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: ENST00000336505
Querying Taster for transcript #2: ENST00000373549
MT speed 0 s - this script 3.366365 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SCAI	polymorphism_automatic	0.004586052519572	simple_aae		affected		A60T	single base exchange	rs589292		show file
SCAI	polymorphism_automatic	0.017090022820064	simple_aae		affected		A37T	single base exchange	rs589292		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.995413947480428 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:127818276C>TN/A show variant in all transcripts IGV

HGNC symbol

SCAI

Ensembl transcript ID

ENST00000373549

Genbank transcript ID

NM_173690

UniProt peptide

Q8N9R8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.178G>A
cDNA.237G>A
g.87510G>A

AA changes

A60T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs589292

database	homozygous (T/T)	heterozygous	allele carriers
1000G	160	840	1000
ExAC	4112	21997	26109

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.002	1
	2.632	1
(flanking)	1.15	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
Donor increased	87513	wt: 0.52 / mu: 0.59	wt: TTGCTCTTAAAGAAA mu: TTACTCTTAAAGAAA	GCTC\|ttaa
Donor increased	87501	wt: 0.73 / mu: 0.84	wt: ACAGGACTGAATTTG mu: ACAGGACTGAATTTA	AGGA\|ctga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000021366

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000035236

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000060865

n/a

Dmelanogaster

no alignment

FBgn0035677

n/a

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000016827

n/a

protein features

start (aa)	end (aa)	feature	details
1	212	REGION	Necessary to inhibit MKL1-induced SRF transcriptional activity (By similarity).	lost
64	64	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
71	173	REGION	Required for interaction with MKL1 (By similarity).	might get lost (downstream of altered splice site)
432	432	CONFLICT	I -> F (in Ref. 1; BAC05217).	might get lost (downstream of altered splice site)
472	492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
553	553	CONFLICT	M -> T (in Ref. 1; BAC05217).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1890 / 1890

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

630 / 630

position of stopcodon in wt / mu cDNA

1949 / 1949

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

60 / 60

chromosome

strand

-1

last intron/exon boundary

1803

theoretical NMD boundary in CDS

1693

length of CDS

1890

coding sequence (CDS) position

178

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

237

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

87510

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

127818276

original gDNA sequence snippet

TTTCTTACAGGACTGAATTTGCTCTTAAAGAAATCATGTCC

altered gDNA sequence snippet

TTTCTTACAGGACTGAATTTACTCTTAAAGAAATCATGTCC

original cDNA sequence snippet

TCACTGAAAAGACTGAATTTGCTCTTAAAGAAATCATGTCC

altered cDNA sequence snippet

TCACTGAAAAGACTGAATTTACTCTTAAAGAAATCATGTCC

wildtype AA sequence

MVRGARQPQQ PRSRLAPRLT GTVEKPPRKR RSSIRGSGDS SHSQSQGERY QHFTEKTEFA
LKEIMSSGGA EDDIPQGERK TVTDFCYLLD KSKQLFNGLR DLPQYGQKQW QSYFGRTFDV
YTKLWKFQQQ HRQVLDNRYG LKRWQIGEIA SKIGQLYYHY YLRTSETSYL NEAFSFYSAI
RQRSYYSQVN KEDRPELVVK KLRYYARFIV VCLLLNKMDV VKDLVKELSD EIEDYTHRFN
TEDQVEWNLV LQEVAAFIEA DPVMVLNDDN TIVITSNRLA ETGAPLLEQG MIVGQLSLAD
ALIIGNCNNQ VKFSELTVDM FRMLQALERE PMNLASQMNK PGMQESADKP TRRENPHKYL
LYKPTFSQLY TFLAASFKEL PANSVLLIYL SATGVFPTGR SDSEGPYDFG GVLTNSNRDI
INGDAIHKRN QSHKEMHCLH PGDLYPFTRK PLFIIVDSSN SVAYKNFTNL FGQPLVCLLS
PTAYPKALQD QSQRGSLFTL FLNNPLMAFL FVSGLSSMRR GLWEKCQEYL RKINRDIAQL
LTHSRSIDQA FLQFFGDEFL RLLLTRFIFC SATMRMHKIF RETRNYPESY PQLPRDETVE
NPHLQKHILE LASILDVRNV FFENTIDDY*

mutated AA sequence

MVRGARQPQQ PRSRLAPRLT GTVEKPPRKR RSSIRGSGDS SHSQSQGERY QHFTEKTEFT
LKEIMSSGGA EDDIPQGERK TVTDFCYLLD KSKQLFNGLR DLPQYGQKQW QSYFGRTFDV
YTKLWKFQQQ HRQVLDNRYG LKRWQIGEIA SKIGQLYYHY YLRTSETSYL NEAFSFYSAI
RQRSYYSQVN KEDRPELVVK KLRYYARFIV VCLLLNKMDV VKDLVKELSD EIEDYTHRFN
TEDQVEWNLV LQEVAAFIEA DPVMVLNDDN TIVITSNRLA ETGAPLLEQG MIVGQLSLAD
ALIIGNCNNQ VKFSELTVDM FRMLQALERE PMNLASQMNK PGMQESADKP TRRENPHKYL
LYKPTFSQLY TFLAASFKEL PANSVLLIYL SATGVFPTGR SDSEGPYDFG GVLTNSNRDI
INGDAIHKRN QSHKEMHCLH PGDLYPFTRK PLFIIVDSSN SVAYKNFTNL FGQPLVCLLS
PTAYPKALQD QSQRGSLFTL FLNNPLMAFL FVSGLSSMRR GLWEKCQEYL RKINRDIAQL
LTHSRSIDQA FLQFFGDEFL RLLLTRFIFC SATMRMHKIF RETRNYPESY PQLPRDETVE
NPHLQKHILE LASILDVRNV FFENTIDDY*

speed

0.65 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: 0.982909977179936 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:127818276C>TN/A show variant in all transcripts IGV

