MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000286744
Querying Taster for transcript #2: ENST00000567476
MT speed 2.5 s - this script 4.538254 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADAMTSL3	polymorphism_automatic	2.78999046088302e-13	simple_aae				V661L	single base exchange	rs4842838		show file
ADAMTSL3	polymorphism_automatic	2.78999046088302e-13	simple_aae				V661L	single base exchange	rs4842838		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999721 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:84582124G>TN/A show variant in all transcripts IGV

HGNC symbol

ADAMTSL3

Ensembl transcript ID

ENST00000286744

Genbank transcript ID

NM_207517

UniProt peptide

P82987

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1981G>T
cDNA.2205G>T
g.259287G>T

AA changes

V661L Score: 32 explain score(s)

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

661

frameshift

known variant

Reference ID: rs4842838

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1214	1006	2220
ExAC	22245	-11723	10522

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.527	0.014
	-0.41	0.014
(flanking)	0.721	0.386

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 marginally increased	259288	wt: 0.9496 / mu: 0.9678 (marginal change - not scored)	wt: ATGCGTGGGAGGTAT mu: ATGCTTGGGAGGTAT	GCGT\|ggga
Donor marginally decreased	259292	wt: 0.4921 / mu: 0.4497 (marginal change - not scored)	wt: GTGGGAGGTATTTGA mu: TTGGGAGGTATTTGA	GGGA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

661

mutated

all conserved

661

Ptroglodytes

all conserved

ENSPTRG00000007394

661

Mmulatta

all conserved

ENSMMUG00000013670

661

Fcatus

no alignment

ENSFCAG00000001257

n/a

Mmusculus

all conserved

ENSMUSG00000070469

674

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000027903

661

Dmelanogaster

not conserved

FBgn0051619

556

KIFLE

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000006128

598

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5076 / 5076

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

1692 / 1692

position of stopcodon in wt / mu cDNA

5300 / 5300

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

225 / 225

chromosome

strand

last intron/exon boundary

5194

theoretical NMD boundary in CDS

4919

length of CDS

5076

coding sequence (CDS) position

1981

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

2205

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

259287

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

84582124

original gDNA sequence snippet

CCCCTTGCACAGCAACATGCGTGGGAGGTATTTGAACCTTT

altered gDNA sequence snippet

CCCCTTGCACAGCAACATGCTTGGGAGGTATTTGAACCTTT

original cDNA sequence snippet

CCCCTTGCACAGCAACATGCGTGGGAGGCCATCAAGAAGCC

altered cDNA sequence snippet

CCCCTTGCACAGCAACATGCTTGGGAGGCCATCAAGAAGCC

wildtype AA sequence

MASWTSPWWV LIGMVFMHSP LPQTTAEKSP GAYFLPEFAL SPQGSFLEDT TGEQFLTYRY
DDQTSRNTRS DEDKDGNWDA WGDWSDCSRT CGGGASYSLR RCLTGRNCEG QNIRYKTCSN
HDCPPDAEDF RAQQCSAYND VQYQGHYYEW LPRYNDPAAP CALKCHAQGQ NLVVELAPKV
LDGTRCNTDS LDMCISGICQ AVGCDRQLGS NAKEDNCGVC AGDGSTCRLV RGQSKSHVSP
EKREENVIAV PLGSRSVRIT VKGPAHLFIE SKTLQGSKGE HSFNSPGVFL VENTTVEFQR
GSERQTFKIP GPLMADFIFK TRYTAAKDSV VQFFFYQPIS HQWRQTDFFP CTVTCGGGYQ
LNSAECVDIR LKRVVPDHYC HYYPENVKPK PKLKECSMDP CPSSDGFKEI MPYDHFQPLP
RWEHNPWTAC SVSCGGGIQR RSFVCVEESM HGEILQVEEW KCMYAPKPKV MQTCNLFDCP
KWIAMEWSQC TVTCGRGLRY RVVLCINHRG EHVGGCNPQL KLHIKEECVI PIPCYKPKEK
SPVEAKLPWL KQAQELEETR IATEEPTFIP EPWSACSTTC GPGVQVREVK CRVLLTFTQT
ETELPEEECE GPKLPTERPC LLEACDESPA SRELDIPLPE DSETTYDWEY AGFTPCTATC
VGGHQEAIAV CLHIQTQQTV NDSLCDMVHR PPAMSQACNT EPCPPRWHVG SWGPCSATCG
VGIQTRDVYC LHPGETPAPP EECRDEKPHA LQACNQFDCP PGWHIEEWQQ CSRTCGGGTQ
NRRVTCRQLL TDGSFLNLSD ELCQGPKASS HKSCARTDCP PHLAVGDWSK CSVSCGVGIQ
RRKQVCQRLA AKGRRIPLSE MMCRDLPGLP LVRSCQMPEC SKIKSEMKTK LGEQGPQILS
VQRVYIQTRE EKRINLTIGS RAYLLPNTSV IIKCPVRRFQ KSLIQWEKDG RCLQNSKRLG
ITKSGSLKIH GLAAPDIGVY RCIAGSAQET VVLKLIGTDN RLIARPALRE PMREYPGMDH
SEANSLGVTW HKMRQMWNNK NDLYLDDDHI SNQPFLRALL GHCSNSAGST NSWELKNKQF
EAAVKQGAYS MDTAQFDELI RNMSQLMETG EVSDDLASQL IYQLVAELAK AQPTHMQWRG
IQEETPPAAQ LRGETGSVSQ SSHAKNSGKL TFKPKGPVLM RQSQPPSISF NKTINSRIGN
TVYITKRTEV INILCDLITP SEATYTWTKD GTLLQPSVKI ILDGTGKIQI QNPTRKEQGI
YECSVANHLG SDVESSSVLY AEAPVILSVE RNITKPEHNH LSVVVGGIVE AALGANVTIR
CPVKGVPQPN ITWLKRGGSL SGNVSLLFNG SLLLQNVSLE NEGTYVCIAT NALGKAVATS
VLHLLERRWP ESRIVFLQGH KKYILQATNT RTNSNDPTGE PPPQEPFWEP GNWSHCSATC
GHLGARIQRP QCVMANGQEV SEALCDHLQK PLAGFEPCNI RDCPARWFTS VWSQCSVSCG
EGYHSRQVTC KRTKANGTVQ VVSPRACAPK DRPLGRKPCF GHPCVQWEPG NRCPGRCMGR
AVRMQQRHTA CQHNSSDSNC DDRKRPTLRR NCTSGACDVC WHTGPWKPCT AACGRGFQSR
KVDCIHTRSC KPVAKRHCVQ KKKPISWRHC LGPSCDRDCT DTTHYCMFVK HLNLCSLDRY
KQRCCQSCQE G*

mutated AA sequence

MASWTSPWWV LIGMVFMHSP LPQTTAEKSP GAYFLPEFAL SPQGSFLEDT TGEQFLTYRY
DDQTSRNTRS DEDKDGNWDA WGDWSDCSRT CGGGASYSLR RCLTGRNCEG QNIRYKTCSN
HDCPPDAEDF RAQQCSAYND VQYQGHYYEW LPRYNDPAAP CALKCHAQGQ NLVVELAPKV
LDGTRCNTDS LDMCISGICQ AVGCDRQLGS NAKEDNCGVC AGDGSTCRLV RGQSKSHVSP
EKREENVIAV PLGSRSVRIT VKGPAHLFIE SKTLQGSKGE HSFNSPGVFL VENTTVEFQR
GSERQTFKIP GPLMADFIFK TRYTAAKDSV VQFFFYQPIS HQWRQTDFFP CTVTCGGGYQ
LNSAECVDIR LKRVVPDHYC HYYPENVKPK PKLKECSMDP CPSSDGFKEI MPYDHFQPLP
RWEHNPWTAC SVSCGGGIQR RSFVCVEESM HGEILQVEEW KCMYAPKPKV MQTCNLFDCP
KWIAMEWSQC TVTCGRGLRY RVVLCINHRG EHVGGCNPQL KLHIKEECVI PIPCYKPKEK
SPVEAKLPWL KQAQELEETR IATEEPTFIP EPWSACSTTC GPGVQVREVK CRVLLTFTQT
ETELPEEECE GPKLPTERPC LLEACDESPA SRELDIPLPE DSETTYDWEY AGFTPCTATC
LGGHQEAIAV CLHIQTQQTV NDSLCDMVHR PPAMSQACNT EPCPPRWHVG SWGPCSATCG
VGIQTRDVYC LHPGETPAPP EECRDEKPHA LQACNQFDCP PGWHIEEWQQ CSRTCGGGTQ
NRRVTCRQLL TDGSFLNLSD ELCQGPKASS HKSCARTDCP PHLAVGDWSK CSVSCGVGIQ
RRKQVCQRLA AKGRRIPLSE MMCRDLPGLP LVRSCQMPEC SKIKSEMKTK LGEQGPQILS
VQRVYIQTRE EKRINLTIGS RAYLLPNTSV IIKCPVRRFQ KSLIQWEKDG RCLQNSKRLG
ITKSGSLKIH GLAAPDIGVY RCIAGSAQET VVLKLIGTDN RLIARPALRE PMREYPGMDH
SEANSLGVTW HKMRQMWNNK NDLYLDDDHI SNQPFLRALL GHCSNSAGST NSWELKNKQF
EAAVKQGAYS MDTAQFDELI RNMSQLMETG EVSDDLASQL IYQLVAELAK AQPTHMQWRG
IQEETPPAAQ LRGETGSVSQ SSHAKNSGKL TFKPKGPVLM RQSQPPSISF NKTINSRIGN
TVYITKRTEV INILCDLITP SEATYTWTKD GTLLQPSVKI ILDGTGKIQI QNPTRKEQGI
YECSVANHLG SDVESSSVLY AEAPVILSVE RNITKPEHNH LSVVVGGIVE AALGANVTIR
CPVKGVPQPN ITWLKRGGSL SGNVSLLFNG SLLLQNVSLE NEGTYVCIAT NALGKAVATS
VLHLLERRWP ESRIVFLQGH KKYILQATNT RTNSNDPTGE PPPQEPFWEP GNWSHCSATC
GHLGARIQRP QCVMANGQEV SEALCDHLQK PLAGFEPCNI RDCPARWFTS VWSQCSVSCG
EGYHSRQVTC KRTKANGTVQ VVSPRACAPK DRPLGRKPCF GHPCVQWEPG NRCPGRCMGR
AVRMQQRHTA CQHNSSDSNC DDRKRPTLRR NCTSGACDVC WHTGPWKPCT AACGRGFQSR
KVDCIHTRSC KPVAKRHCVQ KKKPISWRHC LGPSCDRDCT DTTHYCMFVK HLNLCSLDRY
KQRCCQSCQE G*

speed

1.25 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: 0.999999999999721 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:84582124G>TN/A show variant in all transcripts IGV

HGNC symbol

ADAMTSL3

Ensembl transcript ID

ENST00000567476

Genbank transcript ID

N/A

UniProt peptide

P82987

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1981G>T
cDNA.2203G>T
g.259287G>T

AA changes

V661L Score: 32 explain score(s)

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

661

frameshift

known variant

Reference ID: rs4842838

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1214	1006	2220
ExAC	22245	-11723	10522

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.527	0.014
	-0.41	0.014
(flanking)	0.721	0.386

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 marginally increased	259288	wt: 0.9496 / mu: 0.9678 (marginal change - not scored)	wt: ATGCGTGGGAGGTAT mu: ATGCTTGGGAGGTAT	GCGT\|ggga
Donor marginally decreased	259292	wt: 0.4921 / mu: 0.4497 (marginal change - not scored)	wt: GTGGGAGGTATTTGA mu: TTGGGAGGTATTTGA	GGGA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

661

mutated

all conserved

661

Ptroglodytes

all conserved

ENSPTRG00000007394

661

Mmulatta

all conserved

ENSMMUG00000013670

661

Fcatus

no alignment

ENSFCAG00000001257

n/a

Mmusculus

all conserved

ENSMUSG00000070469

674

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000027903

661

Dmelanogaster

not conserved

FBgn0051619

556

KIFLE

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000006128

598

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5049 / 5049

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

1683 / 1683

position of stopcodon in wt / mu cDNA

5271 / 5271

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

223 / 223

chromosome

strand

last intron/exon boundary

5209

theoretical NMD boundary in CDS

4936

length of CDS

5049

coding sequence (CDS) position

1981

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

2203

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

259287

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

84582124

original gDNA sequence snippet

CCCCTTGCACAGCAACATGCGTGGGAGGTATTTGAACCTTT

altered gDNA sequence snippet

CCCCTTGCACAGCAACATGCTTGGGAGGTATTTGAACCTTT

original cDNA sequence snippet

CCCCTTGCACAGCAACATGCGTGGGAGGCCATCAAGAAGCC

altered cDNA sequence snippet

CCCCTTGCACAGCAACATGCTTGGGAGGCCATCAAGAAGCC

wildtype AA sequence

mutated AA sequence

MASWTSPWWV LIGMVFMHSP LPQTTAEKSP GAYFLPEFAL SPQGSFLEDT TGEQFLTYRY
DDQTSRNTRS DEDKDGNWDA WGDWSDCSRT CGGGASYSLR RCLTGRNCEG QNIRYKTCSN
HDCPPDAEDF RAQQCSAYND VQYQGHYYEW LPRYNDPAAP CALKCHAQGQ NLVVELAPKV
LDGTRCNTDS LDMCISGICQ AVGCDRQLGS NAKEDNCGVC AGDGSTCRLV RGQSKSHVSP
EKREENVIAV PLGSRSVRIT VKGPAHLFIE SKTLQGSKGE HSFNSPGVFL VENTTVEFQR
GSERQTFKIP GPLMADFIFK TRYTAAKDSV VQFFFYQPIS HQWRQTDFFP CTVTCGGGYQ
LNSAECVDIR LKRVVPDHYC HYYPENVKPK PKLKECSMDP CPSSDGFKEI MPYDHFQPLP
RWEHNPWTAC SVSCGGGIQR RSFVCVEESM HGEILQVEEW KCMYAPKPKV MQTCNLFDCP
KWIAMEWSQC TVTCGRGLRY RVVLCINHRG EHVGGCNPQL KLHIKEECVI PIPCYKPKEK
SPVEAKLPWL KQAQELEETR IATEEPTFIP EPWSACSTTC GPGVQVREVK CRVLLTFTQT
ETELPEEECE GPKLPTERPC LLEACDESPA SRELDIPLPE DSETTYDWEY AGFTPCTATC
LGGHQEAIAV CLHIQTQQTV NDSLCDMVHR PPAMSQACNT EPCPPRWHVG SWGPCSATCG
VGIQTRDVYC LHPGETPAPP EECRDEKPHA LQACNQFDCP PGWHIEEWQQ CSRTCGGGTQ
NRRVTCRQLL TDGSFLNLSD ELCQGPKASS HKSCARTDCP PHLAVGDWSK CSVSCGVGIQ
RRKQVCQRLA AKGRRIPLSE MMCRDLPGLP LVRSCQMPEC SKIKSEMKTK LGEQGPQILS
VQRVYIQTRE EKRINLTIGS RAYLLPNTSV IIKCPVRRFQ KSLIQWEKDG RCLQNSKRLG
ITKSGSLKIH GLAAPDIGVY RCIAGSAQET VVLKLIGTDN RLIARPALRE PMREYPGMDH
SEANSLGVTW HKMRQMWNNK NDLYLDDDHI SNQPFLRALL GHCSNSAGST NSWELKNKQF
EAAVKQGAYS MDTAQFDELI RNMSQLMETG EVSDDLASQL IYQLVAELAK AQPTHMQWRG
IQEETPPAAQ LRGETGSVSQ SSHAKNSGKL TFKPKGPVLM RQSQPPSISF NKTINSRIGN
TVYITKRTEV INILCDLITP SEATYTWTKD GTLLQPSVKI ILDGTGKIQI QNPTRKEQGI
YECSVANHLG SDVESSSVLY AEAPVILSVE RNITKPEHNH LSVVVGGIVE AALGANVTIR
CPVKGVPQPN ITWLKRGGSL SGNVSLLFNG SLLLQNVSLE NEGTYVCIAT NALGKAVATS
VLHLLERRWP ESRIVFLQGH KKYILQATNT RTNSNDPTGE PPPQEPFWEP GNWSHCSATC
GHLGARIQRP QCVMANGQEV SEALCDHLQK PLAGFEPCNI RDCPARWFTS VWSQCSVSCG
EGYHSRQVTC KRTKANGTVQ VVSPRACAPK DRPLGRKPCF GHPCVQWEPG NRCPGRCMGR
AVRMQQRHTA CQHNSSDSNC DDRKRPTLRR NCTSGACDVC WHTGPWKPCT AACGRGFQSR
KVDCIHTRSC KPVAKRHCVQ KKKPISWRHC LGPSCDSTYT SQTATNKGAA SHVKRDKPLE
GS*

speed

1.25 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems