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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000532119
Querying Taster for transcript #2: ENST00000528014
Querying Taster for transcript #3: ENST00000292079
Querying Taster for transcript #4: ENST00000260287
Querying Taster for transcript #5: ENST00000532984
Querying Taster for transcript #6: ENST00000579800
MT speed 0 s - this script 4.930701 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FXYD2disease_causing_automatic0.999341783083708simple_aaeaffected0G39Rsingle base exchangers28938168show file
FXYD2disease_causing_automatic0.999341783083708simple_aaeaffected0G39Rsingle base exchangers28938168show file
FXYD2disease_causing_automatic0.999341783083708simple_aaeaffected0G39Rsingle base exchangers28938168show file
FXYD2disease_causing_automatic0.999341783083708simple_aaeaffected0G41Rsingle base exchangers28938168show file
FXYD6-FXYD2disease_causing_automatic1without_aaeaffected0single base exchangers28938168show file
FXYD6-FXYD2disease_causing_automatic1without_aaeaffected0single base exchangers28938168show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999341783083708 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002780)
  • known disease mutation: rs7684 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:117693139C>TN/A show variant in all transcripts   IGV
HGNC symbol FXYD2
Ensembl transcript ID ENST00000532119
Genbank transcript ID N/A
UniProt peptide P54710
alteration type single base exchange
alteration region CDS
DNA changes c.115G>A
cDNA.170G>A
g.6275G>A
AA changes G39R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs28938168
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7684 (pathogenic for Renal hypomagnesemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0920.987
3.0921
(flanking)0.4651
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 increased6275wt: 0.8904 / mu: 0.9018 (marginal change - not scored)wt: CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
mu: CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT		 gtgg|GGCT
Donor gained62710.96mu: TTCATCGTGAGGCTC CATC|gtga
Donor gained62700.49mu: CTTCATCGTGAGGCT TCAT|cgtg
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39GLIFAGLAFIVGLLILLSRRFRCG
mutated  not conserved    39GLIFAGLAFIVRLLILLSRRFRC
Ptroglodytes  no alignment  ENSPTRG00000004327  n/a
Mmulatta  all identical  ENSMMUG00000007796  41GLIFAGLAFIVGLLILLSKRFRC
Fcatus  all identical  ENSFCAG00000011760  88GLIFAALAFVVGLIIILS
Mmusculus  all identical  ENSMUSG00000059412  39GLIFAGLAFVVGLLIILSKRFRC
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000034242  37GLIFAAIAFVVGMLIIFSGRFRC
protein features
start (aa)end (aa)featuredetails 
2946TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 195 / 195
position (AA) of stopcodon in wt / mu AA sequence 65 / 65
position of stopcodon in wt / mu cDNA 250 / 250
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 56 / 56
chromosome 11
strand -1
last intron/exon boundary 257
theoretical NMD boundary in CDS 151
length of CDS 195
coding sequence (CDS) position 115
cDNA position
(for ins/del: last normal base / first normal base)		 170
gDNA position
(for ins/del: last normal base / first normal base)		 6275
chromosomal position
(for ins/del: last normal base / first normal base)		 117693139
original gDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
altered gDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT
original cDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGC
altered cDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGC
wildtype AA sequence MDRWYLGGSP KGDVDPFYYD YETVRNGGLI FAGLAFIVGL LILLSRRFRC GGNKKRRQIN
EDEP*
mutated AA sequence MDRWYLGGSP KGDVDPFYYD YETVRNGGLI FAGLAFIVRL LILLSRRFRC GGNKKRRQIN
EDEP*
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: 0.999341783083708 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002780)
  • known disease mutation: rs7684 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:117693139C>TN/A show variant in all transcripts   IGV
HGNC symbol FXYD2
Ensembl transcript ID ENST00000528014
Genbank transcript ID NM_021603
UniProt peptide P54710
alteration type single base exchange
alteration region CDS
DNA changes c.115G>A
cDNA.283G>A
g.6275G>A
AA changes G39R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs28938168
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7684 (pathogenic for Renal hypomagnesemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0920.987
3.0921
(flanking)0.4651
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 increased6275wt: 0.8904 / mu: 0.9018 (marginal change - not scored)wt: CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
mu: CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT		 gtgg|GGCT
Donor gained62710.96mu: TTCATCGTGAGGCTC CATC|gtga
Donor gained62700.49mu: CTTCATCGTGAGGCT TCAT|cgtg
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39GLIFAGLAFIVGLLILLSRRFRCG
mutated  not conserved    39GLIFAGLAFIVRLLILLSRRFRC
Ptroglodytes  no alignment  ENSPTRG00000004327  n/a
Mmulatta  all identical  ENSMMUG00000007796  41GLIFAGLAFIVGLLILLSKRFRC
Fcatus  all identical  ENSFCAG00000011760  88GLIFAALAFVVGLIIILS
