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: ENST00000463745
Querying Taster for transcript #2: ENST00000335979
Querying Taster for transcript #3: ENST00000394206
MT speed 0 s - this script 4.085714 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ARL6disease_causing_automatic0.999999694534773simple_aaeaffected0G169Asingle base exchangers104893679show file
ARL6disease_causing_automatic0.999999694534773simple_aaeaffected0G169Asingle base exchangers104893679show file
ARL6disease_causing_automatic0.999999694534773simple_aaeaffected0G169Asingle base exchangers104893679show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999694534773 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042296)
  • known disease mutation: rs2041 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97510641G>CN/A show variant in all transcripts   IGV
HGNC symbol ARL6
Ensembl transcript ID ENST00000463745
Genbank transcript ID N/A
UniProt peptide Q9H0F7
alteration type single base exchange
alteration region CDS
DNA changes c.506G>C
cDNA.983G>C
g.27277G>C
AA changes G169A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 169
frameshift no
known variant Reference ID: rs104893679
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2041 (pathogenic for Bardet-Biedl syndrome 3|Bardet-Biedl syndrome 1, modifier of) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1681
3.5711
(flanking)-0.0220.985
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased27269wt: 0.53 / mu: 0.74wt: ATAAAAGGAGAAGGC
mu: ATAAAAGGAGAAGCC		 AAAA|ggag
Donor increased27282wt: 0.67 / mu: 0.86wt: GCTTGCAAGAAGGTG
mu: CCTTGCAAGAAGGTG		 TTGC|aaga
Donor increased27279wt: 0.70 / mu: 0.89wt: AAGGCTTGCAAGAAG
mu: AAGCCTTGCAAGAAG		 GGCT|tgca
Donor marginally increased27270wt: 0.9989 / mu: 0.9990 (marginal change - not scored)wt: TAAAAGGAGAAGGCT
mu: TAAAAGGAGAAGCCT		 AAAG|gaga
Donor gained272750.37mu: GGAGAAGCCTTGCAA AGAA|gcct
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      169HICASDAIKGEGLQEGVDWLQDQI
mutated  not conserved    169HICASDAIKGEALQEGVDWLQDQ
Ptroglodytes  all identical  ENSPTRG00000015139  169HICASDAIKGEGLQEGVDWLQDQ
Mmulatta  all identical  ENSMMUG00000023332  169HICASDAIKGEGLQEGVDWLQDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022722  169HICASDAIKGEGLQEGVDWLQEK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000017239  168HICATDALKGEGLQEGVDWLQDQ
Drerio  all identical  ENSDARG00000032056  169HICASDAVKGEGLLEGVDWLQDQ
Dmelanogaster  all identical  FBgn0034446  171HICSSSAISGEGLGEGVQWLI
Celegans  all identical  C38D4.8  169SIHSTCALTGDGLDKAMQQLSAE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
164167TURNmight get lost (downstream of altered splice site)
170180HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 561 / 561
position (AA) of stopcodon in wt / mu AA sequence 187 / 187
position of stopcodon in wt / mu cDNA 1038 / 1038
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 478 / 478
chromosome 3
strand 1
last intron/exon boundary 1013
theoretical NMD boundary in CDS 485
length of CDS 561
coding sequence (CDS) position 506
cDNA position
(for ins/del: last normal base / first normal base)		 983
gDNA position
(for ins/del: last normal base / first normal base)		 27277
chromosomal position
(for ins/del: last normal base / first normal base)		 97510641
original gDNA sequence snippet TGATGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACT
altered gDNA sequence snippet TGATGCCATAAAAGGAGAAGCCTTGCAAGAAGGTGTAGACT
original cDNA sequence snippet TGATGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACT
altered cDNA sequence snippet TGATGCCATAAAAGGAGAAGCCTTGCAAGAAGGTGTAGACT
wildtype AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGL QEGVDWLQDQ
IQTVKT*
mutated AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEAL QEGVDWLQDQ
IQTVKT*
speed 1.09 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: 0.999999694534773 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042296)
  • known disease mutation: rs2041 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97510641G>CN/A show variant in all transcripts   IGV
HGNC symbol ARL6
Ensembl transcript ID ENST00000335979
Genbank transcript ID NM_032146
UniProt peptide Q9H0F7
alteration type single base exchange
alteration region CDS
DNA changes c.506G>C
cDNA.859G>C
g.27277G>C
AA changes G169A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 169
frameshift no
known variant Reference ID: rs104893679
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2041 (pathogenic for Bardet-Biedl syndrome 3|Bardet-Biedl syndrome 1, modifier of) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1681
3.5711
(flanking)-0.0220.985
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased27269wt: 0.53 / mu: 0.74wt: ATAAAAGGAGAAGGC
mu: ATAAAAGGAGAAGCC		 AAAA|ggag
Donor increased27282wt: 0.67 / mu: 0.86wt: GCTTGCAAGAAGGTG
mu: CCTTGCAAGAAGGTG		 TTGC|aaga
Donor increased27279wt: 0.70 / mu: 0.89wt: AAGGCTTGCAAGAAG
mu: AAGCCTTGCAAGAAG		 GGCT|tgca
Donor marginally increased27270wt: 0.9989 / mu: 0.9990 (marginal change - not scored)wt: TAAAAGGAGAAGGCT
mu: TAAAAGGAGAAGCCT		 AAAG|gaga
Donor gained272750.37mu: GGAGAAGCCTTGCAA AGAA|gcct
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      169HICASDAIKGEGLQEGVDWLQDQI
mutated  not conserved    169HICASDAIKGEALQEGVDWLQDQ
Ptroglodytes  all identical  ENSPTRG00000015139  169HICASDAIKGEGLQEGVDWLQDQ
Mmulatta  all identical  ENSMMUG00000023332  169HICASDAIKGEGLQEGVDWLQDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022722  169HICASDAIKGEGLQEGVDWLQEK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000017239  168HICATDALKGEGLQEGVDWLQDQ
Drerio  all identical  ENSDARG00000032056  169HICASDAVKGEGLLEGVDWLQDQ
Dmelanogaster  all identical  FBgn0034446  171HICSSSAISGEGLGEGVQWLI
Celegans  all identical  C38D4.8  169SIHSTCALTGDGLDKAMQQLSAE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
164167TURNmight get lost (downstream of altered splice site)
170180HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 561 / 561
position (AA) of stopcodon in wt / mu AA sequence 187 / 187
position of stopcodon in wt / mu cDNA 914 / 914
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 354 / 354
chromosome 3
strand 1
last intron/exon boundary 889
theoretical NMD boundary in CDS 485
length of CDS 561
coding sequence (CDS) position 506
cDNA position
(for ins/del: last normal base / first normal base)		 859
gDNA position
(for ins/del: last normal base / first normal base)		 27277
chromosomal position
(for ins/del: last normal base / first normal base)		 97510641
original gDNA sequence snippet TGATGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACT
altered gDNA sequence snippet TGATGCCATAAAAGGAGAAGCCTTGCAAGAAGGTGTAGACT
original cDNA sequence snippet TGATGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACT
altered cDNA sequence snippet TGATGCCATAAAAGGAGAAGCCTTGCAAGAAGGTGTAGACT
wildtype AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGL QEGVDWLQDQ
IQTVKT*
mutated AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEAL QEGVDWLQDQ
IQTVKT*
speed 1.05 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: 0.999999694534773 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042296)
  • known disease mutation: rs2041 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97510641G>CN/A show variant in all transcripts   IGV
HGNC symbol ARL6
Ensembl transcript ID ENST00000394206
Genbank transcript ID NM_177976
UniProt peptide Q9H0F7
alteration type single base exchange
alteration region CDS
DNA changes c.506G>C
cDNA.819G>C
g.27277G>C
AA changes G169A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 169
frameshift no
known variant Reference ID: rs104893679
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2041 (pathogenic for Bardet-Biedl syndrome 3|Bardet-Biedl syndrome 1, modifier of) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042296)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1681
3.5711
(flanking)-0.0220.985
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased27269wt: 0.53 / mu: 0.74wt: ATAAAAGGAGAAGGC
mu: ATAAAAGGAGAAGCC		 AAAA|ggag
Donor increased27282wt: 0.67 / mu: 0.86wt: GCTTGCAAGAAGGTG
mu: CCTTGCAAGAAGGTG		 TTGC|aaga
Donor increased27279wt: 0.70 / mu: 0.89wt: AAGGCTTGCAAGAAG
mu: AAGCCTTGCAAGAAG		 GGCT|tgca
Donor marginally increased27270wt: 0.9989 / mu: 0.9990 (marginal change - not scored)wt: TAAAAGGAGAAGGCT
mu: TAAAAGGAGAAGCCT		 AAAG|gaga
Donor gained272750.37mu: GGAGAAGCCTTGCAA AGAA|gcct
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      169HICASDAIKGEGLQEGVDWLQDQI
mutated  not conserved    169HICASDAIKGEALQEGVDWLQDQ
Ptroglodytes  all identical  ENSPTRG00000015139  169HICASDAIKGEGLQEGVDWLQDQ
Mmulatta  all identical  ENSMMUG00000023332  169HICASDAIKGEGLQEGVDWLQDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022722  169HICASDAIKGEGLQEGVDWLQEK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000017239  168HICATDALKGEGLQEGVDWLQDQ
Drerio  all identical  ENSDARG00000032056  169HICASDAVKGEGLLEGVDWLQDQ
Dmelanogaster  all identical  FBgn0034446  171HICSSSAISGEGLGEGVQWLI
Celegans  all identical  C38D4.8  169SIHSTCALTGDGLDKAMQQLSAE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
164167TURNmight get lost (downstream of altered splice site)
170180HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 561 / 561
position (AA) of stopcodon in wt / mu AA sequence 187 / 187
position of stopcodon in wt / mu cDNA 874 / 874
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 314 / 314
chromosome 3
strand 1
last intron/exon boundary 849
theoretical NMD boundary in CDS 485
length of CDS 561
coding sequence (CDS) position 506
cDNA position
(for ins/del: last normal base / first normal base)		 819
gDNA position
(for ins/del: last normal base / first normal base)		 27277
chromosomal position
(for ins/del: last normal base / first normal base)		 97510641
original gDNA sequence snippet TGATGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACT
altered gDNA sequence snippet TGATGCCATAAAAGGAGAAGCCTTGCAAGAAGGTGTAGACT
original cDNA sequence snippet TGATGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACT
altered cDNA sequence snippet TGATGCCATAAAAGGAGAAGCCTTGCAAGAAGGTGTAGACT
wildtype AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGL QEGVDWLQDQ
IQTVKT*
mutated AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEAL QEGVDWLQDQ
IQTVKT*
speed 0.91 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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