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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000540691
Querying Taster for transcript #2: ENST00000539106
Querying Taster for transcript #3: ENST00000222307
MT speed 2.1 s - this script 3.758833 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KXD1	polymorphism_automatic	2.55795384873636e-12	simple_aae		affected		P157A	single base exchange	rs7648		show file
KXD1	polymorphism_automatic	2.55795384873636e-12	simple_aae		affected		P157A	single base exchange	rs7648		show file
KXD1	polymorphism_automatic	2.55795384873636e-12	simple_aae		affected		P157A	single base exchange	rs7648		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997442 (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)

chr19:18679379C>GN/A show variant in all transcripts IGV

HGNC symbol

KXD1

Ensembl transcript ID

ENST00000540691

Genbank transcript ID

NM_001171948

UniProt peptide

Q9BQD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.469C>G
cDNA.774C>G
g.10808C>G

AA changes

P157A Score: 27 explain score(s)

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

157

frameshift

known variant

Reference ID: rs7648

database	homozygous (G/G)	heterozygous	allele carriers
1000G	647	1022	1669
ExAC	17866	-2965	14901

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.177	0
	0.293	0.001
(flanking)	1.462	0.004

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	10806	wt: 0.2893 / mu: 0.2989 (marginal change - not scored)	wt: CGAGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCA mu: CGAGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCA	tcca\|GCCT
Acc increased	10801	wt: 0.48 / mu: 0.56	wt: GGCTTCGAGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGC mu: GGCTTCGAGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGC	ccat\|GTCC

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

157

mutated

not conserved

157

Ptroglodytes

all identical

ENSPTRG00000010713

106

Mmulatta

all identical

ENSMMUG00000016078

157

Fcatus

not conserved

ENSFCAG00000009743

157

Mmusculus

no alignment

ENSMUSG00000055553

n/a

Ggallus

not conserved

ENSGALG00000021619

156

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000051934

159

Dmelanogaster

not conserved

FBgn0036291

180

STK

Celegans

no alignment

C13F10.2

n/a

Xtropicalis

not conserved

ENSXETG00000023203

161

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

531 / 531

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

177 / 177

position of stopcodon in wt / mu cDNA

836 / 836

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

306 / 306

chromosome

strand

last intron/exon boundary

607

theoretical NMD boundary in CDS

251

length of CDS

531

coding sequence (CDS) position

469

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

774

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

10808

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

18679379

original gDNA sequence snippet

AGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCAAC

altered gDNA sequence snippet

AGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCAAC

original cDNA sequence snippet

AGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCAAC

altered cDNA sequence snippet

AGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCAAC

wildtype AA sequence

MDLPDSASRV FCGRILSMVN TDDVNAIILA QKNMLDRFEK TNEMLLNFNN LSSARLQQMS
ERFLHHTRTL VEMKRDLDSI FRRIRTLKGK LARQHPEAFS HIPEASFLEE EDEDPIPPST
TTTIATSEQS TGSCDTSPDT VSPSLSPGFE DLSHVQPGSP AINGRSQTDD EEMTGE*

mutated AA sequence

MDLPDSASRV FCGRILSMVN TDDVNAIILA QKNMLDRFEK TNEMLLNFNN LSSARLQQMS
ERFLHHTRTL VEMKRDLDSI FRRIRTLKGK LARQHPEAFS HIPEASFLEE EDEDPIPPST
TTTIATSEQS TGSCDTSPDT VSPSLSPGFE DLSHVQAGSP AINGRSQTDD EEMTGE*

speed

0.90 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: 0.999999999997442 (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)

chr19:18679379C>GN/A show variant in all transcripts IGV

HGNC symbol

KXD1

Ensembl transcript ID

ENST00000539106

Genbank transcript ID

NM_001171949

UniProt peptide

Q9BQD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.469C>G
cDNA.678C>G
g.10808C>G

AA changes

P157A Score: 27 explain score(s)

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

157

frameshift

known variant

Reference ID: rs7648

database	homozygous (G/G)	heterozygous	allele carriers
1000G	647	1022	1669
ExAC	17866	-2965	14901

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.177	0
	0.293	0.001
(flanking)	1.462	0.004

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	10806	wt: 0.2893 / mu: 0.2989 (marginal change - not scored)	wt: CGAGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCA mu: CGAGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCA	tcca\|GCCT
Acc increased	10801	wt: 0.48 / mu: 0.56	wt: GGCTTCGAGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGC mu: GGCTTCGAGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGC	ccat\|GTCC

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

157

mutated

not conserved

157

Ptroglodytes

all identical

ENSPTRG00000010713

106

Mmulatta

all identical

ENSMMUG00000016078

157

Fcatus

not conserved

ENSFCAG00000009743

157

Mmusculus

no alignment

ENSMUSG00000055553

n/a

Ggallus

not conserved

ENSGALG00000021619

156

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000051934

159

Dmelanogaster

not conserved

FBgn0036291

180

STK

Celegans

no alignment

C13F10.2

n/a

Xtropicalis

not conserved

ENSXETG00000023203

161

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

531 / 531

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

177 / 177

position of stopcodon in wt / mu cDNA

740 / 740

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

210 / 210

chromosome

strand

last intron/exon boundary

511

theoretical NMD boundary in CDS

251

length of CDS

531

coding sequence (CDS) position

469

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

678

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

10808

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

18679379

original gDNA sequence snippet

AGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCAAC

altered gDNA sequence snippet

AGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCAAC

original cDNA sequence snippet

AGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCAAC

altered cDNA sequence snippet

AGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCAAC

wildtype AA sequence

MDLPDSASRV FCGRILSMVN TDDVNAIILA QKNMLDRFEK TNEMLLNFNN LSSARLQQMS
ERFLHHTRTL VEMKRDLDSI FRRIRTLKGK LARQHPEAFS HIPEASFLEE EDEDPIPPST
TTTIATSEQS TGSCDTSPDT VSPSLSPGFE DLSHVQPGSP AINGRSQTDD EEMTGE*

mutated AA sequence

MDLPDSASRV FCGRILSMVN TDDVNAIILA QKNMLDRFEK TNEMLLNFNN LSSARLQQMS
ERFLHHTRTL VEMKRDLDSI FRRIRTLKGK LARQHPEAFS HIPEASFLEE EDEDPIPPST
TTTIATSEQS TGSCDTSPDT VSPSLSPGFE DLSHVQAGSP AINGRSQTDD EEMTGE*

speed

0.38 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997442 (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)

chr19:18679379C>GN/A show variant in all transcripts IGV

HGNC symbol

KXD1

Ensembl transcript ID

ENST00000222307

Genbank transcript ID

NM_024069

UniProt peptide

Q9BQD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.469C>G
cDNA.643C>G
g.10808C>G

AA changes

P157A Score: 27 explain score(s)

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

157

frameshift

known variant

Reference ID: rs7648

database	homozygous (G/G)	heterozygous	allele carriers
1000G	647	1022	1669
ExAC	17866	-2965	14901

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.177	0
	0.293	0.001
(flanking)	1.462	0.004

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	10806	wt: 0.2893 / mu: 0.2989 (marginal change - not scored)	wt: CGAGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCA mu: CGAGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCA	tcca\|GCCT
Acc increased	10801	wt: 0.48 / mu: 0.56	wt: GGCTTCGAGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGC mu: GGCTTCGAGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGC	ccat\|GTCC

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

157

mutated

not conserved

157

Ptroglodytes

all identical

ENSPTRG00000010713

106

Mmulatta

all identical

ENSMMUG00000016078

157

Fcatus

not conserved

ENSFCAG00000009743

157

Mmusculus

no alignment

ENSMUSG00000055553

n/a

Ggallus

not conserved

ENSGALG00000021619

156

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000051934

159

Dmelanogaster

not conserved

FBgn0036291

180

STK

Celegans

no alignment

C13F10.2

n/a

Xtropicalis

not conserved

ENSXETG00000023203

161

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

531 / 531

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

177 / 177

position of stopcodon in wt / mu cDNA

705 / 705

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

175 / 175

chromosome

strand

last intron/exon boundary

476

theoretical NMD boundary in CDS

251

length of CDS

531

coding sequence (CDS) position

469

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

643

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

10808

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

18679379

original gDNA sequence snippet

AGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCAAC

altered gDNA sequence snippet

AGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCAAC

original cDNA sequence snippet

AGGACCTGTCCCATGTCCAGCCTGGCTCCCCAGCCATCAAC

altered cDNA sequence snippet

AGGACCTGTCCCATGTCCAGGCTGGCTCCCCAGCCATCAAC

wildtype AA sequence

MDLPDSASRV FCGRILSMVN TDDVNAIILA QKNMLDRFEK TNEMLLNFNN LSSARLQQMS
ERFLHHTRTL VEMKRDLDSI FRRIRTLKGK LARQHPEAFS HIPEASFLEE EDEDPIPPST
TTTIATSEQS TGSCDTSPDT VSPSLSPGFE DLSHVQPGSP AINGRSQTDD EEMTGE*

mutated AA sequence

MDLPDSASRV FCGRILSMVN TDDVNAIILA QKNMLDRFEK TNEMLLNFNN LSSARLQQMS
ERFLHHTRTL VEMKRDLDSI FRRIRTLKGK LARQHPEAFS HIPEASFLEE EDEDPIPPST
TTTIATSEQS TGSCDTSPDT VSPSLSPGFE DLSHVQAGSP AINGRSQTDD EEMTGE*

speed

0.82 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems