MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000377905
Querying Taster for transcript #2: ENST00000439485
Querying Taster for transcript #3: ENST00000397076
MT speed 0 s - this script 3.77251 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SLC17A4	polymorphism_automatic	6.84610146350906e-11	simple_aae		affected		A142T	single base exchange	rs11754288		show file
SLC17A4	polymorphism_automatic	2.1153301332788e-10	simple_aae		affected		A142T	single base exchange	rs11754288		show file
SLC17A4	polymorphism_automatic	4.73883043916601e-10	simple_aae		affected		A372T	single base exchange	rs11754288		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999931539 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:25776949G>AN/A show variant in all transcripts IGV

HGNC symbol

SLC17A4

Ensembl transcript ID

ENST00000439485

Genbank transcript ID

N/A

UniProt peptide

Q9Y2C5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.424G>A
cDNA.502G>A
g.22023G>A

AA changes

A142T Score: 58 explain score(s)

position(s) of altered AA
if AA alteration in CDS

142

frameshift

known variant

Reference ID: rs11754288

database	homozygous (A/A)	heterozygous	allele carriers
1000G	245	812	1057
ExAC	9199	14369	23568

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.496	0.005
	-0.673	0
(flanking)	0.772	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc increased	22026	wt: 0.60 / mu: 0.75	wt: TCAGGAAACTCTTCACTGCCATTGGTAAGGGAGAGACTGGA mu: TCAGGAAACTCTTCACTACCATTGGTAAGGGAGAGACTGGA	gcca\|TTGG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

142

mutated

not conserved

142

Ptroglodytes

all identical

ENSPTRG00000017791

372

Mmulatta

all identical

ENSMMUG00000002579

372

Fcatus

not conserved

ENSFCAG00000014669

143

Mmusculus

all identical

ENSMUSG00000021336

369

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000086739

379

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
149	169	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
171	191	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
203	223	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
230	250	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	312	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
332	352	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
368	388	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
398	418	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
431	451	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
461	481	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

position (AA) of stopcodon in wt / mu AA sequence

268 / 268

position of stopcodon in wt / mu cDNA

882 / 882

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

79 / 79

chromosome

strand

last intron/exon boundary

748

theoretical NMD boundary in CDS

619

length of CDS

804

coding sequence (CDS) position

424

cDNA position
(for ins/del: last normal base / first normal base)

502

gDNA position
(for ins/del: last normal base / first normal base)

22023

chromosomal position
(for ins/del: last normal base / first normal base)

25776949

original gDNA sequence snippet

CCATCAGGAAACTCTTCACTGCCATTGGTAAGGGAGAGACT

altered gDNA sequence snippet

CCATCAGGAAACTCTTCACTACCATTGGTAAGGGAGAGACT

original cDNA sequence snippet

CCATCAGGAAACTCTTCACTGCCATTGGGGTTCTCTTCCCA

altered cDNA sequence snippet

CCATCAGGAAACTCTTCACTACCATTGGGGTTCTCTTCCCA

wildtype AA sequence

MSTGPDVKAT VGDISSDGNL NVAQEECSRK GFCSVRHGLA LILQLCNFSI YTQQMNLSIA
IPAMVNNTAP PSQPNASTER PSTDSQGYWN ETLKEFKAMS GILSALPFVV GCICIILGGL
LADFLLSRKI LRLITIRKLF TAIGVLFPSV ILVSLPWVRS SHSMTMTFLV LSSAISSFCE
SGALVNFLDI APRYTGFLKG LLQVFAHIAG AISPTAAGFF ISQDSEFGWR NVFLLSAAVN
ISGLVFYLIF GRADVQDWAK EQTFTHL*

mutated AA sequence

MSTGPDVKAT VGDISSDGNL NVAQEECSRK GFCSVRHGLA LILQLCNFSI YTQQMNLSIA
IPAMVNNTAP PSQPNASTER PSTDSQGYWN ETLKEFKAMS GILSALPFVV GCICIILGGL
LADFLLSRKI LRLITIRKLF TTIGVLFPSV ILVSLPWVRS SHSMTMTFLV LSSAISSFCE
SGALVNFLDI APRYTGFLKG LLQVFAHIAG AISPTAAGFF ISQDSEFGWR NVFLLSAAVN
ISGLVFYLIF GRADVQDWAK EQTFTHL*

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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999788467 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:25776949G>AN/A show variant in all transcripts IGV

HGNC symbol

SLC17A4

Ensembl transcript ID

ENST00000397076

Genbank transcript ID

N/A

UniProt peptide

Q9Y2C5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.424G>A
cDNA.726G>A
g.22023G>A

AA changes

A142T Score: 58 explain score(s)

position(s) of altered AA
if AA alteration in CDS

142

frameshift

known variant

Reference ID: rs11754288

database	homozygous (A/A)	heterozygous	allele carriers
1000G	245	812	1057
ExAC	9199	14369	23568

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.496	0.005
	-0.673	0
(flanking)	0.772	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc increased	22026	wt: 0.60 / mu: 0.75	wt: TCAGGAAACTCTTCACTGCCATTGGTAAGGGAGAGACTGGA mu: TCAGGAAACTCTTCACTACCATTGGTAAGGGAGAGACTGGA	gcca\|TTGG
Donor marginally increased	22028	wt: 0.9752 / mu: 0.9898 (marginal change - not scored)	wt: GCCATTGGTAAGGGA mu: ACCATTGGTAAGGGA	CATT\|ggta

distance from splice site

127

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

142

mutated

not conserved

142

Ptroglodytes

all identical

ENSPTRG00000017791

372

Mmulatta

all identical

ENSMMUG00000002579

372

Fcatus

no alignment

ENSFCAG00000014669

n/a

Mmusculus

all identical

ENSMUSG00000021336

369

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000086739

379

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
149	169	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
171	191	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
203	223	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
230	250	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	312	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
332	352	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
368	388	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
398	418	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
431	451	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
461	481	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

666 / 666

position (AA) of stopcodon in wt / mu AA sequence

222 / 222

position of stopcodon in wt / mu cDNA

968 / 968

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

303 / 303

chromosome

strand

last intron/exon boundary

1885

theoretical NMD boundary in CDS

1532

length of CDS

666

coding sequence (CDS) position

424

cDNA position
(for ins/del: last normal base / first normal base)

726

gDNA position
(for ins/del: last normal base / first normal base)

22023

chromosomal position
(for ins/del: last normal base / first normal base)

25776949

original gDNA sequence snippet

CCATCAGGAAACTCTTCACTGCCATTGGTAAGGGAGAGACT

altered gDNA sequence snippet

CCATCAGGAAACTCTTCACTACCATTGGTAAGGGAGAGACT

original cDNA sequence snippet

CCATCAGGAAACTCTTCACTGCCATTGGTAAGGGAGAGACT

altered cDNA sequence snippet

CCATCAGGAAACTCTTCACTACCATTGGTAAGGGAGAGACT

wildtype AA sequence

MNLSIAIPAM VNNTAPPSQP NASTERPSTD SQGYWNETLK EFKAMDCSPG WSLPIRAMIK
SLPLWAILVS YFCEYWLFYT IMAYTPTYIS SVLQANLRDS GILSALPFVV GCICIILGGL
LADFLLSRKI LRLITIRKLF TAIGKGETGH RGERGKLRAA FSLLCVCPPT PGVLFPSVIL
VSLPWVRSSH SMTMTFLVLS SAISSFCESG ALVNFLDIAP R*

mutated AA sequence

MNLSIAIPAM VNNTAPPSQP NASTERPSTD SQGYWNETLK EFKAMDCSPG WSLPIRAMIK
SLPLWAILVS YFCEYWLFYT IMAYTPTYIS SVLQANLRDS GILSALPFVV GCICIILGGL
LADFLLSRKI LRLITIRKLF TTIGKGETGH RGERGKLRAA FSLLCVCPPT PGVLFPSVIL
VSLPWVRSSH SMTMTFLVLS SAISSFCESG ALVNFLDIAP R*

speed

0.76 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999526117 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:25776949G>AN/A show variant in all transcripts IGV

HGNC symbol

SLC17A4

Ensembl transcript ID

ENST00000377905

Genbank transcript ID

NM_005495

UniProt peptide

Q9Y2C5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1114G>A
cDNA.1233G>A
g.22023G>A

AA changes

A372T Score: 58 explain score(s)

position(s) of altered AA
if AA alteration in CDS

372

frameshift

known variant

Reference ID: rs11754288

database	homozygous (A/A)	heterozygous	allele carriers
1000G	245	812	1057
ExAC	9199	14369	23568

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.496	0.005
	-0.673	0
(flanking)	0.772	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc increased	22026	wt: 0.60 / mu: 0.75	wt: TCAGGAAACTCTTCACTGCCATTGGTAAGGGAGAGACTGGA mu: TCAGGAAACTCTTCACTACCATTGGTAAGGGAGAGACTGGA	gcca\|TTGG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

372

mutated

not conserved

372

Ptroglodytes

all identical

ENSPTRG00000017791

372

Mmulatta

all identical

ENSMMUG00000002579

372

Fcatus

no alignment

ENSFCAG00000014669

n/a

Mmusculus

all identical

ENSMUSG00000021336

369

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000086739

379

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
368	388	TRANSMEM	Helical; (Potential).	lost
398	418	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
431	451	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
461	481	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1494 / 1494

position (AA) of stopcodon in wt / mu AA sequence

498 / 498

position of stopcodon in wt / mu cDNA

1613 / 1613

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

120 / 120

chromosome

strand

last intron/exon boundary

1479

theoretical NMD boundary in CDS

1309

length of CDS

1494

coding sequence (CDS) position

1114

cDNA position
(for ins/del: last normal base / first normal base)

1233

gDNA position
(for ins/del: last normal base / first normal base)

22023

chromosomal position
(for ins/del: last normal base / first normal base)

25776949

original gDNA sequence snippet

CCATCAGGAAACTCTTCACTGCCATTGGTAAGGGAGAGACT

altered gDNA sequence snippet

CCATCAGGAAACTCTTCACTACCATTGGTAAGGGAGAGACT

original cDNA sequence snippet

CCATCAGGAAACTCTTCACTGCCATTGGGGTTCTCTTCCCA

altered cDNA sequence snippet

CCATCAGGAAACTCTTCACTACCATTGGGGTTCTCTTCCCA

wildtype AA sequence

MSTGPDVKAT VGDISSDGNL NVAQEECSRK GFCSVRHGLA LILQLCNFSI YTQQMNLSIA
IPAMVNNTAP PSQPNASTER PSTDSQGYWN ETLKEFKAMA PAYDWSPEIQ GIILSSLNYG
SFLAPIPSGY VAGIFGAKYV VGAGLFISSF LTLFIPLAAN AGVALLIVLR IVQGIAQVMV
LTGQYSIWVK WAPPLERSQL TTIAGSGSML GSFIVLLAGG LLCQTIGWPY VFYIFGGIGC
ACCPLWFPLI YDDPVNHPFI SAGEKRYIVC SLAQQDCSPG WSLPIRAMIK SLPLWAILVS
YFCEYWLFYT IMAYTPTYIS SVLQANLRDS GILSALPFVV GCICIILGGL LADFLLSRKI
LRLITIRKLF TAIGVLFPSV ILVSLPWVRS SHSMTMTFLV LSSAISSFCE SGALVNFLDI
APRYTGFLKG LLQVFAHIAG AISPTAAGFF ISQDSEFGWR NVFLLSAAVN ISGLVFYLIF
GRADVQDWAK EQTFTHL*

mutated AA sequence

MSTGPDVKAT VGDISSDGNL NVAQEECSRK GFCSVRHGLA LILQLCNFSI YTQQMNLSIA
IPAMVNNTAP PSQPNASTER PSTDSQGYWN ETLKEFKAMA PAYDWSPEIQ GIILSSLNYG
SFLAPIPSGY VAGIFGAKYV VGAGLFISSF LTLFIPLAAN AGVALLIVLR IVQGIAQVMV
LTGQYSIWVK WAPPLERSQL TTIAGSGSML GSFIVLLAGG LLCQTIGWPY VFYIFGGIGC
ACCPLWFPLI YDDPVNHPFI SAGEKRYIVC SLAQQDCSPG WSLPIRAMIK SLPLWAILVS
YFCEYWLFYT IMAYTPTYIS SVLQANLRDS GILSALPFVV GCICIILGGL LADFLLSRKI
LRLITIRKLF TTIGVLFPSV ILVSLPWVRS SHSMTMTFLV LSSAISSFCE SGALVNFLDI
APRYTGFLKG LLQVFAHIAG AISPTAAGFF ISQDSEFGWR NVFLLSAAVN ISGLVFYLIF
GRADVQDWAK EQTFTHL*

speed

0.92 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems