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 4.883235 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADSL	disease_causing	0.999999817632252	simple_aae		affected		R204Q	single base exchange	rs28941471		show file
ADSL	disease_causing	0.999999864474822	simple_aae		affected		R190Q	single base exchange	rs28941471		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999817632252 (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known as potential disease variant: rs2465 (probable pathogenic)
known disease mutation at this position (HGMD CM990119)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40754954G>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.611G>A
cDNA.642G>A
g.12448G>A

AA changes

R204Q Score: 43 explain score(s)

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

204

frameshift

known variant

Reference ID: rs28941471

database	homozygous (A/A)	heterozygous	allele carriers
1000G	0	5	5
ExAC	0	8	8

known as potential disease variant: rs2465 (probable pathogenic for Adenylosuccinate lyase deficiency|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990119)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990119)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990119)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.767	1
	2.356	0.983
(flanking)	-1.709	0.071

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 gained	12444	0.33	mu: AGCGTGTCCAAGATG	CGTG\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

204

mutated

all conserved

204

Ptroglodytes

all identical

ENSPTRG00000014407

190

Mmulatta

all identical

ENSMMUG00000005341

Fcatus

all identical

ENSFCAG00000004798

190

Mmusculus

all identical

ENSMUSG00000022407

190

Ggallus

all identical

ENSGALG00000012034

191

Trubripes

all identical

ENSTRUG00000001024

206

Drerio

all identical

ENSDARG00000017049

188

Dmelanogaster

not conserved

FBgn0038467

185

Celegans

all identical

R06C7.5

186

Xtropicalis

all identical

ENSXETG00000006328

209

protein features

start (aa)	end (aa)	feature	details
201	204	STRAND		lost
206	211	HELIX		might get lost (downstream of altered splice site)
212	214	TURN		might get lost (downstream of altered splice site)
216	229	HELIX		might get lost (downstream of altered splice site)
240	242	STRAND		might get lost (downstream of altered splice site)
246	274	HELIX		might get lost (downstream of altered splice site)
277	279	STRAND		might get lost (downstream of altered splice site)
295	295	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
299	313	HELIX		might get lost (downstream of altered splice site)
316	323	HELIX		might get lost (downstream of altered splice site)
331	333	HELIX		might get lost (downstream of altered splice site)
334	360	HELIX		might get lost (downstream of altered splice site)
366	380	HELIX		might get lost (downstream of altered splice site)
382	389	HELIX		might get lost (downstream of altered splice site)
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

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

611

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

642

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

12448

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

40754954

original gDNA sequence snippet

CCAGAACTTGAAGCGTGTCCGAGATGACCTGCGCTTCCGGG

altered gDNA sequence snippet

CCAGAACTTGAAGCGTGTCCAAGATGACCTGCGCTTCCGGG

original cDNA sequence snippet

CCAGAACTTGAAGCGTGTCCGAGATGACCTGCGCTTCCGGG

altered cDNA sequence snippet

CCAGAACTTGAAGCGTGTCCAAGATGACCTGCGCTTCCGGG

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 KRVQDDLRFR 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*

speed

1.34 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: 0.999999864474822 (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known as potential disease variant: rs2465 (probable pathogenic)
known disease mutation at this position (HGMD CM990119)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:40754954G>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.569G>A
cDNA.625G>A
g.12448G>A

AA changes

R190Q Score: 43 explain score(s)

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

190

frameshift

known variant

Reference ID: rs28941471

database	homozygous (A/A)	heterozygous	allele carriers
1000G	0	5	5
ExAC	0	8	8

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.767	1
	2.356	0.983
(flanking)	-1.709	0.071

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 gained	12444	0.33	mu: AGCGTGTCCAAGATG	CGTG\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

190

mutated

all conserved

190

Ptroglodytes

all identical

ENSPTRG00000014407

190

Mmulatta

all identical

ENSMMUG00000005341

Fcatus

all identical

ENSFCAG00000004798

190

Mmusculus

all identical

ENSMUSG00000022407

190

Ggallus

all identical

ENSGALG00000012034

191

Trubripes

all identical

ENSTRUG00000001024

206

Drerio

all identical

ENSDARG00000017049

188

Dmelanogaster

not conserved

FBgn0038467

185

Celegans

all identical

R06C7.5

186

Xtropicalis

all identical

ENSXETG00000006328

209

protein features

start (aa)	end (aa)	feature	details
168	192	HELIX		lost
201	204	STRAND		might get lost (downstream of altered splice site)
206	211	HELIX		might get lost (downstream of altered splice site)
212	214	TURN		might get lost (downstream of altered splice site)
216	229	HELIX		might get lost (downstream of altered splice site)
240	242	STRAND		might get lost (downstream of altered splice site)
246	274	HELIX		might get lost (downstream of altered splice site)
277	279	STRAND		might get lost (downstream of altered splice site)
295	295	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
299	313	HELIX		might get lost (downstream of altered splice site)
316	323	HELIX		might get lost (downstream of altered splice site)
331	333	HELIX		might get lost (downstream of altered splice site)
334	360	HELIX		might get lost (downstream of altered splice site)
366	380	HELIX		might get lost (downstream of altered splice site)
382	389	HELIX		might get lost (downstream of altered splice site)
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

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

569

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

625

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

12448

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

40754954

original gDNA sequence snippet

CCAGAACTTGAAGCGTGTCCGAGATGACCTGCGCTTCCGGG

altered gDNA sequence snippet

CCAGAACTTGAAGCGTGTCCAAGATGACCTGCGCTTCCGGG

original cDNA sequence snippet

CCAGAACTTGAAGCGTGTCCGAGATGACCTGCGCTTCCGGG

altered cDNA sequence snippet

CCAGAACTTGAAGCGTGTCCAAGATGACCTGCGCTTCCGGG

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
MDLQNLKRVQ 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*

speed

1.38 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems