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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000303097
Querying Taster for transcript #2: ENST00000394222
Querying Taster for transcript #3: ENST00000471138
Querying Taster for transcript #4: ENST00000535334
Querying Taster for transcript #5: ENST00000539730
MT speed 0 s - this script 3.972215 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ARL13Bdisease_causing_automatic0.999999999682436simple_aae0R200Csingle base exchangers121912608show file
ARL13Bdisease_causing_automatic0.999999999682436simple_aae0R200Csingle base exchangers121912608show file
ARL13Bdisease_causing_automatic0.999999999894654simple_aae0R93Csingle base exchangers121912608show file
ARL13Bdisease_causing_automatic0.999999999894654simple_aae0R97Csingle base exchangers121912608show file
ARL13Bdisease_causing_automatic1without_aae0single base exchangers121912608show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999682436 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM085245)
  • known disease mutation: rs1993 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:93755507C>TN/A show variant in all transcripts   IGV
HGNC symbol ARL13B
Ensembl transcript ID ENST00000394222
Genbank transcript ID N/A
UniProt peptide Q3SXY8
alteration type single base exchange
alteration region CDS
DNA changes c.598C>T
cDNA.873C>T
g.56525C>T
AA changes R200C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 200
frameshift no
known variant Reference ID: rs121912608
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1993 (pathogenic for Joubert syndrome 8) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1650.996
4.0961
(flanking)5.751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 92
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      200VIARDFDALNERIQKETTEQRALE
mutated  not conserved    200VIARDFDALNECIQKETTEQRAL
Ptroglodytes  all identical  ENSPTRG00000015129  200VIARDFDALNERIQKETTEQRAL
Mmulatta  all identical  ENSMMUG00000020335  201VIARDFDALNERIQKDTTEQRAL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022911  200IIAKDFDALSERIQKDTTEQRAL
Ggallus  all identical  ENSGALG00000015412  201IIAKDFDALNERIQRDTTEQKAY
Trubripes  all identical  ENSTRUG00000013035  200TINLDYEIIAERVSKDTAEQQAQ
Drerio  all identical  ENSDARG00000012763  200NIAKDYEAISERVQKDTAEQKAQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000032383  200VIAKDFEALHERVQKETAEQRAQ
protein features
start (aa)end (aa)featuredetails 
192245COILEDPotential.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1287 / 1287
position (AA) of stopcodon in wt / mu AA sequence 429 / 429
position of stopcodon in wt / mu cDNA 1562 / 1562
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 276 / 276
chromosome 3
strand 1
last intron/exon boundary 1486
theoretical NMD boundary in CDS 1160
length of CDS 1287
coding sequence (CDS) position 598
cDNA position
(for ins/del: last normal base / first normal base)		 873
gDNA position
(for ins/del: last normal base / first normal base)		 56525
chromosomal position
(for ins/del: last normal base / first normal base)		 93755507
original gDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered gDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
original cDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered cDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
wildtype AA sequence MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA PTVGFSKINL
RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD EERMEETKEA MSEMLRHPRI
SGKPILVLAN KQDKEGALGE ADVIECLSLE KLVNEHKCLC QIEPCSAISG YGKKIDKSIK
KGLYWLLHVI ARDFDALNER IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL
DGTSGLAELD PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK LRMKRNHRVE
PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET HHNDFYRKPL PPLAVPQRPN
SDAHDVIS*
mutated AA sequence MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA PTVGFSKINL
RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD EERMEETKEA MSEMLRHPRI
SGKPILVLAN KQDKEGALGE ADVIECLSLE KLVNEHKCLC QIEPCSAISG YGKKIDKSIK
KGLYWLLHVI ARDFDALNEC IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL
DGTSGLAELD PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK LRMKRNHRVE
PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET HHNDFYRKPL PPLAVPQRPN
SDAHDVIS*
speed 0.42 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