HGNC symbol

SCAI

Ensembl transcript ID

ENST00000336505

Genbank transcript ID

NM_001144877

UniProt peptide

Q8N9R8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.109G>A
cDNA.168G>A
g.87510G>A

AA changes

A37T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs589292

database	homozygous (T/T)	heterozygous	allele carriers
1000G	160	840	1000
ExAC	4112	21997	26109

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.002	1
	2.632	1
(flanking)	1.15	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
Donor increased	87513	wt: 0.52 / mu: 0.59	wt: TTGCTCTTAAAGAAA mu: TTACTCTTAAAGAAA	GCTC\|ttaa
Donor increased	87501	wt: 0.73 / mu: 0.84	wt: ACAGGACTGAATTTG mu: ACAGGACTGAATTTA	AGGA\|ctga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000021366

RGSAFLFCFIFTSWMNEHMFSYR

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000035236

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000060865

n/a

Dmelanogaster

all conserved

FBgn0035677

269

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000016827

n/a

protein features

start (aa)	end (aa)	feature	details
1	212	REGION	Necessary to inhibit MKL1-induced SRF transcriptional activity (By similarity).	lost
64	64	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
71	173	REGION	Required for interaction with MKL1 (By similarity).	might get lost (downstream of altered splice site)
432	432	CONFLICT	I -> F (in Ref. 1; BAC05217).	might get lost (downstream of altered splice site)
472	492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
553	553	CONFLICT	M -> T (in Ref. 1; BAC05217).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1821 / 1821

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

607 / 607

position of stopcodon in wt / mu cDNA

1880 / 1880

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

60 / 60

chromosome

strand

-1

last intron/exon boundary

1734

theoretical NMD boundary in CDS

1624

length of CDS

1821

coding sequence (CDS) position

109

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

168

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

87510

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

127818276

original gDNA sequence snippet

TTTCTTACAGGACTGAATTTGCTCTTAAAGAAATCATGTCC

altered gDNA sequence snippet

TTTCTTACAGGACTGAATTTACTCTTAAAGAAATCATGTCC

original cDNA sequence snippet

GGAGAAGCAGGACTGAATTTGCTCTTAAAGAAATCATGTCC

altered cDNA sequence snippet

GGAGAAGCAGGACTGAATTTACTCTTAAAGAAATCATGTCC

wildtype AA sequence

MVRGARQPQQ PRSRLAPRLT GTVEKPPRKR RSRTEFALKE IMSSGGAEDD IPQGERKTVT
DFCYLLDKSK QLFNGLRDLP QYGQKQWQSY FGRTFDVYTK LWKFQQQHRQ VLDNRYGLKR
WQIGEIASKI GQLYYHYYLR TSETSYLNEA FSFYSAIRQR SYYSQVNKED RPELVVKKLR
YYARFIVVCL LLNKMDVVKD LVKELSDEIE DYTHRFNTED QVEWNLVLQE VAAFIEADPV
MVLNDDNTIV ITSNRLAETG APLLEQGMIV GQLSLADALI IGNCNNQVKF SELTVDMFRM
LQALEREPMN LASQMNKPGM QESADKPTRR ENPHKYLLYK PTFSQLYTFL AASFKELPAN
SVLLIYLSAT GVFPTGRSDS EGPYDFGGVL TNSNRDIING DAIHKRNQSH KEMHCLHPGD
LYPFTRKPLF IIVDSSNSVA YKNFTNLFGQ PLVCLLSPTA YPKALQDQSQ RGSLFTLFLN
NPLMAFLFVS GLSSMRRGLW EKCQEYLRKI NRDIAQLLTH SRSIDQAFLQ FFGDEFLRLL
LTRFIFCSAT MRMHKIFRET RNYPESYPQL PRDETVENPH LQKHILELAS ILDVRNVFFE
NTIDDY*

mutated AA sequence

MVRGARQPQQ PRSRLAPRLT GTVEKPPRKR RSRTEFTLKE IMSSGGAEDD IPQGERKTVT
DFCYLLDKSK QLFNGLRDLP QYGQKQWQSY FGRTFDVYTK LWKFQQQHRQ VLDNRYGLKR
WQIGEIASKI GQLYYHYYLR TSETSYLNEA FSFYSAIRQR SYYSQVNKED RPELVVKKLR
YYARFIVVCL LLNKMDVVKD LVKELSDEIE DYTHRFNTED QVEWNLVLQE VAAFIEADPV
MVLNDDNTIV ITSNRLAETG APLLEQGMIV GQLSLADALI IGNCNNQVKF SELTVDMFRM
LQALEREPMN LASQMNKPGM QESADKPTRR ENPHKYLLYK PTFSQLYTFL AASFKELPAN
SVLLIYLSAT GVFPTGRSDS EGPYDFGGVL TNSNRDIING DAIHKRNQSH KEMHCLHPGD
LYPFTRKPLF IIVDSSNSVA YKNFTNLFGQ PLVCLLSPTA YPKALQDQSQ RGSLFTLFLN
NPLMAFLFVS GLSSMRRGLW EKCQEYLRKI NRDIAQLLTH SRSIDQAFLQ FFGDEFLRLL
LTRFIFCSAT MRMHKIFRET RNYPESYPQL PRDETVENPH LQKHILELAS ILDVRNVFFE
NTIDDY*

speed

0.66 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems