MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000389048
Querying Taster for transcript #2: ENST00000431873
MT speed 0 s - this script 3.915164 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALK	disease_causing_automatic	0.999999999626037	simple_aae			0	I1250T	single base exchange	rs113994092		show file
ALK	disease_causing_automatic	1	without_aae			0		single base exchange	rs113994092		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999626037 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM088295)
known disease mutation: rs21867 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:29432739A>GN/A show variant in all transcripts IGV

HGNC symbol

ALK

Ensembl transcript ID

ENST00000389048

Genbank transcript ID

NM_004304

UniProt peptide

Q9UM73

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3749T>C
cDNA.4656T>C
g.711694T>C

AA changes

I1250T Score: 89 explain score(s)

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

1250

frameshift

known variant

Reference ID: rs113994092
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs21867 (pathogenic for Neuroblastoma|Neuroblastoma 3) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM088295)

known disease mutation at this position, please check HGMD for details (HGMD ID CM088295)
known disease mutation at this position, please check HGMD for details (HGMD ID CM088295)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.686	1
	4.681	1
(flanking)	4.681	1

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	711688	wt: 0.9860 / mu: 0.9873 (marginal change - not scored)	wt: ATGCATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACT mu: ATGCATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACT	ccag\|AGAC
Acc marginally increased	711689	wt: 0.8350 / mu: 0.9027 (marginal change - not scored)	wt: TGCATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACTG mu: TGCATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACTG	caga\|GACA
Acc marginally increased	711686	wt: 0.9836 / mu: 0.9866 (marginal change - not scored)	wt: AAATGCATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAA mu: AAATGCATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAA	tccc\|AGAG
Acc marginally increased	711691	wt: 0.8268 / mu: 0.8585 (marginal change - not scored)	wt: CATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACTGCC mu: CATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACTGCC	gaga\|CATT
Donor marginally increased	711689	wt: 0.8036 / mu: 0.8789 (marginal change - not scored)	wt: CCCAGAGACATTGCT mu: CCCAGAGACACTGCT	CAGA\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1250

mutated

not conserved

1250

Ptroglodytes

all identical

ENSPTRG00000011796

1246

Mmulatta

all identical

ENSMMUG00000010265

1249

Fcatus

all identical

ENSFCAG00000001792

1251

Mmusculus

all identical

ENSMUSG00000055471

1254

Ggallus

all identical

ENSGALG00000009034

825

Trubripes

no homologue

Drerio

all identical

ENSDARG00000095833

723

Dmelanogaster

all identical

FBgn0040505

1327

Celegans

all identical

T10H9.2

1107

Xtropicalis

all identical

ENSXETG00000031142

819

protein features

start (aa)	end (aa)	feature	details
1060	1620	TOPO_DOM	Cytoplasmic (Potential).	lost
1116	1392	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4863 / 4863