disease causing

 Model: simple_aae, prob: 0.999999999682436 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM085245)
  • known disease mutation: rs1993 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:93755507C>TN/A show variant in all transcripts   IGV
HGNC symbol ARL13B
Ensembl transcript ID ENST00000471138
Genbank transcript ID N/A
UniProt peptide Q3SXY8
alteration type single base exchange
alteration region CDS
DNA changes c.598C>T
cDNA.867C>T
g.56525C>T
AA changes R200C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 200
frameshift no
known variant Reference ID: rs121912608
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1993 (pathogenic for Joubert syndrome 8) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1650.996
4.0961
(flanking)5.751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 92
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      200VIARDFDALNERIQKETTEQRALE
mutated  not conserved    200VIARDFDALNECIQKETTEQRAL
Ptroglodytes  all identical  ENSPTRG00000015129  200VIARDFDALNERIQKETTEQRAL
Mmulatta  all identical  ENSMMUG00000020335  201VIARDFDALNERIQKDTTEQRAL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022911  200IIAKDFDALSERIQKDTTEQRAL
Ggallus  all identical  ENSGALG00000015412  201IIAKDFDALNERIQRDTTEQKAY
Trubripes  all identical  ENSTRUG00000013035  200TINLDYEIIAERVSKDTAEQQAQ
Drerio  all identical  ENSDARG00000012763  200NIAKDYEAISERVQKDTAEQKAQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000032383  200VIAKDFEALHERVQKETAEQRAQ
protein features
start (aa)end (aa)featuredetails 
192245COILEDPotential.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1287 / 1287
position (AA) of stopcodon in wt / mu AA sequence 429 / 429
position of stopcodon in wt / mu cDNA 1556 / 1556
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 270 / 270
chromosome 3
strand 1
last intron/exon boundary 1594
theoretical NMD boundary in CDS 1274
length of CDS 1287
coding sequence (CDS) position 598
cDNA position
(for ins/del: last normal base / first normal base)		 867
gDNA position
(for ins/del: last normal base / first normal base)		 56525
chromosomal position
(for ins/del: last normal base / first normal base)		 93755507
original gDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered gDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
original cDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered cDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
wildtype AA sequence MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA PTVGFSKINL
RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD EERMEETKEA MSEMLRHPRI
SGKPILVLAN KQDKEGALGE ADVIECLSLE KLVNEHKCLC QIEPCSAISG YGKKIDKSIK
KGLYWLLHVI ARDFDALNER IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL
DGTSGLAELD PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK LRMKRNHRVE
PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET HHNDFYRKPL PPLAVPQRPN
SDAHDVIS*
mutated AA sequence MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA PTVGFSKINL
RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD EERMEETKEA MSEMLRHPRI
SGKPILVLAN KQDKEGALGE ADVIECLSLE KLVNEHKCLC QIEPCSAISG YGKKIDKSIK
KGLYWLLHVI ARDFDALNEC IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL
DGTSGLAELD PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK LRMKRNHRVE
PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET HHNDFYRKPL PPLAVPQRPN
SDAHDVIS*
speed 0.59 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

disease causing

 Model: simple_aae, prob: 0.999999999894654 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM085245)
  • known disease mutation: rs1993 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:93755507C>TN/A show variant in all transcripts   IGV
HGNC symbol ARL13B
Ensembl transcript ID ENST00000303097
Genbank transcript ID NM_144996
UniProt peptide Q3SXY8
alteration type single base exchange
alteration region CDS
DNA changes c.277C>T
cDNA.559C>T
g.56525C>T
AA changes R93C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 93
frameshift no
known variant Reference ID: rs121912608
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1993 (pathogenic for Joubert syndrome 8) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1650.996
4.0961
(flanking)5.751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 92
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      93VIARDFDALNERIQKETTEQRALE
mutated  not conserved    93VIARDFDALNECIQKETTEQRAL
Ptroglodytes  all identical  ENSPTRG00000015129  200VIARDFDALNERIQKETTEQRAL
Mmulatta  all identical  ENSMMUG00000020335  201VIARDFDALNERIQKDTTEQRAL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022911  200IIAKDFDALSERIQKDTTEQRAL
Ggallus  all identical  ENSGALG00000015412  201IIAKDFDALNERIQRDTTEQKAY
Trubripes  all identical  ENSTRUG00000013035  200TINLDYEIIAERVSKDTAEQQAQ
Drerio  all identical  ENSDARG00000012763  200NIAKDYEAISERVQKDTAEQKAQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000032383  200VIAKDFEALHERVQKETAEQRAQ
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 966 / 966
position (AA) of stopcodon in wt / mu AA sequence 322 / 322
position of stopcodon in wt / mu cDNA 1248 / 1248
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 283 / 283
chromosome 3
strand 1
last intron/exon boundary 1172
theoretical NMD boundary in CDS 839
length of CDS 966
coding sequence (CDS) position 277
cDNA position
(for ins/del: last normal base / first normal base)		 559
gDNA position
(for ins/del: last normal base / first normal base)		 56525
chromosomal position
(for ins/del: last normal base / first normal base)		 93755507
original gDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered gDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
original cDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered cDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
wildtype AA sequence MFSLMASCCG WFKRWREPVR LANKQDKEGA LGEADVIECL SLEKLVNEHK CLCQIEPCSA
ISGYGKKIDK SIKKGLYWLL HVIARDFDAL NERIQKETTE QRALEEQEKQ ERAERVRKLR
EERKQNEQEQ AELDGTSGLA ELDPEPTNPF QPIASVIIEN EGKLEREKKN QKMEKDSDGC
HLKHKMEHEQ IETQGQVNHN GQKNNEFGLV ENYKEALTQQ LKNEDETDRP SLESANGKKK
TKKLRMKRNH RVEPLNIDDC APESPTPPPP PPPVGWGTPK VTRLPKLEPL GETHHNDFYR
KPLPPLAVPQ RPNSDAHDVI S*
mutated AA sequence MFSLMASCCG WFKRWREPVR LANKQDKEGA LGEADVIECL SLEKLVNEHK CLCQIEPCSA
ISGYGKKIDK SIKKGLYWLL HVIARDFDAL NECIQKETTE QRALEEQEKQ ERAERVRKLR
EERKQNEQEQ AELDGTSGLA ELDPEPTNPF QPIASVIIEN EGKLEREKKN QKMEKDSDGC
HLKHKMEHEQ IETQGQVNHN GQKNNEFGLV ENYKEALTQQ LKNEDETDRP SLESANGKKK
TKKLRMKRNH RVEPLNIDDC APESPTPPPP PPPVGWGTPK VTRLPKLEPL GETHHNDFYR
KPLPPLAVPQ RPNSDAHDVI S*
speed 0.56 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