Mmusculus  all identical  ENSMUSG00000059412  39GLIFAGLAFVVGLLIILSKRFRC
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000034242  37GLIFAAIAFVVGMLIIFSGRFRC
protein features
start (aa)end (aa)featuredetails 
2946TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 195 / 195
position (AA) of stopcodon in wt / mu AA sequence 65 / 65
position of stopcodon in wt / mu cDNA 363 / 363
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 169 / 169
chromosome 11
strand -1
last intron/exon boundary 370
theoretical NMD boundary in CDS 151
length of CDS 195
coding sequence (CDS) position 115
cDNA position
(for ins/del: last normal base / first normal base)		 283
gDNA position
(for ins/del: last normal base / first normal base)		 6275
chromosomal position
(for ins/del: last normal base / first normal base)		 117693139
original gDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
altered gDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT
original cDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGC
altered cDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGC
wildtype AA sequence MDRWYLGGSP KGDVDPFYYD YETVRNGGLI FAGLAFIVGL LILLSRRFRC GGNKKRRQIN
EDEP*
mutated AA sequence MDRWYLGGSP KGDVDPFYYD YETVRNGGLI FAGLAFIVRL LILLSRRFRC GGNKKRRQIN
EDEP*
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

disease causing

 Model: simple_aae, prob: 0.999341783083708 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002780)
  • known disease mutation: rs7684 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:117693139C>TN/A show variant in all transcripts   IGV
HGNC symbol FXYD2
Ensembl transcript ID ENST00000260287
Genbank transcript ID N/A
UniProt peptide P54710
alteration type single base exchange
alteration region CDS
DNA changes c.115G>A
cDNA.194G>A
g.6275G>A
AA changes G39R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs28938168
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7684 (pathogenic for Renal hypomagnesemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0920.987
3.0921
(flanking)0.4651
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 increased6275wt: 0.8904 / mu: 0.9018 (marginal change - not scored)wt: CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
mu: CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT		 gtgg|GGCT
Donor gained62710.96mu: TTCATCGTGAGGCTC CATC|gtga
Donor gained62700.49mu: CTTCATCGTGAGGCT TCAT|cgtg
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39GLIFAGLAFIVGLLILLSRRFRCG
mutated  not conserved    39GLIFAGLAFIVRLLILLSRRFRC
Ptroglodytes  no alignment  ENSPTRG00000004327  n/a
Mmulatta  all identical  ENSMMUG00000007796  41GLIFAGLAFIVGLLILLSKRFRC
Fcatus  all identical  ENSFCAG00000011760  88GLIFAALAFVVGLIIILS
Mmusculus  all identical  ENSMUSG00000059412  39GLIFAGLAFVVGLLIILSKRFRC
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000034242  37GLIFAAIAFVVGMLIIFSGRFRC
protein features
start (aa)end (aa)featuredetails 
2946TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 195 / 195
position (AA) of stopcodon in wt / mu AA sequence 65 / 65
position of stopcodon in wt / mu cDNA 274 / 274
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 80 / 80
chromosome 11
strand -1
last intron/exon boundary 281
theoretical NMD boundary in CDS 151
length of CDS 195
coding sequence (CDS) position 115
cDNA position
(for ins/del: last normal base / first normal base)		 194
gDNA position
(for ins/del: last normal base / first normal base)		 6275
chromosomal position
(for ins/del: last normal base / first normal base)		 117693139
original gDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
altered gDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT
original cDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGC
altered cDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGC
wildtype AA sequence MDRWYLGGSP KGDVDPFYYD YETVRNGGLI FAGLAFIVGL LILLSRRFRC GGNKKRRQIN
EDEP*
mutated AA sequence MDRWYLGGSP KGDVDPFYYD YETVRNGGLI FAGLAFIVRL LILLSRRFRC GGNKKRRQIN
EDEP*
speed 0.54 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: 0.999341783083708 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002780)
  • known disease mutation: rs7684 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:117693139C>TN/A show variant in all transcripts   IGV
HGNC symbol FXYD2
Ensembl transcript ID ENST00000292079
Genbank transcript ID NM_001680
UniProt peptide P54710
alteration type single base exchange
alteration region CDS
DNA changes c.121G>A
cDNA.187G>A
g.6275G>A
AA changes G41R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 41
frameshift no
known variant Reference ID: rs28938168
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7684 (pathogenic for Renal hypomagnesemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0920.987
3.0921
(flanking)0.4651
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 increased6275wt: 0.8904 / mu: 0.9018 (marginal change - not scored)wt: CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
mu: CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT		 gtgg|GGCT
Donor gained62710.96mu: TTCATCGTGAGGCTC CATC|gtga
Donor gained62700.49mu: CTTCATCGTGAGGCT TCAT|cgtg
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      41GLIFAGLAFIVGLLILLSRRFRCG
mutated  not conserved    41GLIFAGLAFIVRLLILLSRRFRC
Ptroglodytes  no alignment  ENSPTRG00000004327  n/a
Mmulatta  all identical  ENSMMUG00000007796  41GLIFAGLAFIVGLLILLSKRFRC
Fcatus  all identical  ENSFCAG00000011760  80GLIFAALAFVVGLIIILS
Mmusculus  all identical  ENSMUSG00000059412  39GLIFAGLAFVVGLLIILSKRFRC
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000034242  37GLIFAAIAFVVGMLIIFSGRFRC
protein features
start (aa)end (aa)featuredetails 
2946TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 201 / 201
position (AA) of stopcodon in wt / mu AA sequence 67 / 67
position of stopcodon in wt / mu cDNA 267 / 267
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 67 / 67
chromosome 11
strand -1
last intron/exon boundary 274
theoretical NMD boundary in CDS 157
length of CDS 201
coding sequence (CDS) position 121
cDNA position
(for ins/del: last normal base / first normal base)		 187
gDNA position
(for ins/del: last normal base / first normal base)		 6275
chromosomal position
(for ins/del: last normal base / first normal base)		 117693139
original gDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
altered gDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT
original cDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGC
altered cDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGC
wildtype AA sequence MTGLSMDGGG SPKGDVDPFY YDYETVRNGG LIFAGLAFIV GLLILLSRRF RCGGNKKRRQ
INEDEP*
mutated AA sequence MTGLSMDGGG SPKGDVDPFY YDYETVRNGG LIFAGLAFIV RLLILLSRRF RCGGNKKRRQ
INEDEP*
speed 0.99 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 CM002780)
  • known disease mutation: rs7684 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:117693139C>TN/A show variant in all transcripts   IGV
HGNC symbol FXYD6-FXYD2
Ensembl transcript ID ENST00000532984
Genbank transcript ID NM_001243598
UniProt peptide Q9H0Q3
alteration type single base exchange
alteration region intron
DNA changes g.54244G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28938168
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7684 (pathogenic for Renal hypomagnesemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0920.987
3.0921
(flanking)0.4651
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 increased54244wt: 0.8904 / mu: 0.9018 (marginal change - not scored)wt: CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
mu: CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT		 gtgg|GGCT
Donor gained542390.49mu: CTTCATCGTGAGGCT TCAT|cgtg
Donor gained542400.96mu: TTCATCGTGAGGCTC CATC|gtga
distance from splice site 255
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features no protein features affected
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 82 / 82
chromosome 11
strand -1
last intron/exon boundary 461
theoretical NMD boundary in CDS 329
length of CDS 339
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)		 54244
chromosomal position
(for ins/del: last normal base / first normal base)		 117693139
original gDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
altered gDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MELVLVFLCS LLAPMVLASA AEKEKEMDPF HYDYQTLRIG GLVFAVVLFS VGILLILRPQ
EMRKPRWRTS SPPMQQSPRK QRTEVQPSGG RRQPQGGRGP VLLWQKIPLW GQ*
mutated AA sequence N/A
speed 0.70 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 CM002780)
  • known disease mutation: rs7684 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:117693139C>TN/A show variant in all transcripts   IGV
HGNC symbol FXYD6-FXYD2
Ensembl transcript ID ENST00000579800
Genbank transcript ID NM_001243598
UniProt peptide Q9H0Q3
alteration type single base exchange
alteration region intron
DNA changes g.54244G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28938168
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7684 (pathogenic for Renal hypomagnesemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002780)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0920.987
3.0921
(flanking)0.4651
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 increased54244wt: 0.8904 / mu: 0.9018 (marginal change - not scored)wt: CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
mu: CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT		 gtgg|GGCT
Donor gained542390.49mu: CTTCATCGTGAGGCT TCAT|cgtg
Donor gained542400.96mu: TTCATCGTGAGGCTC CATC|gtga
distance from splice site 255
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features no protein features affected
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 82 / 82
chromosome 11
strand -1
last intron/exon boundary 461
theoretical NMD boundary in CDS 329
length of CDS 339
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)		 54244
chromosomal position
(for ins/del: last normal base / first normal base)		 117693139
original gDNA sequence snippet CTGGACTGGCCTTCATCGTGGGGCTCCTCATCCTCCTCAGT
altered gDNA sequence snippet CTGGACTGGCCTTCATCGTGAGGCTCCTCATCCTCCTCAGT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MELVLVFLCS LLAPMVLASA AEKEKEMDPF HYDYQTLRIG GLVFAVVLFS VGILLILRPQ
EMRKPRWRTS SPPMQQSPRK QRTEVQPSGG RRQPQGGRGP VLLWQKIPLW GQ*
mutated AA sequence N/A
speed 0.75 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