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: ENST00000317578
Querying Taster for transcript #2: ENST00000560160
MT speed 0 s - this script 4.669522 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SIX5	polymorphism_automatic	0.00238499730078501	simple_aae		affected		V255M	single base exchange	rs2341097		show file
SIX5	polymorphism_automatic	0.00290888868717498	simple_aae		affected		V693M	single base exchange	rs2341097		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.997615002699215 (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)

chr19:46268902C>TN/A show variant in all transcripts IGV

HGNC symbol

SIX5

Ensembl transcript ID

ENST00000560160

Genbank transcript ID

N/A

UniProt peptide

Q8N196

alteration type

single base exchange

alteration region

CDS

DNA changes

c.763G>A
cDNA.1054G>A
g.3240G>A

AA changes

V255M Score: 21 explain score(s)

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

255

frameshift

known variant

Reference ID: rs2341097

database	homozygous (T/T)	heterozygous	allele carriers
1000G	232	1029	1261
ExAC	6513	19741	26254

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.035	0.847
	0.441	0.386
(flanking)	-0.899	0.092

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 increased	3243	wt: 0.24 / mu: 0.43	wt: CACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCCGAC mu: CACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCCGAC	gtgc\|TGAG
Acc marginally increased	3240	wt: 0.2034 / mu: 0.2320 (marginal change - not scored)	wt: GGACACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCC mu: GGACACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCC	accg\|TGCT
Donor marginally increased	3241	wt: 0.9816 / mu: 0.9930 (marginal change - not scored)	wt: CACCGTGCTGAGGCT mu: CACCATGCTGAGGCT	CCGT\|gctg
Donor gained	3236	0.40	mu: CCCCACACCATGCTG	CCAC\|acca

distance from splice site

468

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

255

mutated

all conserved

255

Ptroglodytes

all identical

ENSPTRG00000033681

663

Mmulatta

all identical

ENSMMUG00000016455

694

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040841

680

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000011163

622

Drerio

not conserved

ENSDARG00000068406

902

Dmelanogaster

no alignment

FBgn0027364

n/a

Celegans

no alignment

C10G8.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
201	260	DNA_BIND	Homeobox.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

906 / 906

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

302 / 302

position of stopcodon in wt / mu cDNA

1197 / 1197

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

292 / 292

chromosome

strand

-1

last intron/exon boundary

587

theoretical NMD boundary in CDS

245

length of CDS

906

coding sequence (CDS) position

763

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

1054

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

3240

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

46268902

original gDNA sequence snippet

GGACACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCC

altered gDNA sequence snippet

GGACACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCC

original cDNA sequence snippet

GGACACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCC

altered cDNA sequence snippet

GGACACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCC

wildtype AA sequence

MRPSGPAAAR LAQWTSIDCA RSSRCPRPSG TARRQSTASR SAPAQRSRPA TAATATPRRT
RSAAWPHSPA CRSRRSATGS RTGDSATGPG PEAARPARGN FLLANPVSGS PIVTGVALQQ
GKIILTATFP TSMLVSQVLP PAPGLALPLK PETAISVPEG GLPVAPSPAL PEAHALGTLS
AQQPPPAAAT TSSTSLPFSP DSPGLLPNFP APPPEGLMLS PAAVPVWSAG LELSAGTEGL
LEAEKGLGTQ APHTVLRLPD PDPEGLLLGA TAGGEVDEGL EAEAKVLTQL QSVPVEEPLE
L*

mutated AA sequence

MRPSGPAAAR LAQWTSIDCA RSSRCPRPSG TARRQSTASR SAPAQRSRPA TAATATPRRT
RSAAWPHSPA CRSRRSATGS RTGDSATGPG PEAARPARGN FLLANPVSGS PIVTGVALQQ
GKIILTATFP TSMLVSQVLP PAPGLALPLK PETAISVPEG GLPVAPSPAL PEAHALGTLS
AQQPPPAAAT TSSTSLPFSP DSPGLLPNFP APPPEGLMLS PAAVPVWSAG LELSAGTEGL
LEAEKGLGTQ APHTMLRLPD PDPEGLLLGA TAGGEVDEGL EAEAKVLTQL QSVPVEEPLE
L*

speed

1.37 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: 0.997091111312825 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:46268902C>TN/A show variant in all transcripts IGV

HGNC symbol

SIX5

Ensembl transcript ID

ENST00000317578

Genbank transcript ID

NM_175875

UniProt peptide

Q8N196

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2077G>A
cDNA.2116G>A
g.3240G>A

AA changes

V693M Score: 21 explain score(s)

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

693

frameshift

known variant

Reference ID: rs2341097

database	homozygous (T/T)	heterozygous	allele carriers
1000G	232	1029	1261
ExAC	6513	19741	26254

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.035	0.847
	0.441	0.386
(flanking)	-0.899	0.092

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 increased	3243	wt: 0.24 / mu: 0.43	wt: CACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCCGAC mu: CACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCCGAC	gtgc\|TGAG
Acc marginally increased	3240	wt: 0.2034 / mu: 0.2320 (marginal change - not scored)	wt: GGACACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCC mu: GGACACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCC	accg\|TGCT
Donor marginally increased	3241	wt: 0.9816 / mu: 0.9930 (marginal change - not scored)	wt: CACCGTGCTGAGGCT mu: CACCATGCTGAGGCT	CCGT\|gctg
Donor gained	3236	0.40	mu: CCCCACACCATGCTG	CCAC\|acca

distance from splice site

468

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

693

mutated

all conserved

693

Ptroglodytes

all identical

ENSPTRG00000033681

663

Mmulatta

all identical

ENSMMUG00000016455

694

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040841

680

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000011163

623

Drerio

all identical

ENSDARG00000068406

717

Dmelanogaster

no alignment

FBgn0027364

n/a

Celegans

no alignment

C10G8.6

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2220 / 2220

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

740 / 740

position of stopcodon in wt / mu cDNA

2259 / 2259

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

40 / 40

chromosome

strand

-1

last intron/exon boundary

1649

theoretical NMD boundary in CDS

1559

length of CDS

2220

coding sequence (CDS) position

2077

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

2116

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

3240

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

46268902

original gDNA sequence snippet

GGACACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCC

altered gDNA sequence snippet

GGACACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCC

original cDNA sequence snippet

GGACACAGGCCCCCCACACCGTGCTGAGGCTGCCAGACCCC

altered cDNA sequence snippet

GGACACAGGCCCCCCACACCATGCTGAGGCTGCCAGACCCC

wildtype AA sequence

MATLPAEPSA GPAAGGEAVA AAAATEEEEE EARQLLQTLQ AAEGEAAAAA GAGAGAAAAG
AEGPGSPGVP GSPPEAASEP PTGLRFSPEQ VACVCEALLQ AGHAGRLSRF LGALPPAERL
RGSDPVLRAR ALVAFQRGEY AELYRLLESR PFPAAHHAFL QDLYLRARYH EAERARGRAL
GAVDKYRLRK KFPLPKTIWD GEETVYCFKE RSRAALKACY RGNRYPTPDE KRRLATLTGL
SLTQVSNWFK NRRQRDRTGA GGGAPCKSES DGNPTTEDES SRSPEDLERG AAPVSAEAAA
QGSIFLAGTG PPAPCPASSS ILVNGSFLAA SGSPAVLLNG GPVIINGLAL GEASSLGPLL
LTGGGGAPPP QPSPQGASET KTSLVLDPQT GEVRLEEAQS EAPETKGAQV AAPGPALGEE
VLGPLAQVVP GPPTAATFPL PPGPVPAVAA PQVVPLSPPP GYPTGLSPTS PLLNLPQVVP
TSQVVTLPQA VGPLQLLAAG PGSPVKVAAA AGPANVHLIN SGVGVTALQL PSATAPGNFL
LANPVSGSPI VTGVALQQGK IILTATFPTS MLVSQVLPPA PGLALPLKPE TAISVPEGGL
PVAPSPALPE AHALGTLSAQ QPPPAAATTS STSLPFSPDS PGLLPNFPAP PPEGLMLSPA
AVPVWSAGLE LSAGTEGLLE AEKGLGTQAP HTVLRLPDPD PEGLLLGATA GGEVDEGLEA
EAKVLTQLQS VPVEEPLEL*

mutated AA sequence

MATLPAEPSA GPAAGGEAVA AAAATEEEEE EARQLLQTLQ AAEGEAAAAA GAGAGAAAAG
AEGPGSPGVP GSPPEAASEP PTGLRFSPEQ VACVCEALLQ AGHAGRLSRF LGALPPAERL
RGSDPVLRAR ALVAFQRGEY AELYRLLESR PFPAAHHAFL QDLYLRARYH EAERARGRAL
GAVDKYRLRK KFPLPKTIWD GEETVYCFKE RSRAALKACY RGNRYPTPDE KRRLATLTGL
SLTQVSNWFK NRRQRDRTGA GGGAPCKSES DGNPTTEDES SRSPEDLERG AAPVSAEAAA
QGSIFLAGTG PPAPCPASSS ILVNGSFLAA SGSPAVLLNG GPVIINGLAL GEASSLGPLL
LTGGGGAPPP QPSPQGASET KTSLVLDPQT GEVRLEEAQS EAPETKGAQV AAPGPALGEE
VLGPLAQVVP GPPTAATFPL PPGPVPAVAA PQVVPLSPPP GYPTGLSPTS PLLNLPQVVP
TSQVVTLPQA VGPLQLLAAG PGSPVKVAAA AGPANVHLIN SGVGVTALQL PSATAPGNFL
LANPVSGSPI VTGVALQQGK IILTATFPTS MLVSQVLPPA PGLALPLKPE TAISVPEGGL
PVAPSPALPE AHALGTLSAQ QPPPAAATTS STSLPFSPDS PGLLPNFPAP PPEGLMLSPA
AVPVWSAGLE LSAGTEGLLE AEKGLGTQAP HTMLRLPDPD PEGLLLGATA GGEVDEGLEA
EAKVLTQLQS VPVEEPLEL*

speed

1.36 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems