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: ENST00000368011
Querying Taster for transcript #2: ENST00000392192
MT speed 0 s - this script 3.170665 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KLHDC9	polymorphism_automatic	2.29635799264827e-09	simple_aae				S171R	single base exchange	rs11576830		show file
KLHDC9	polymorphism_automatic	2.29635799264827e-09	simple_aae				S171R	single base exchange	rs11576830		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999997703642 (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)

chr1:161068836A>CN/A show variant in all transcripts IGV

HGNC symbol

KLHDC9

Ensembl transcript ID

ENST00000368011

Genbank transcript ID

NM_152366

UniProt peptide

Q8NEP7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.511A>C
cDNA.653A>C
g.686A>C

AA changes

S171R Score: 110 explain score(s)

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

171

frameshift

known variant

Reference ID: rs11576830

database	homozygous (C/C)	heterozygous	allele carriers
1000G	171	856	1027
ExAC	3954	21143	25097

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.992	0.002
	-1.246	0.001
(flanking)	0.76	0.131

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

171

mutated

not conserved

171

Ptroglodytes

all identical

ENSPTRG00000001568

171

Mmulatta

all identical

ENSMMUG00000002007

171

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000045259

171

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012703

158

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1050 / 1050

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

350 / 350

position of stopcodon in wt / mu cDNA

1192 / 1192

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

143 / 143

chromosome

strand

last intron/exon boundary

1029

theoretical NMD boundary in CDS

836

length of CDS

1050

coding sequence (CDS) position

511

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

653

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

686

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

161068836

original gDNA sequence snippet

ACACATTAAGGCTGGACCCCAGCGCCCGCACCTATTGGTAT

altered gDNA sequence snippet

ACACATTAAGGCTGGACCCCCGCGCCCGCACCTATTGGTAT

original cDNA sequence snippet

ACACATTAAGGCTGGACCCCAGCGCCCGCACCTATTGCTAC

altered cDNA sequence snippet

ACACATTAAGGCTGGACCCCCGCGCCCGCACCTATTGCTAC

wildtype AA sequence

MAVAVPPGRA AGSGWAWRPV ARDALLARAF HSCTELRGRF YLVGGLLAGG AREPSSDTVV
FDPARGQAVR LGARGSPPRS HHDAAPVDGR WLCVVGGWDG SRRLATVTAL DTERGVWEAW
TGTPGDCPPA GLSSHTCTRI SDRELQVAGR EGGIHTQRRY GSIYTLRLDP SARTYCYKQE
GCHTASRSGH CAALLQTPGP HPGHQLLLFG GCNLAEPEVA GHWSHGKIKE EPPVAPHLME
QLARLVSSGQ GSQKGPHGLR HHSCSVVGPF AVLFGGETLT RARDTICNDL YIYDTRTSPP
LWFHFPCADR GMKRMGHRTC LWNDQLYLVG GFGEDGRTAS PQVCILDFI*

mutated AA sequence

MAVAVPPGRA AGSGWAWRPV ARDALLARAF HSCTELRGRF YLVGGLLAGG AREPSSDTVV
FDPARGQAVR LGARGSPPRS HHDAAPVDGR WLCVVGGWDG SRRLATVTAL DTERGVWEAW
TGTPGDCPPA GLSSHTCTRI SDRELQVAGR EGGIHTQRRY GSIYTLRLDP RARTYCYKQE
GCHTASRSGH CAALLQTPGP HPGHQLLLFG GCNLAEPEVA GHWSHGKIKE EPPVAPHLME
QLARLVSSGQ GSQKGPHGLR HHSCSVVGPF AVLFGGETLT RARDTICNDL YIYDTRTSPP
LWFHFPCADR GMKRMGHRTC LWNDQLYLVG GFGEDGRTAS PQVCILDFI*

speed

0.59 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: 0.999999997703642 (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)

chr1:161068836A>CN/A show variant in all transcripts IGV

HGNC symbol

KLHDC9

Ensembl transcript ID

ENST00000392192

Genbank transcript ID

NM_001007255

UniProt peptide

Q8NEP7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.511A>C
cDNA.653A>C
g.686A>C

AA changes

S171R Score: 110 explain score(s)

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

171

frameshift

known variant

Reference ID: rs11576830

database	homozygous (C/C)	heterozygous	allele carriers
1000G	171	856	1027
ExAC	3954	21143	25097

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.992	0.002
	-1.246	0.001
(flanking)	0.76	0.131

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

171

mutated

not conserved

171

Ptroglodytes

all identical

ENSPTRG00000001568

171

Mmulatta

all identical

ENSMMUG00000002007

171

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000045259

171

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012703

158

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

867 / 867

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

289 / 289

position of stopcodon in wt / mu cDNA

1009 / 1009

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

143 / 143

chromosome

strand

last intron/exon boundary

1048

theoretical NMD boundary in CDS

855

length of CDS

867

coding sequence (CDS) position

511

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

653

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

686

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

161068836

original gDNA sequence snippet

ACACATTAAGGCTGGACCCCAGCGCCCGCACCTATTGGTAT

altered gDNA sequence snippet

ACACATTAAGGCTGGACCCCCGCGCCCGCACCTATTGGTAT

original cDNA sequence snippet

ACACATTAAGGCTGGACCCCAGCGCCCGCACCTATTGCTAC

altered cDNA sequence snippet

ACACATTAAGGCTGGACCCCCGCGCCCGCACCTATTGCTAC

wildtype AA sequence

MAVAVPPGRA AGSGWAWRPV ARDALLARAF HSCTELRGRF YLVGGLLAGG AREPSSDTVV
FDPARGQAVR LGARGSPPRS HHDAAPVDGR WLCVVGGWDG SRRLATVTAL DTERGVWEAW
TGTPGDCPPA GLSSHTCTRI SDRELQVAGR EGGIHTQRRY GSIYTLRLDP SARTYCYKQE
GCHTASRSGH CAALLQTPGP HPGHQLLLFG GCNLAEPEVA GHWSHGKIKS FLSPQGGTTC
CSSFDGTACK ACEQWAGVPE GAPWTTASLM FCGRALCCAV WWRNSDQS*

mutated AA sequence

MAVAVPPGRA AGSGWAWRPV ARDALLARAF HSCTELRGRF YLVGGLLAGG AREPSSDTVV
FDPARGQAVR LGARGSPPRS HHDAAPVDGR WLCVVGGWDG SRRLATVTAL DTERGVWEAW
TGTPGDCPPA GLSSHTCTRI SDRELQVAGR EGGIHTQRRY GSIYTLRLDP RARTYCYKQE
GCHTASRSGH CAALLQTPGP HPGHQLLLFG GCNLAEPEVA GHWSHGKIKS FLSPQGGTTC
CSSFDGTACK ACEQWAGVPE GAPWTTASLM FCGRALCCAV WWRNSDQS*

speed

0.63 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems