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: ENST00000265808
Querying Taster for transcript #2: ENST00000276373
Querying Taster for transcript #3: ENST00000519026
Querying Taster for transcript #4: ENST00000381608
Querying Taster for transcript #5: ENST00000440926
Querying Taster for transcript #6: ENST00000437980
MT speed 1.68 s - this script 3.585444 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SLC18A1polymorphism_automatic8.5650375680757e-12simple_aaeaffectedT4Psingle base exchangers2270641show file
SLC18A1polymorphism_automatic8.5650375680757e-12simple_aaeaffectedT4Psingle base exchangers2270641show file
SLC18A1polymorphism_automatic8.5650375680757e-12simple_aaeaffectedT4Psingle base exchangers2270641show file
SLC18A1polymorphism_automatic8.5650375680757e-12simple_aaeaffectedT4Psingle base exchangers2270641show file
SLC18A1polymorphism_automatic8.5650375680757e-12simple_aaeaffectedT4Psingle base exchangers2270641show file
SLC18A1polymorphism_automatic8.5650375680757e-12simple_aaeaffectedT4Psingle base exchangers2270641show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999991435 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM057213)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:20038466T>GN/A show variant in all transcripts   IGV
HGNC symbol SLC18A1
Ensembl transcript ID ENST00000265808
Genbank transcript ID NM_001142324
UniProt peptide P54219
alteration type single base exchange
alteration region CDS
DNA changes c.10A>C
cDNA.390A>C
g.2252A>C
AA changes T4P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 4
frameshift no
known variant Reference ID: rs2270641
databasehomozygous (G/G)heterozygousallele carriers
1000G1868611047
ExAC29231234615269

known disease mutation at this position, please check HGMD for details (HGMD ID CM057213)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2780
0.2390.003
(flanking)1.1290.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2246wt: 0.24 / mu: 0.36wt: CCAGTCCGGCCATCACCATGCTCCGGACCATTCTGGATGCT
mu: CCAGTCCGGCCATCACCATGCTCCGGCCCATTCTGGATGCT		 atgc|TCCG
Acc increased2261wt: 0.26 / mu: 0.73wt: CCATGCTCCGGACCATTCTGGATGCTCCCCAGCGGTTGCTG
mu: CCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGCTG		 ctgg|ATGC
Acc gained22590.51mu: CACCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGC ttct|GGAT
distance from splice site 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      4 MLRTILDAPQRLLKEG
mutated  not conserved    4 MLRPILDAPQRLLKEGRASRQL
Ptroglodytes  all identical  ENSPTRG00000020039  4 MLRTVLDAPQRLLKEGRASRQL
Mmulatta  all identical  ENSMMUG00000019999  4 MLRTVLVAPQRLLKEGRASRQL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000036330  4 MFQVVLGAPQRLLKEGRQSRKL
Ggallus  no alignment  ENSGALG00000001693  n/a
Trubripes  no alignment  ENSTRUG00000012619  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0260964  n/a
Celegans  no alignment  W01C8.6  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121TOPO_DOMCytoplasmic (Potential).lost
2242TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
43138TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
5858CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8787CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
104104CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
139158TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
159167TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
168188TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
189197TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
198218TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
219227TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
228250TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
251256TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
257279TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
280299TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
300319TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320335TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
336360TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
361365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
366386TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
387397TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
398418TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
419422TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
423443TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
444448TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
449470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471525TOPO_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 1482 / 1482
position (AA) of stopcodon in wt / mu AA sequence 494 / 494
position of stopcodon in wt / mu cDNA 1862 / 1862
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 381 / 381
chromosome 8
strand -1
last intron/exon boundary 1749
theoretical NMD boundary in CDS 1318
length of CDS 1482
coding sequence (CDS) position 10
cDNA position
(for ins/del: last normal base / first normal base)		 390
gDNA position
(for ins/del: last normal base / first normal base)		 2252
chromosomal position
(for ins/del: last normal base / first normal base)		 20038466
original gDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered gDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
original cDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered cDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
wildtype AA sequence MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGLAF LPASVSYLIG TNLFGVLANK MGRWLCSLIG MLVVGTSLLC VPLAHNIFGL
IGPNAGLGLA IGMVDSSMMP IMGHLVDLRH TSVYGSVYAI ADVAFCMGFA IGPSTGGAIV
KAIGFPWLMV ITGVINIVYA PLCYYLRSPP AKEEKLAILS QDCPMETRMY ATQKPTKEFP
LGEDSDEEPD HEE*
mutated AA sequence MLRPILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGLAF LPASVSYLIG TNLFGVLANK MGRWLCSLIG MLVVGTSLLC VPLAHNIFGL
IGPNAGLGLA IGMVDSSMMP IMGHLVDLRH TSVYGSVYAI ADVAFCMGFA IGPSTGGAIV
KAIGFPWLMV ITGVINIVYA PLCYYLRSPP AKEEKLAILS QDCPMETRMY ATQKPTKEFP
LGEDSDEEPD HEE*
speed 0.10 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: 0.999999999991435 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM057213)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:20038466T>GN/A show variant in all transcripts   IGV
HGNC symbol SLC18A1
Ensembl transcript ID ENST00000276373
Genbank transcript ID NM_003053
UniProt peptide P54219
alteration type single base exchange
alteration region CDS
DNA changes c.10A>C
cDNA.277A>C
g.2252A>C
AA changes T4P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 4
frameshift no
known variant Reference ID: rs2270641
databasehomozygous (G/G)heterozygousallele carriers
1000G1868611047
ExAC29231234615269

known disease mutation at this position, please check HGMD for details (HGMD ID CM057213)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2780
0.2390.003
(flanking)1.1290.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2246wt: 0.24 / mu: 0.36wt: CCAGTCCGGCCATCACCATGCTCCGGACCATTCTGGATGCT
mu: CCAGTCCGGCCATCACCATGCTCCGGCCCATTCTGGATGCT		 atgc|TCCG
Acc increased2261wt: 0.26 / mu: 0.73wt: CCATGCTCCGGACCATTCTGGATGCTCCCCAGCGGTTGCTG
mu: CCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGCTG		 ctgg|ATGC
Acc gained22590.51mu: CACCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGC ttct|GGAT
distance from splice site 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      4 MLRTILDAPQRLLKEG
mutated  not conserved    4 MLRPILDAPQRLLKEGRASRQL
Ptroglodytes  all identical  ENSPTRG00000020039  4 MLRTVLDAPQRLLKEGRASRQL
Mmulatta  all identical  ENSMMUG00000019999  4 MLRTVLVAPQRLLKEGRASRQL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000036330  4 MFQVVLGAPQRLLKEGRQSRKL
Ggallus  no alignment  ENSGALG00000001693  n/a
Trubripes  no alignment  ENSTRUG00000012619  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0260964  n/a
Celegans  no alignment  W01C8.6  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121TOPO_DOMCytoplasmic (Potential).lost
2242TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
43138TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
5858CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8787CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
104104CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
139158TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
159167TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
168188TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
189197TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
198218TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
219227TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
228250TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
251256TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
257279TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
280299TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
300319TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320335TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
336360TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
361365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
366386TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
387397TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
398418TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
419422TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
423443TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
444448TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
449470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471525TOPO_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 1578 / 1578
position (AA) of stopcodon in wt / mu AA sequence 526 / 526
position of stopcodon in wt / mu cDNA 1845 / 1845
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 268 / 268
chromosome 8
strand -1
last intron/exon boundary 1732
theoretical NMD boundary in CDS 1414
length of CDS 1578
coding sequence (CDS) position 10
cDNA position
(for ins/del: last normal base / first normal base)		 277
gDNA position
(for ins/del: last normal base / first normal base)		 2252
chromosomal position
(for ins/del: last normal base / first normal base)		 20038466
original gDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered gDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
original cDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered cDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
wildtype AA sequence MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGPSTGGA IVKAIGFPWL MVITGVINIV YAPLCYYLRS
PPAKEEKLAI LSQDCPMETR MYATQKPTKE FPLGEDSDEE PDHEE*
mutated AA sequence MLRPILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGPSTGGA IVKAIGFPWL MVITGVINIV YAPLCYYLRS
PPAKEEKLAI LSQDCPMETR MYATQKPTKE FPLGEDSDEE PDHEE*
speed 0.10 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: 0.999999999991435 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM057213)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:20038466T>GN/A show variant in all transcripts   IGV
HGNC symbol SLC18A1
Ensembl transcript ID ENST00000519026
Genbank transcript ID N/A
UniProt peptide P54219
alteration type single base exchange
alteration region CDS
DNA changes c.10A>C
cDNA.243A>C
g.2252A>C
AA changes T4P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 4
frameshift no
known variant Reference ID: rs2270641
databasehomozygous (G/G)heterozygousallele carriers
1000G1868611047
ExAC29231234615269

known disease mutation at this position, please check HGMD for details (HGMD ID CM057213)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2780
0.2390.003
(flanking)1.1290.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2246wt: 0.24 / mu: 0.36wt: CCAGTCCGGCCATCACCATGCTCCGGACCATTCTGGATGCT
mu: CCAGTCCGGCCATCACCATGCTCCGGCCCATTCTGGATGCT		 atgc|TCCG
Acc increased2261wt: 0.26 / mu: 0.73wt: CCATGCTCCGGACCATTCTGGATGCTCCCCAGCGGTTGCTG
mu: CCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGCTG		 ctgg|ATGC
Acc gained22590.51mu: CACCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGC ttct|GGAT
distance from splice site 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      4 MLRTILDAPQRLLKEG
mutated  not conserved    4 MLRPILDAPQRLLKEGRASRQL
Ptroglodytes  all identical  ENSPTRG00000020039  4 MLRTVLDAPQRLLKEGRASRQL
Mmulatta  all identical  ENSMMUG00000019999  4 MLRTVLVAPQRLLKEGRASRQL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000036330  4 MFQVVLGAPQRLLKEGRQSRKL
Ggallus  no alignment  ENSGALG00000001693  n/a
Trubripes  no alignment  ENSTRUG00000012619  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0260964  n/a
Celegans  no alignment  W01C8.6  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121TOPO_DOMCytoplasmic (Potential).lost
2242TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
43138TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
5858CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8787CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
104104CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
139158TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
159167TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
168188TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
189197TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
198218TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
219227TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
228250TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
251256TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
257279TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
280299TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
300319TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320335TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
336360TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
361365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
366386TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
387397TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
398418TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
419422TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
423443TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
444448TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
449470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471525TOPO_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 1482 / 1482
position (AA) of stopcodon in wt / mu AA sequence 494 / 494
position of stopcodon in wt / mu cDNA 1715 / 1715
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 234 / 234
chromosome 8
strand -1
last intron/exon boundary 1602
theoretical NMD boundary in CDS 1318
length of CDS 1482
coding sequence (CDS) position 10
cDNA position
(for ins/del: last normal base / first normal base)		 243
gDNA position
(for ins/del: last normal base / first normal base)		 2252
chromosomal position
(for ins/del: last normal base / first normal base)		 20038466
original gDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered gDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
original cDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered cDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
wildtype AA sequence MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGLAF LPASVSYLIG TNLFGVLANK MGRWLCSLIG MLVVGTSLLC VPLAHNIFGL
IGPNAGLGLA IGMVDSSMMP IMGHLVDLRH TSVYGSVYAI ADVAFCMGFA IGPSTGGAIV
KAIGFPWLMV ITGVINIVYA PLCYYLRSPP AKEEKLAILS QDCPMETRMY ATQKPTKEFP
LGEDSDEEPD HEE*
mutated AA sequence MLRPILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGLAF LPASVSYLIG TNLFGVLANK MGRWLCSLIG MLVVGTSLLC VPLAHNIFGL
IGPNAGLGLA IGMVDSSMMP IMGHLVDLRH TSVYGSVYAI ADVAFCMGFA IGPSTGGAIV
KAIGFPWLMV ITGVINIVYA PLCYYLRSPP AKEEKLAILS QDCPMETRMY ATQKPTKEFP
LGEDSDEEPD HEE*
speed 1.25 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: 0.999999999991435 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM057213)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:20038466T>GN/A show variant in all transcripts   IGV
HGNC symbol SLC18A1
Ensembl transcript ID ENST00000381608
Genbank transcript ID N/A
UniProt peptide P54219
alteration type single base exchange
alteration region CDS
DNA changes c.10A>C
cDNA.10A>C
g.2252A>C
AA changes T4P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 4
frameshift no
known variant Reference ID: rs2270641
databasehomozygous (G/G)heterozygousallele carriers
1000G1868611047
ExAC29231234615269

known disease mutation at this position, please check HGMD for details (HGMD ID CM057213)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2780
0.2390.003
(flanking)1.1290.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2246wt: 0.24 / mu: 0.36wt: CCAGTCCGGCCATCACCATGCTCCGGACCATTCTGGATGCT
mu: CCAGTCCGGCCATCACCATGCTCCGGCCCATTCTGGATGCT		 atgc|TCCG
Acc increased2261wt: 0.26 / mu: 0.73wt: CCATGCTCCGGACCATTCTGGATGCTCCCCAGCGGTTGCTG
mu: CCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGCTG		 ctgg|ATGC
Acc gained22590.51mu: CACCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGC ttct|GGAT
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      4 MLRTILDAPQRLLKEG
mutated  not conserved    4 MLRPILDAPQRLLKEGRASRQL
Ptroglodytes  all identical  ENSPTRG00000020039  4 MLRTVLDAPQRLLKEGRASRQL
Mmulatta  all identical  ENSMMUG00000019999  4 MLRTVLVAPQRLLKEGRASRQL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000036330  4 MFQVVLGAPQRLLKEGRQSRKL
Ggallus  no alignment  ENSGALG00000001693  n/a
Trubripes  no alignment  ENSTRUG00000012619  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0260964  n/a
Celegans  no alignment  W01C8.6  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121TOPO_DOMCytoplasmic (Potential).lost
2242TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
43138TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
5858CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8787CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
104104CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
139158TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
159167TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
168188TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
189197TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
198218TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
219227TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
228250TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
251256TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
257279TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
280299TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
300319TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320335TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
336360TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
361365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
366386TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
387397TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
398418TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
419422TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
423443TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
444448TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
449470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471525TOPO_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 1419 / 1419
position (AA) of stopcodon in wt / mu AA sequence 473 / 473
position of stopcodon in wt / mu cDNA 1419 / 1419
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 8
strand -1
last intron/exon boundary 1331
theoretical NMD boundary in CDS 1280
length of CDS 1419
coding sequence (CDS) position 10
cDNA position
(for ins/del: last normal base / first normal base)		 10
gDNA position
(for ins/del: last normal base / first normal base)		 2252
chromosomal position
(for ins/del: last normal base / first normal base)		 20038466
original gDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered gDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
original cDNA sequence snippet ATGCTCCGGACCATTCTGGATGCTCCCCAG
altered cDNA sequence snippet ATGCTCCGGCCCATTCTGGATGCTCCCCAG
wildtype AA sequence MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGYSESGL PHGDPDVCNP EAHEGISSGG GQ*
mutated AA sequence MLRPILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGYSESGL PHGDPDVCNP EAHEGISSGG GQ*
speed 0.08 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: 0.999999999991435 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM057213)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:20038466T>GN/A show variant in all transcripts   IGV
HGNC symbol SLC18A1
Ensembl transcript ID ENST00000440926
Genbank transcript ID NM_001135691
UniProt peptide P54219
alteration type single base exchange
alteration region CDS
DNA changes c.10A>C
cDNA.481A>C
g.2252A>C
AA changes T4P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 4
frameshift no
known variant Reference ID: rs2270641
databasehomozygous (G/G)heterozygousallele carriers
1000G1868611047
ExAC29231234615269

known disease mutation at this position, please check HGMD for details (HGMD ID CM057213)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2780
0.2390.003
(flanking)1.1290.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2246wt: 0.24 / mu: 0.36wt: CCAGTCCGGCCATCACCATGCTCCGGACCATTCTGGATGCT
mu: CCAGTCCGGCCATCACCATGCTCCGGCCCATTCTGGATGCT		 atgc|TCCG
Acc increased2261wt: 0.26 / mu: 0.73wt: CCATGCTCCGGACCATTCTGGATGCTCCCCAGCGGTTGCTG
mu: CCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGCTG		 ctgg|ATGC
Acc gained22590.51mu: CACCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGC ttct|GGAT
distance from splice site 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      4 MLRTILDAPQRLLKEG
mutated  not conserved    4 MLRPILDAPQRLLKEGRASRQL
Ptroglodytes  all identical  ENSPTRG00000020039  4 MLRTVLDAPQRLLKEGRASRQL
Mmulatta  all identical  ENSMMUG00000019999  4 MLRTVLVAPQRLLKEGRASRQL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000036330  4 MFQVVLGAPQRLLKEGRQSRKL
Ggallus  no alignment  ENSGALG00000001693  n/a
Trubripes  no alignment  ENSTRUG00000012619  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0260964  n/a
Celegans  no alignment  W01C8.6  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121TOPO_DOMCytoplasmic (Potential).lost
2242TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
43138TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
5858CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8787CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
104104CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
139158TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
159167TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
168188TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
189197TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
198218TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
219227TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
228250TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
251256TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
257279TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
280299TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
300319TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320335TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
336360TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
361365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
366386TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
387397TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
398418TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
419422TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
423443TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
444448TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
449470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471525TOPO_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 1578 / 1578
position (AA) of stopcodon in wt / mu AA sequence 526 / 526
position of stopcodon in wt / mu cDNA 2049 / 2049
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 472 / 472
chromosome 8
strand -1
last intron/exon boundary 1936
theoretical NMD boundary in CDS 1414
length of CDS 1578
coding sequence (CDS) position 10
cDNA position
(for ins/del: last normal base / first normal base)		 481
gDNA position
(for ins/del: last normal base / first normal base)		 2252
chromosomal position
(for ins/del: last normal base / first normal base)		 20038466
original gDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered gDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
original cDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered cDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
wildtype AA sequence MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGPSTGGA IVKAIGFPWL MVITGVINIV YAPLCYYLRS
PPAKEEKLAI LSQDCPMETR MYATQKPTKE FPLGEDSDEE PDHEE*
mutated AA sequence MLRPILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGPSTGGA IVKAIGFPWL MVITGVINIV YAPLCYYLRS
PPAKEEKLAI LSQDCPMETR MYATQKPTKE FPLGEDSDEE PDHEE*
speed 0.08 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: 0.999999999991435 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM057213)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:20038466T>GN/A show variant in all transcripts   IGV
HGNC symbol SLC18A1
Ensembl transcript ID ENST00000437980
Genbank transcript ID NM_001142325
UniProt peptide P54219
alteration type single base exchange
alteration region CDS
DNA changes c.10A>C
cDNA.481A>C
g.2252A>C
AA changes T4P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 4
frameshift no
known variant Reference ID: rs2270641
databasehomozygous (G/G)heterozygousallele carriers
1000G1868611047
ExAC29231234615269

known disease mutation at this position, please check HGMD for details (HGMD ID CM057213)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2780
0.2390.003
(flanking)1.1290.02
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2246wt: 0.24 / mu: 0.36wt: CCAGTCCGGCCATCACCATGCTCCGGACCATTCTGGATGCT
mu: CCAGTCCGGCCATCACCATGCTCCGGCCCATTCTGGATGCT		 atgc|TCCG
Acc increased2261wt: 0.26 / mu: 0.73wt: CCATGCTCCGGACCATTCTGGATGCTCCCCAGCGGTTGCTG
mu: CCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGCTG		 ctgg|ATGC
Acc gained22590.51mu: CACCATGCTCCGGCCCATTCTGGATGCTCCCCAGCGGTTGC ttct|GGAT
distance from splice site 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      4 MLRTILDAPQRLLKEG
mutated  not conserved    4 MLRPILDAPQRLLKEGRASRQL
Ptroglodytes  all identical  ENSPTRG00000020039  4 MLRTVLDAPQRLLKEGRASRQL
Mmulatta  all identical  ENSMMUG00000019999  4 MLRTVLVAPQRLLKEGRASRQL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000036330  4 MFQVVLGAPQRLLKEGRQSRKL
Ggallus  no alignment  ENSGALG00000001693  n/a
Trubripes  no alignment  ENSTRUG00000012619  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0260964  n/a
Celegans  no alignment  W01C8.6  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121TOPO_DOMCytoplasmic (Potential).lost
2242TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
43138TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
5858CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8787CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
104104CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
139158TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
159167TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
168188TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
189197TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
198218TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
219227TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
228250TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
251256TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
257279TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
280299TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
300319TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320335TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
336360TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
361365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
366386TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
387397TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
398418TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
419422TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
423443TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
444448TOPO_DOMLumenal, vesicle (Potential).might get lost (downstream of altered splice site)
449470TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
471525TOPO_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 1419 / 1419
position (AA) of stopcodon in wt / mu AA sequence 473 / 473
position of stopcodon in wt / mu cDNA 1890 / 1890
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 472 / 472
chromosome 8
strand -1
last intron/exon boundary 1802
theoretical NMD boundary in CDS 1280
length of CDS 1419
coding sequence (CDS) position 10
cDNA position
(for ins/del: last normal base / first normal base)		 481
gDNA position
(for ins/del: last normal base / first normal base)		 2252
chromosomal position
(for ins/del: last normal base / first normal base)		 20038466
original gDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered gDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
original cDNA sequence snippet CGGCCATCACCATGCTCCGGACCATTCTGGATGCTCCCCAG
altered cDNA sequence snippet CGGCCATCACCATGCTCCGGCCCATTCTGGATGCTCCCCAG
wildtype AA sequence MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGYSESGL PHGDPDVCNP EAHEGISSGG GQ*
mutated AA sequence MLRPILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS
LHLGHAGSSP HALASPAFST IFSFFNNNTV AVEESVPSGI AWMNDTASTI PPPATEAISA
HKNNCLQGTG FLEEEITRVG VLFASKAVMQ LLVNPFVGPL TNRIGYHIPM FAGFVIMFLS
TVMFAFSGTY TLLFVARTLQ GIGSSFSSVA GLGMLASVYT DDHERGRAMG TALGGLALGL
LVGAPFGSVM YEFVGKSAPF LILAFLALLD GALQLCILQP SKVSPESAKG TPLFMLLKDP
YILVAAGSIC FANMGVAILE PTLPIWMMQT MCSPKWQLGL AFLPASVSYL IGTNLFGVLA
NKMGRWLCSL IGMLVVGTSL LCVPLAHNIF GLIGPNAGLG LAIGMVDSSM MPIMGHLVDL
RHTSVYGSVY AIADVAFCMG FAIGYSESGL PHGDPDVCNP EAHEGISSGG GQ*
speed 0.07 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