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

1621 / 1621

position of stopcodon in wt / mu cDNA

5770 / 5770

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

908 / 908

chromosome

strand

-1

last intron/exon boundary

5072

theoretical NMD boundary in CDS

4114

length of CDS

4863

coding sequence (CDS) position

3749

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

4656

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

711694

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

29432739

original gDNA sequence snippet

TTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACTGCCTCT

altered gDNA sequence snippet

TTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACTGCCTCT

original cDNA sequence snippet

CCACTTCATCCACCGAGACATTGCTGCCAGAAACTGCCTCT

altered cDNA sequence snippet

CCACTTCATCCACCGAGACACTGCTGCCAGAAACTGCCTCT

wildtype AA sequence

MGAIGLLWLL PLLLSTAAVG SGMGTGQRAG SPAAGPPLQP REPLSYSRLQ RKSLAVDFVV
PSLFRVYARD LLLPPSSSEL KAGRPEARGS LALDCAPLLR LLGPAPGVSW TAGSPAPAEA
RTLSRVLKGG SVRKLRRAKQ LVLELGEEAI LEGCVGPPGE AAVGLLQFNL SELFSWWIRQ
GEGRLRIRLM PEKKASEVGR EGRLSAAIRA SQPRLLFQIF GTGHSSLESP TNMPSPSPDY
FTWNLTWIMK DSFPFLSHRS RYGLECSFDF PCELEYSPPL HDLRNQSWSW RRIPSEEASQ
MDLLDGPGAE RSKEMPRGSF LLLNTSADSK HTILSPWMRS SSEHCTLAVS VHRHLQPSGR
YIAQLLPHNE AAREILLMPT PGKHGWTVLQ GRIGRPDNPF RVALEYISSG NRSLSAVDFF
ALKNCSEGTS PGSKMALQSS FTCWNGTVLQ LGQACDFHQD CAQGEDESQM CRKLPVGFYC
NFEDGFCGWT QGTLSPHTPQ WQVRTLKDAR FQDHQDHALL LSTTDVPASE SATVTSATFP
APIKSSPCEL RMSWLIRGVL RGNVSLVLVE NKTGKEQGRM VWHVAAYEGL SLWQWMVLPL
LDVSDRFWLQ MVAWWGQGSR AIVAFDNISI SLDCYLTISG EDKILQNTAP KSRNLFERNP
NKELKPGENS PRQTPIFDPT VHWLFTTCGA SGPHGPTQAQ CNNAYQNSNL SVEVGSEGPL
KGIQIWKVPA TDTYSISGYG AAGGKGGKNT MMRSHGVSVL GIFNLEKDDM LYILVGQQGE
DACPSTNQLI QKVCIGENNV IEEEIRVNRS VHEWAGGGGG GGGATYVFKM KDGVPVPLII
AAGGGGRAYG AKTDTFHPER LENNSSVLGL NGNSGAAGGG GGWNDNTSLL WAGKSLQEGA
TGGHSCPQAM KKWGWETRGG FGGGGGGCSS GGGGGGYIGG NAASNNDPEM DGEDGVSFIS
PLGILYTPAL KVMEGHGEVN IKHYLNCSHC EVDECHMDPE SHKVICFCDH GTVLAEDGVS
CIVSPTPEPH LPLSLILSVV TSALVAALVL AFSGIMIVYR RKHQELQAMQ MELQSPEYKL
SKLRTSTIMT DYNPNYCFAG KTSSISDLKE VPRKNITLIR GLGHGAFGEV YEGQVSGMPN
DPSPLQVAVK TLPEVCSEQD ELDFLMEALI ISKFNHQNIV RCIGVSLQSL PRFILLELMA
GGDLKSFLRE TRPRPSQPSS LAMLDLLHVA RDIACGCQYL EENHFIHRDI AARNCLLTCP
GPGRVAKIGD FGMARDIYRA SYYRKGGCAM LPVKWMPPEA FMEGIFTSKT DTWSFGVLLW
EIFSLGYMPY PSKSNQEVLE FVTSGGRMDP PKNCPGPVYR IMTQCWQHQP EDRPNFAIIL
ERIEYCTQDP DVINTALPIE YGPLVEEEEK VPVRPKDPEG VPPLLVSQQA KREEERSPAA
PPPLPTTSSG KAAKKPTAAE ISVRVPRGPA VEGGHVNMAF SQSNPPSELH KVHGSRNKPT
SLWNPTYGSW FTEKPTKKNN PIAKKEPHDR GNLGLEGSCT VPPNVATGRL PGASLLLEPS
SLTANMKEVP LFRLRHFPCG NVNYGYQQQG LPLEAATAPG AGHYEDTILK SKNSMNQPGP
*

