV TERWRLPPLG TPVPPALYCQ ATMRLPGLEL
SHRQAIPASK PAGDQLPAAL WTSSAVLGLL LLALPTYHLW KRCRHLAEDD THPPASLRLL
PQVSAWAGLR GTGQVGISPS *
mutated AA sequence N/A
speed 0.84 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

Problems