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 3.36163 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADSL	disease_causing_automatic	0.999999999952266	simple_aae		affected	0	R426H	single base exchange	rs119450941		show file
ADSL	disease_causing_automatic	0.999999999952266	simple_aae		affected	0	R440H	single base exchange	rs119450941		show file
ADSL	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs119450941		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999952266 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990123)
known disease mutation: rs2462 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40760969G>AN/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.1277G>A
cDNA.1333G>A
g.18463G>A

AA changes

R426H Score: 29 explain score(s)

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

426

frameshift

known variant

Reference ID: rs119450941

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	31	31

known disease mutation: rs2462 (pathogenic for Adenylosuccinate lyase deficiency|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990123)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990123)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990123)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.452	1
	5.525	0.999
(flanking)	-2.575	0.041

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
Donor increased	18465	wt: 0.52 / mu: 0.63	wt: AGCGTATCCAGGTTG mu: AGCATATCCAGGTTG	CGTA\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

426

mutated

not conserved

426

Ptroglodytes

all identical

ENSPTRG00000014407

426

Mmulatta

all identical

ENSMMUG00000005341

305

Fcatus

all identical

ENSFCAG00000004798

426

Mmusculus

all identical

ENSMUSG00000022407

426

Ggallus

all identical

ENSGALG00000012034

427

Trubripes

all identical

ENSTRUG00000001024

442

Drerio

all identical

ENSDARG00000017049

424

Dmelanogaster

all identical

FBgn0038467

421

Celegans

all conserved

R06C7.5

422

Xtropicalis

all identical

ENSXETG00000006328

445

protein features

start (aa)	end (aa)	feature	details
423	429	HELIX		lost
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

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

1277

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

1333

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

18463

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

40760969

original gDNA sequence snippet

TGACAATGACCTCATAGAGCGTATCCAGGTTGATGCCTACT

altered gDNA sequence snippet

TGACAATGACCTCATAGAGCATATCCAGGTTGATGCCTACT

original cDNA sequence snippet

TGACAATGACCTCATAGAGCGTATCCAGGTTGATGCCTACT

altered cDNA sequence snippet

TGACAATGACCTCATAGAGCATATCCAGGTTGATGCCTACT

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
NDLIEHIQVD AYFSPIHSQL DHLLDPSSFT GRASQQVQRF LEEEVYPLLK PYESVMKVKA
ELCL*

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

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999952266 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990123)
known disease mutation: rs2462 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40760969G>AN/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.1319G>A
cDNA.1350G>A
g.18463G>A

AA changes

R440H Score: 29 explain score(s)

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

440

frameshift

known variant

Reference ID: rs119450941

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	31	31

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.452	1
	5.525	0.999
(flanking)	-2.575	0.041

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
Donor increased	18465	wt: 0.52 / mu: 0.63	wt: AGCGTATCCAGGTTG mu: AGCATATCCAGGTTG	CGTA\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

440

mutated

not conserved

440

Ptroglodytes

all identical

ENSPTRG00000014407

426

Mmulatta

all identical

ENSMMUG00000005341

306

Fcatus

all identical

ENSFCAG00000004798

426

Mmusculus

all identical

ENSMUSG00000022407

426

Ggallus

all identical

ENSGALG00000012034

427

Trubripes

all identical

ENSTRUG00000001024

442

Drerio

all identical

ENSDARG00000017049

424

Dmelanogaster

all identical

FBgn0038467

421

Celegans

all conserved

R06C7.5

422

Xtropicalis

all identical

ENSXETG00000006328

445

protein features

start (aa)	end (aa)	feature	details
440	443	HELIX		lost
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

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

1319

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

1350

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

18463

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

40760969

original gDNA sequence snippet

TGACAATGACCTCATAGAGCGTATCCAGGTTGATGCCTACT

altered gDNA sequence snippet

TGACAATGACCTCATAGAGCATATCCAGGTTGATGCCTACT

original cDNA sequence snippet

TGACAATGACCTCATAGAGCGTATCCAGGTTGATGCCTACT

altered cDNA sequence snippet

TGACAATGACCTCATAGAGCATATCCAGGTTGATGCCTACT

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 EGGDNDLIEH IQVDAYFSPI HSQLDHLLDP SSFTGRASQQ VQRFLEEEVY
PLLKPYESVM KVKAELCL*

speed

0.31 s

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 CM990123)
known disease mutation: rs2462 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40760969G>AN/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.18463G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs119450941

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	31	31

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.452	1
	5.525	0.999
(flanking)	-2.575	0.041

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
Donor increased	18465	wt: 0.52 / mu: 0.63	wt: AGCGTATCCAGGTTG mu: AGCATATCCAGGTTG	CGTA\|tcca

distance from splice site

600

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)

18463

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

40760969

original gDNA sequence snippet

TGACAATGACCTCATAGAGCGTATCCAGGTTGATGCCTACT

altered gDNA sequence snippet

TGACAATGACCTCATAGAGCATATCCAGGTTGATGCCTACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.28 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