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: ENST00000391805
Querying Taster for transcript #2: ENST00000309958
Querying Taster for transcript #3: ENST00000358789
MT speed 0 s - this script 3.597927 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KLK10	polymorphism_automatic	0	simple_aae		affected		S50A	single base exchange	rs3745535		show file
KLK10	polymorphism_automatic	0	simple_aae		affected		S50A	single base exchange	rs3745535		show file
KLK10	polymorphism_automatic	0	simple_aae		affected		S50A	single base exchange	rs3745535		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr19:51520487A>CN/A show variant in all transcripts IGV

HGNC symbol

KLK10

Ensembl transcript ID

ENST00000391805

Genbank transcript ID

NM_001077500

UniProt peptide

O43240

alteration type

single base exchange

alteration region

CDS

DNA changes

c.148T>G
cDNA.268T>G
g.2945T>G

AA changes

S50A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs3745535

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1301	875	2176
ExAC	23374	-13981	9393

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SP1, Transcription Factor, SP1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.327	0
	-0.587	0
(flanking)	0.191	0.001

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 gained	2944	0.56	mu: TATGGCGCCCCGTGC	TGGC\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000011367

Mmulatta

all conserved

ENSMMUG00000015451

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000030693

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000003166

n/a

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
47	274	DOMAIN	Peptidase S1.	lost
52	52	DISULFID	By similarity.	might get lost (downstream of altered splice site)
71	71	DISULFID	By similarity.	might get lost (downstream of altered splice site)
86	86	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
87	87	DISULFID	By similarity.	might get lost (downstream of altered splice site)
137	137	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
162	162	DISULFID	By similarity.	might get lost (downstream of altered splice site)
169	169	DISULFID	By similarity.	might get lost (downstream of altered splice site)
201	201	DISULFID	By similarity.	might get lost (downstream of altered splice site)
215	215	DISULFID	By similarity.	might get lost (downstream of altered splice site)
225	225	DISULFID	By similarity.	might get lost (downstream of altered splice site)
229	229	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
235	235	DISULFID	By similarity.	might get lost (downstream of altered splice site)
250	250	DISULFID	By similarity.	might get lost (downstream of altered splice site)
263	263	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

831 / 831

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

277 / 277

position of stopcodon in wt / mu cDNA

951 / 951

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

121 / 121

chromosome

strand

-1

last intron/exon boundary

799

theoretical NMD boundary in CDS

628

length of CDS

831

coding sequence (CDS) position

148

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

268

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

2945

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

51520487

original gDNA sequence snippet

TGGACCCCGAAGCCTATGGCTCCCCGTGCGCGCGCGGCTCG

altered gDNA sequence snippet

TGGACCCCGAAGCCTATGGCGCCCCGTGCGCGCGCGGCTCG

original cDNA sequence snippet

TGGACCCCGAAGCCTATGGCTCCCCGTGCGCGCGCGGCTCG

altered cDNA sequence snippet

TGGACCCCGAAGCCTATGGCGCCCCGTGCGCGCGCGGCTCG

wildtype AA sequence

MRAPHLHLSA ASGARALAKL LPLLMAQLWA AEAALLPQND TRLDPEAYGS PCARGSQPWQ
VSLFNGLSFH CAGVLVDQSW VLTAAHCGNK PLWARVGDDH LLLLQGEQLR RTTRSVVHPK
YHQGSGPILP RRTDEHDLML LKLARPVVLG PRVRALQLPY RCAQPGDQCQ VAGWGTTAAR
RVKYNKGLTC SSITILSPKE CEVFYPGVVT NNMICAGLDR GQDPCQSDSG GPLVCDETLQ
GILSWGVYPC GSAQHPAVYT QICKYMSWIN KVIRSN*

mutated AA sequence

MRAPHLHLSA ASGARALAKL LPLLMAQLWA AEAALLPQND TRLDPEAYGA PCARGSQPWQ
VSLFNGLSFH CAGVLVDQSW VLTAAHCGNK PLWARVGDDH LLLLQGEQLR RTTRSVVHPK
YHQGSGPILP RRTDEHDLML LKLARPVVLG PRVRALQLPY RCAQPGDQCQ VAGWGTTAAR
RVKYNKGLTC SSITILSPKE CEVFYPGVVT NNMICAGLDR GQDPCQSDSG GPLVCDETLQ
GILSWGVYPC GSAQHPAVYT QICKYMSWIN KVIRSN*

speed

0.47 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: 1 (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)

chr19:51520487A>CN/A show variant in all transcripts IGV

HGNC symbol

KLK10

Ensembl transcript ID

ENST00000309958

Genbank transcript ID

NM_002776

UniProt peptide

O43240

alteration type

single base exchange

alteration region

CDS

DNA changes

c.148T>G
cDNA.367T>G
g.2945T>G

AA changes

S50A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs3745535

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1301	875	2176
ExAC	23374	-13981	9393

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.327	0
	-0.587	0
(flanking)	0.191	0.001

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 gained	2944	0.56	mu: TATGGCGCCCCGTGC	TGGC\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000011367

Mmulatta

all conserved

ENSMMUG00000015451

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000030693

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000003166

n/a

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
47	274	DOMAIN	Peptidase S1.	lost
52	52	DISULFID	By similarity.	might get lost (downstream of altered splice site)
71	71	DISULFID	By similarity.	might get lost (downstream of altered splice site)
86	86	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
87	87	DISULFID	By similarity.	might get lost (downstream of altered splice site)
137	137	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
162	162	DISULFID	By similarity.	might get lost (downstream of altered splice site)
169	169	DISULFID	By similarity.	might get lost (downstream of altered splice site)
201	201	DISULFID	By similarity.	might get lost (downstream of altered splice site)
215	215	DISULFID	By similarity.	might get lost (downstream of altered splice site)
225	225	DISULFID	By similarity.	might get lost (downstream of altered splice site)
229	229	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
235	235	DISULFID	By similarity.	might get lost (downstream of altered splice site)
250	250	DISULFID	By similarity.	might get lost (downstream of altered splice site)
263	263	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

831 / 831

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

277 / 277

position of stopcodon in wt / mu cDNA

1050 / 1050

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

220 / 220

chromosome

strand

-1

last intron/exon boundary

898

theoretical NMD boundary in CDS

628

length of CDS

831

coding sequence (CDS) position

148

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

367

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

2945

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

51520487

original gDNA sequence snippet

TGGACCCCGAAGCCTATGGCTCCCCGTGCGCGCGCGGCTCG

altered gDNA sequence snippet

TGGACCCCGAAGCCTATGGCGCCCCGTGCGCGCGCGGCTCG

original cDNA sequence snippet

TGGACCCCGAAGCCTATGGCTCCCCGTGCGCGCGCGGCTCG

altered cDNA sequence snippet

TGGACCCCGAAGCCTATGGCGCCCCGTGCGCGCGCGGCTCG

wildtype AA sequence

mutated AA sequence

speed

0.81 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr19:51520487A>CN/A show variant in all transcripts IGV

HGNC symbol

KLK10

Ensembl transcript ID

ENST00000358789

Genbank transcript ID

N/A

UniProt peptide

O43240

alteration type

single base exchange

alteration region

CDS

DNA changes

c.148T>G
cDNA.229T>G
g.2945T>G

AA changes

S50A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs3745535

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1301	875	2176
ExAC	23374	-13981	9393

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.327	0
	-0.587	0
(flanking)	0.191	0.001

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 gained	2944	0.56	mu: TATGGCGCCCCGTGC	TGGC\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000011367

Mmulatta

all conserved

ENSMMUG00000015451

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000030693

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000003166

n/a

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
47	274	DOMAIN	Peptidase S1.	lost
52	52	DISULFID	By similarity.	might get lost (downstream of altered splice site)
71	71	DISULFID	By similarity.	might get lost (downstream of altered splice site)
86	86	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
87	87	DISULFID	By similarity.	might get lost (downstream of altered splice site)
137	137	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
162	162	DISULFID	By similarity.	might get lost (downstream of altered splice site)
169	169	DISULFID	By similarity.	might get lost (downstream of altered splice site)
201	201	DISULFID	By similarity.	might get lost (downstream of altered splice site)
215	215	DISULFID	By similarity.	might get lost (downstream of altered splice site)
225	225	DISULFID	By similarity.	might get lost (downstream of altered splice site)
229	229	ACT_SITE	Charge relay system (By similarity).	might get lost (downstream of altered splice site)
235	235	DISULFID	By similarity.	might get lost (downstream of altered splice site)
250	250	DISULFID	By similarity.	might get lost (downstream of altered splice site)
263	263	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

831 / 831

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

277 / 277

position of stopcodon in wt / mu cDNA

912 / 912

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

82 / 82

chromosome

strand

-1

last intron/exon boundary

760

theoretical NMD boundary in CDS

628

length of CDS

831

coding sequence (CDS) position

148

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

229

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

2945

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

51520487

original gDNA sequence snippet

TGGACCCCGAAGCCTATGGCTCCCCGTGCGCGCGCGGCTCG

altered gDNA sequence snippet

TGGACCCCGAAGCCTATGGCGCCCCGTGCGCGCGCGGCTCG

original cDNA sequence snippet

TGGACCCCGAAGCCTATGGCTCCCCGTGCGCGCGCGGCTCG

altered cDNA sequence snippet

TGGACCCCGAAGCCTATGGCGCCCCGTGCGCGCGCGGCTCG

wildtype AA sequence

mutated AA sequence

speed

0.76 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