disease causing

 Model: simple_aae, prob: 0.999999999894654 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM085245)
  • known disease mutation: rs1993 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:93755507C>TN/A show variant in all transcripts   IGV
HGNC symbol ARL13B
Ensembl transcript ID ENST00000535334
Genbank transcript ID NM_001174150
UniProt peptide Q3SXY8
alteration type single base exchange
alteration region CDS
DNA changes c.289C>T
cDNA.812C>T
g.56525C>T
AA changes R97C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 97
frameshift no
known variant Reference ID: rs121912608
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1993 (pathogenic for Joubert syndrome 8) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1650.996
4.0961
(flanking)5.751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 92
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      97VIARDFDALNERIQKETTEQRALE
mutated  not conserved    97VIARDFDALNECIQKETTEQRAL
Ptroglodytes  all identical  ENSPTRG00000015129  200VIARDFDALNERIQKETTEQRAL
Mmulatta  all identical  ENSMMUG00000020335  201VIARDFDALNERIQKDTTEQRAL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022911  200IIAKDFDALSERIQKDTTEQRAL
Ggallus  all identical  ENSGALG00000015412  201IIAKDFDALNERIQRDTTEQKAY
Trubripes  all identical  ENSTRUG00000013035  200TINLDYEIIAERVSKDTAEQQAQ
Drerio  all identical  ENSDARG00000012763  200NIAKDYEAISERVQKDTAEQKAQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000032383  200VIAKDFEALHERVQKETAEQRAQ
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 978 / 978
position (AA) of stopcodon in wt / mu AA sequence 326 / 326
position of stopcodon in wt / mu cDNA 1501 / 1501
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 524 / 524
chromosome 3
strand 1
last intron/exon boundary 1425
theoretical NMD boundary in CDS 851
length of CDS 978
coding sequence (CDS) position 289
cDNA position
(for ins/del: last normal base / first normal base)		 812
gDNA position
(for ins/del: last normal base / first normal base)		 56525
chromosomal position
(for ins/del: last normal base / first normal base)		 93755507
original gDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered gDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
original cDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered cDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
wildtype AA sequence MEETKEAMSE MLRHPRISGK PILVLANKQD KEGALGEADV IECLSLEKLV NEHKCLCQIE
PCSAISGYGK KIDKSIKKGL YWLLHVIARD FDALNERIQK ETTEQRALEE QEKQERAERV
RKLREERKQN EQEQAELDGT SGLAELDPEP TNPFQPIASV IIENEGKLER EKKNQKMEKD
SDGCHLKHKM EHEQIETQGQ VNHNGQKNNE FGLVENYKEA LTQQLKNEDE TDRPSLESAN
GKKKTKKLRM KRNHRVEPLN IDDCAPESPT PPPPPPPVGW GTPKVTRLPK LEPLGETHHN
DFYRKPLPPL AVPQRPNSDA HDVIS*
mutated AA sequence MEETKEAMSE MLRHPRISGK PILVLANKQD KEGALGEADV IECLSLEKLV NEHKCLCQIE
PCSAISGYGK KIDKSIKKGL YWLLHVIARD FDALNECIQK ETTEQRALEE QEKQERAERV
RKLREERKQN EQEQAELDGT SGLAELDPEP TNPFQPIASV IIENEGKLER EKKNQKMEKD
SDGCHLKHKM EHEQIETQGQ VNHNGQKNNE FGLVENYKEA LTQQLKNEDE TDRPSLESAN
GKKKTKKLRM KRNHRVEPLN IDDCAPESPT PPPPPPPVGW GTPKVTRLPK LEPLGETHHN
DFYRKPLPPL AVPQRPNSDA HDVIS*
speed 0.59 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

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM085245)
  • known disease mutation: rs1993 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:93755507C>TN/A show variant in all transcripts   IGV
HGNC symbol ARL13B
Ensembl transcript ID ENST00000539730
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.622C>T
g.56525C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121912608
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1993 (pathogenic for Joubert syndrome 8) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085245)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1650.996
4.0961
(flanking)5.751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 92
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 862 / 862
chromosome 3
strand 1
last intron/exon boundary 1235
theoretical NMD boundary in CDS 323
length of CDS 450
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 622
gDNA position
(for ins/del: last normal base / first normal base)		 56525
chromosomal position
(for ins/del: last normal base / first normal base)		 93755507
original gDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered gDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
original cDNA sequence snippet ACTTTGATGCCTTAAATGAACGCATCCAAAAAGAGACAACA
altered cDNA sequence snippet ACTTTGATGCCTTAAATGAATGCATCCAAAAAGAGACAACA
wildtype AA sequence MEKDSDGCHL KHKMEHEQIE TQGQVNHNGQ KNNEFGLVEN YKEALTQQLK NEDETDRPSL
ESANGKKKTK KLRMKRNHRV EPLNIDDCAP ESPTPPPPPP PVGWGTPKVT RLPKLEPLGE
THHNDFYRKP LPPLAVPQRP NSDAHDVIS*
mutated AA sequence N/A
speed 0.73 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