mutated AA sequence

MGAIGLLWLL PLLLSTAAVG SGMGTGQRAG SPAAGPPLQP REPLSYSRLQ RKSLAVDFVV
PSLFRVYARD LLLPPSSSEL KAGRPEARGS LALDCAPLLR LLGPAPGVSW TAGSPAPAEA
RTLSRVLKGG SVRKLRRAKQ LVLELGEEAI LEGCVGPPGE AAVGLLQFNL SELFSWWIRQ
GEGRLRIRLM PEKKASEVGR EGRLSAAIRA SQPRLLFQIF GTGHSSLESP TNMPSPSPDY
FTWNLTWIMK DSFPFLSHRS RYGLECSFDF PCELEYSPPL HDLRNQSWSW RRIPSEEASQ
MDLLDGPGAE RSKEMPRGSF LLLNTSADSK HTILSPWMRS SSEHCTLAVS VHRHLQPSGR
YIAQLLPHNE AAREILLMPT PGKHGWTVLQ GRIGRPDNPF RVALEYISSG NRSLSAVDFF
ALKNCSEGTS PGSKMALQSS FTCWNGTVLQ LGQACDFHQD CAQGEDESQM CRKLPVGFYC
NFEDGFCGWT QGTLSPHTPQ WQVRTLKDAR FQDHQDHALL LSTTDVPASE SATVTSATFP
APIKSSPCEL RMSWLIRGVL RGNVSLVLVE NKTGKEQGRM VWHVAAYEGL SLWQWMVLPL
LDVSDRFWLQ MVAWWGQGSR AIVAFDNISI SLDCYLTISG EDKILQNTAP KSRNLFERNP
NKELKPGENS PRQTPIFDPT VHWLFTTCGA SGPHGPTQAQ CNNAYQNSNL SVEVGSEGPL
KGIQIWKVPA TDTYSISGYG AAGGKGGKNT MMRSHGVSVL GIFNLEKDDM LYILVGQQGE
DACPSTNQLI QKVCIGENNV IEEEIRVNRS VHEWAGGGGG GGGATYVFKM KDGVPVPLII
AAGGGGRAYG AKTDTFHPER LENNSSVLGL NGNSGAAGGG GGWNDNTSLL WAGKSLQEGA
TGGHSCPQAM KKWGWETRGG FGGGGGGCSS GGGGGGYIGG NAASNNDPEM DGEDGVSFIS
PLGILYTPAL KVMEGHGEVN IKHYLNCSHC EVDECHMDPE SHKVICFCDH GTVLAEDGVS
CIVSPTPEPH LPLSLILSVV TSALVAALVL AFSGIMIVYR RKHQELQAMQ MELQSPEYKL
SKLRTSTIMT DYNPNYCFAG KTSSISDLKE VPRKNITLIR GLGHGAFGEV YEGQVSGMPN
DPSPLQVAVK TLPEVCSEQD ELDFLMEALI ISKFNHQNIV RCIGVSLQSL PRFILLELMA
GGDLKSFLRE TRPRPSQPSS LAMLDLLHVA RDIACGCQYL EENHFIHRDT AARNCLLTCP
GPGRVAKIGD FGMARDIYRA SYYRKGGCAM LPVKWMPPEA FMEGIFTSKT DTWSFGVLLW
EIFSLGYMPY PSKSNQEVLE FVTSGGRMDP PKNCPGPVYR IMTQCWQHQP EDRPNFAIIL
ERIEYCTQDP DVINTALPIE YGPLVEEEEK VPVRPKDPEG VPPLLVSQQA KREEERSPAA
PPPLPTTSSG KAAKKPTAAE ISVRVPRGPA VEGGHVNMAF SQSNPPSELH KVHGSRNKPT
SLWNPTYGSW FTEKPTKKNN PIAKKEPHDR GNLGLEGSCT VPPNVATGRL PGASLLLEPS
SLTANMKEVP LFRLRHFPCG NVNYGYQQQG LPLEAATAPG AGHYEDTILK SKNSMNQPGP
*

speed

1.10 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

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 CM088295)
known disease mutation: rs21867 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:29432739A>GN/A show variant in all transcripts IGV

HGNC symbol

ALK

Ensembl transcript ID

ENST00000431873

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.711694T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.686	1
	4.681	1
(flanking)	4.681	1

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	711688	wt: 0.9860 / mu: 0.9873 (marginal change - not scored)	wt: ATGCATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACT mu: ATGCATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACT	ccag\|AGAC
Acc marginally increased	711689	wt: 0.8350 / mu: 0.9027 (marginal change - not scored)	wt: TGCATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACTG mu: TGCATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACTG	caga\|GACA
Acc marginally increased	711686	wt: 0.9836 / mu: 0.9866 (marginal change - not scored)	wt: AAATGCATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAA mu: AAATGCATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAA	tccc\|AGAG
Acc marginally increased	711691	wt: 0.8268 / mu: 0.8585 (marginal change - not scored)	wt: CATTTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACTGCC mu: CATTTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACTGCC	gaga\|CATT
Donor marginally increased	711689	wt: 0.8036 / mu: 0.8789 (marginal change - not scored)	wt: CCCAGAGACATTGCT mu: CCCAGAGACACTGCT	CAGA\|gaca

distance from splice site

1828

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

793

theoretical NMD boundary in CDS

742

length of CDS

1353

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)

711694

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

29432739

original gDNA sequence snippet

TTCCTTTCTTCCCAGAGACATTGCTGCCAGAAACTGCCTCT

altered gDNA sequence snippet

TTCCTTTCTTCCCAGAGACACTGCTGCCAGAAACTGCCTCT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.87 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems