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: ENST00000216194
Querying Taster for transcript #2: ENST00000342312
Querying Taster for transcript #3: ENST00000454266
MT speed 0 s - this script 3.673843 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADSL	disease_causing_automatic	0.206945119012031	simple_aae		affected	0	S438P	single base exchange	rs119450940		show file
ADSL	disease_causing_automatic	0.206945119012031	simple_aae		affected	0	S452P	single base exchange	rs119450940		show file
ADSL	disease_causing_automatic	0.99999999891328	without_aae		affected	0		single base exchange	rs119450940		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.206945119012031 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM920008)
known disease mutation: rs2461 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40761004T>CN/A show variant in all transcripts IGV

HGNC symbol

ADSL

Ensembl transcript ID

ENST00000216194

Genbank transcript ID

NM_000026

UniProt peptide

P30566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1312T>C
cDNA.1368T>C
g.18498T>C

AA changes

S438P Score: 74 explain score(s)

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

438

frameshift

known variant

Reference ID: rs119450940
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2461 (pathogenic for Adenylosuccinate lyase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920008)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920008)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920008)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.012	0.938
	1.246	0.952
(flanking)	1.586	0.952

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 marginally increased	18499	wt: 0.5057 / mu: 0.5123 (marginal change - not scored)	wt: CTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTGG mu: CTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTGG	actc\|CCAG
Acc increased	18495	wt: 0.77 / mu: 0.86	wt: ATGCCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTA mu: ATGCCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTA	attc\|ACTC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

438

mutated

not conserved

438

Ptroglodytes

all identical

ENSPTRG00000014407

438

Mmulatta

all identical

ENSMMUG00000005341

317

Fcatus

all identical

ENSFCAG00000004798

438

Mmusculus

all identical

ENSMUSG00000022407

438

Ggallus

not conserved

ENSGALG00000012034

439

Trubripes

not conserved

ENSTRUG00000001024

454

Drerio

not conserved

ENSDARG00000017049

436

Dmelanogaster

not conserved

FBgn0038467

433

Celegans

not conserved

R06C7.5

431

Xtropicalis

all conserved

ENSXETG00000006328

457

protein features

start (aa)	end (aa)	feature	details
434	437	HELIX		might get lost (downstream of altered splice site)
440	443	HELIX		might get lost (downstream of altered splice site)
446	449	HELIX		might get lost (downstream of altered splice site)
453	463	HELIX		might get lost (downstream of altered splice site)
465	469	HELIX		might get lost (downstream of altered splice site)
470	472	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1455 / 1455

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

485 / 485

position of stopcodon in wt / mu cDNA

1511 / 1511

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

57 / 57

chromosome

strand

last intron/exon boundary

1425

theoretical NMD boundary in CDS

1318

length of CDS

1455

coding sequence (CDS) position

1312

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

1368

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

18498

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

40761004

original gDNA sequence snippet

CCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTG

altered gDNA sequence snippet

CCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTG

original cDNA sequence snippet

CCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTG

altered cDNA sequence snippet

CCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTG

wildtype AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTD
LIILRNALDL LLPKLARVIS RLADFAKERA SLPTLGFTHF QPAQLTTVGK RCCLWIQDLC
MDLQNLKRVR DDLRFRGVKG TTGTQASFLQ LFEGDDHKVE QLDKMVTEKA GFKRAFIITG
QTYTRKVDIE VLSVLASLGA SVHKICTDIR LLANLKEMEE PFEKQQIGSS AMPYKRNPMR
SERCCSLARH LMTLVMDPLQ TASVQWFERT LDDSANRRIC LAEAFLTADT ILNTLQNISE
GLVVYPKVIE RRIRQELPFM ATENIIMAMV KAGGSRQDCH EKIRVLSQQA ASVVKQEGGD
NDLIERIQVD AYFSPIHSQL DHLLDPSSFT GRASQQVQRF LEEEVYPLLK PYESVMKVKA
ELCL*

mutated AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTD
LIILRNALDL LLPKLARVIS RLADFAKERA SLPTLGFTHF QPAQLTTVGK RCCLWIQDLC
MDLQNLKRVR DDLRFRGVKG TTGTQASFLQ LFEGDDHKVE QLDKMVTEKA GFKRAFIITG
QTYTRKVDIE VLSVLASLGA SVHKICTDIR LLANLKEMEE PFEKQQIGSS AMPYKRNPMR
SERCCSLARH LMTLVMDPLQ TASVQWFERT LDDSANRRIC LAEAFLTADT ILNTLQNISE
GLVVYPKVIE RRIRQELPFM ATENIIMAMV KAGGSRQDCH EKIRVLSQQA ASVVKQEGGD
NDLIERIQVD AYFSPIHPQL DHLLDPSSFT GRASQQVQRF LEEEVYPLLK PYESVMKVKA
ELCL*

speed

0.79 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

disease causing

Model: simple_aae, prob: 0.206945119012031 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM920008)
known disease mutation: rs2461 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40761004T>CN/A show variant in all transcripts IGV

HGNC symbol

ADSL

Ensembl transcript ID

ENST00000454266

Genbank transcript ID

N/A

UniProt peptide

P30566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1354T>C
cDNA.1385T>C
g.18498T>C

AA changes

S452P Score: 74 explain score(s)

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

452

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.012	0.938
	1.246	0.952
(flanking)	1.586	0.952

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 marginally increased	18499	wt: 0.5057 / mu: 0.5123 (marginal change - not scored)	wt: CTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTGG mu: CTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTGG	actc\|CCAG
Acc increased	18495	wt: 0.77 / mu: 0.86	wt: ATGCCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTA mu: ATGCCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTA	attc\|ACTC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

452

mutated

not conserved

452

Ptroglodytes

all identical

ENSPTRG00000014407

438

Mmulatta

all identical

ENSMMUG00000005341

317

Fcatus

all identical

ENSFCAG00000004798

438

Mmusculus

all identical

ENSMUSG00000022407

438

Ggallus

not conserved

ENSGALG00000012034

439

Trubripes

not conserved

ENSTRUG00000001024

454

Drerio

not conserved

ENSDARG00000017049

436

Dmelanogaster

not conserved

FBgn0038467

433

Celegans

not conserved

R06C7.5

434

Xtropicalis

all conserved

ENSXETG00000006328

457

protein features

start (aa)	end (aa)	feature	details
453	463	HELIX		might get lost (downstream of altered splice site)
465	469	HELIX		might get lost (downstream of altered splice site)
470	472	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1497 / 1497

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

499 / 499

position of stopcodon in wt / mu cDNA

1528 / 1528

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

32 / 32

chromosome

strand

last intron/exon boundary

1442

theoretical NMD boundary in CDS

1360

length of CDS

1497

coding sequence (CDS) position

1354

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

1385

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

18498

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

40761004

original gDNA sequence snippet

CCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTG

altered gDNA sequence snippet

CCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTG

original cDNA sequence snippet

CCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTG

altered cDNA sequence snippet

CCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTG

wildtype AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTS
LILSRGVIKA YCNLRLPGSD SSPVSVSQLA RVISRLADFA KERASLPTLG FTHFQPAQLT
TVGKRCCLWI QDLCMDLQNL KRVRDDLRFR GVKGTTGTQA SFLQLFEGDD HKVEQLDKMV
TEKAGFKRAF IITGQTYTRK VDIEVLSVLA SLGASVHKIC TDIRLLANLK EMEEPFEKQQ
IGSSAMPYKR NPMRSERCCS LARHLMTLVM DPLQTASVQW FERTLDDSAN RRICLAEAFL
TADTILNTLQ NISEGLVVYP KVIERRIRQE LPFMATENII MAMVKAGGSR QDCHEKIRVL
SQQAASVVKQ EGGDNDLIER IQVDAYFSPI HSQLDHLLDP SSFTGRASQQ VQRFLEEEVY
PLLKPYESVM KVKAELCL*

mutated AA sequence

MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTS
LILSRGVIKA YCNLRLPGSD SSPVSVSQLA RVISRLADFA KERASLPTLG FTHFQPAQLT
TVGKRCCLWI QDLCMDLQNL KRVRDDLRFR GVKGTTGTQA SFLQLFEGDD HKVEQLDKMV
TEKAGFKRAF IITGQTYTRK VDIEVLSVLA SLGASVHKIC TDIRLLANLK EMEEPFEKQQ
IGSSAMPYKR NPMRSERCCS LARHLMTLVM DPLQTASVQW FERTLDDSAN RRICLAEAFL
TADTILNTLQ NISEGLVVYP KVIERRIRQE LPFMATENII MAMVKAGGSR QDCHEKIRVL
SQQAASVVKQ EGGDNDLIER IQVDAYFSPI HPQLDHLLDP SSFTGRASQQ VQRFLEEEVY
PLLKPYESVM KVKAELCL*

speed

0.76 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 0.99999999891328 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM920008)
known disease mutation: rs2461 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40761004T>CN/A show variant in all transcripts IGV

HGNC symbol

ADSL

Ensembl transcript ID

ENST00000342312

Genbank transcript ID

NM_001123378

UniProt peptide

P30566

alteration type

single base exchange

alteration region

intron

DNA changes

g.18498T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.012	0.938
	1.246	0.952
(flanking)	1.586	0.952

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 marginally increased	18499	wt: 0.5057 / mu: 0.5123 (marginal change - not scored)	wt: CTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTGG mu: CTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTGG	actc\|CCAG
Acc increased	18495	wt: 0.77 / mu: 0.86	wt: ATGCCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTA mu: ATGCCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTA	attc\|ACTC

distance from splice site

635

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
396	416	HELIX		might get lost (downstream of altered splice site)
423	429	HELIX		might get lost (downstream of altered splice site)
431	433	HELIX		might get lost (downstream of altered splice site)
434	437	HELIX		might get lost (downstream of altered splice site)
440	443	HELIX		might get lost (downstream of altered splice site)
446	449	HELIX		might get lost (downstream of altered splice site)
453	463	HELIX		might get lost (downstream of altered splice site)
465	469	HELIX		might get lost (downstream of altered splice site)
470	472	HELIX		might get lost (downstream of altered splice site)

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

28 / 28

chromosome

strand

last intron/exon boundary

1219

theoretical NMD boundary in CDS

1141

length of CDS

1278

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)

18498

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

40761004

original gDNA sequence snippet

CCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTG

altered gDNA sequence snippet

CCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.64 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems