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: ENST00000295201
Querying Taster for transcript #2: ENST00000427593
MT speed 0 s - this script 3.462086 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TEKT4	polymorphism_automatic	4.45160900364172e-08	simple_aae		affected		S100G	single base exchange	rs11164112		show file
TEKT4	polymorphism_automatic	4.45160900364172e-08	simple_aae		affected		S100G	single base exchange	rs11164112		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999995548391 (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)

chr2:95537622A>GN/A show variant in all transcripts IGV

HGNC symbol

TEKT4

Ensembl transcript ID

ENST00000295201

Genbank transcript ID

NM_144705

UniProt peptide

Q8WW24

alteration type

single base exchange

alteration region

CDS

DNA changes

c.298A>G
cDNA.435A>G
g.445A>G

AA changes

S100G Score: 56 explain score(s)

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

100

frameshift

known variant

Reference ID: rs11164112

database	homozygous (G/G)	heterozygous	allele carriers
1000G	469	1203	1672
ExAC	7382	18003	25385

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.35	0.912
	-0.332	0.889
(flanking)	0.161	0.924

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	439	wt: 0.22 / mu: 0.75	wt: AGGACACGCACAGCT mu: AGGACACGCACGGCT	GACA\|cgca
Donor marginally increased	447	wt: 0.9647 / mu: 0.9669 (marginal change - not scored)	wt: CACAGCTGGAAGTCG mu: CACGGCTGGAAGTCG	CAGC\|tgga

distance from splice site

201

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

not conserved

100

Ptroglodytes

not conserved

ENSPTRG00000012206

100

Mmulatta

not conserved

ENSMMUG00000022534

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000024175

112

Ggallus

not conserved

ENSGALG00000005247

122

Trubripes

not conserved

ENSTRUG00000006068

122

Drerio

not conserved

ENSDARG00000028899

117

Dmelanogaster

not conserved

FBgn0028902

248

Celegans

not conserved

R02E12.4

287

Xtropicalis

not conserved

ENSXETG00000016064

122

protein features

start (aa)	end (aa)	feature	details
102	180	COILED	Potential.	might get lost (downstream of altered splice site)
310	336	COILED	Potential.	might get lost (downstream of altered splice site)
363	411	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1308 / 1308

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

436 / 436

position of stopcodon in wt / mu cDNA

1445 / 1445

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

138 / 138

chromosome

strand

last intron/exon boundary

1229

theoretical NMD boundary in CDS

1041

length of CDS

1308

coding sequence (CDS) position

298

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

435

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

445

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

95537622

original gDNA sequence snippet

AGCGACTGCAGGACACGCACAGCTGGAAGTCGGAGCTGCAG

altered gDNA sequence snippet

AGCGACTGCAGGACACGCACGGCTGGAAGTCGGAGCTGCAG

original cDNA sequence snippet

AGCGACTGCAGGACACGCACAGCTGGAAGTCGGAGCTGCAG

altered cDNA sequence snippet

AGCGACTGCAGGACACGCACGGCTGGAAGTCGGAGCTGCAG

wildtype AA sequence

MAQTVPPCEL PCKEYDVARN TGAYTSSGLA TASFRTSKYL LEEWFQNCYA RYHQAFADRD
QSERQRHESQ QLATETQALA QRTQQDSTRT VGERLQDTHS WKSELQREME ALAAETNLLL
AQKQRLERAL DATEVPFSIT TDNLQCRERR EHPNLVRDHV ETELLKEAEL IRNIQELLKR
TIMQAVSQIR LNREHKETCE MDWSDKMEAY NIDETCGRHH SQSTEVQAHP YSTTFQESAS
TPETRAKFTQ DNLCRAQRER LASANLRVLV DCILRDTSED LRLQCDAVNL AFGRRCEELE
DARYKLHHHL HKTLREITDQ EHNVAALKQA IKDKEAPLHV AQTRLYLRSH RPNMELCRDA
AQFRLLSEVE ELNMSLTALR EKLLEAEQSL RNLEDIHMSL EKDIAAMTNS LFIDRQKCMA
HRTRYPTILQ LAGYQ*

mutated AA sequence

MAQTVPPCEL PCKEYDVARN TGAYTSSGLA TASFRTSKYL LEEWFQNCYA RYHQAFADRD
QSERQRHESQ QLATETQALA QRTQQDSTRT VGERLQDTHG WKSELQREME ALAAETNLLL
AQKQRLERAL DATEVPFSIT TDNLQCRERR EHPNLVRDHV ETELLKEAEL IRNIQELLKR
TIMQAVSQIR LNREHKETCE MDWSDKMEAY NIDETCGRHH SQSTEVQAHP YSTTFQESAS
TPETRAKFTQ DNLCRAQRER LASANLRVLV DCILRDTSED LRLQCDAVNL AFGRRCEELE
DARYKLHHHL HKTLREITDQ EHNVAALKQA IKDKEAPLHV AQTRLYLRSH RPNMELCRDA
AQFRLLSEVE ELNMSLTALR EKLLEAEQSL RNLEDIHMSL EKDIAAMTNS LFIDRQKCMA
HRTRYPTILQ LAGYQ*

speed

0.76 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: 0.99999995548391 (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)

chr2:95537622A>GN/A show variant in all transcripts IGV

HGNC symbol

TEKT4

Ensembl transcript ID

ENST00000427593

Genbank transcript ID

N/A

UniProt peptide

Q8WW24

alteration type

single base exchange

alteration region

CDS

DNA changes

c.298A>G
cDNA.370A>G
g.445A>G

AA changes

S100G Score: 56 explain score(s)

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

100

frameshift

known variant

Reference ID: rs11164112

database	homozygous (G/G)	heterozygous	allele carriers
1000G	469	1203	1672
ExAC	7382	18003	25385

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.35	0.912
	-0.332	0.889
(flanking)	0.161	0.924

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	439	wt: 0.22 / mu: 0.75	wt: AGGACACGCACAGCT mu: AGGACACGCACGGCT	GACA\|cgca
Donor marginally increased	447	wt: 0.9647 / mu: 0.9669 (marginal change - not scored)	wt: CACAGCTGGAAGTCG mu: CACGGCTGGAAGTCG	CAGC\|tgga

distance from splice site

201

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

100

mutated

not conserved

100

Ptroglodytes

not conserved

ENSPTRG00000012206

100

Mmulatta

not conserved

ENSMMUG00000022534

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000024175

112

Ggallus

not conserved

ENSGALG00000005247

122

Trubripes

not conserved

ENSTRUG00000006068

122

Drerio

not conserved

ENSDARG00000028899

117

Dmelanogaster

not conserved

FBgn0028902

248

Celegans

not conserved

R02E12.4

287

Xtropicalis

not conserved

ENSXETG00000016064

122

protein features

start (aa)	end (aa)	feature	details
102	180	COILED	Potential.	might get lost (downstream of altered splice site)
310	336	COILED	Potential.	might get lost (downstream of altered splice site)
363	411	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

678 / 678

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

226 / 226

position of stopcodon in wt / mu cDNA

750 / 750

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

73 / 73

chromosome

strand

last intron/exon boundary

571

theoretical NMD boundary in CDS

448

length of CDS

678

coding sequence (CDS) position

298

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

370

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

445

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

95537622

original gDNA sequence snippet

AGCGACTGCAGGACACGCACAGCTGGAAGTCGGAGCTGCAG

altered gDNA sequence snippet

AGCGACTGCAGGACACGCACGGCTGGAAGTCGGAGCTGCAG

original cDNA sequence snippet

AGCGACTGCAGGACACGCACAGCTGGAAGTCGGAGCTGCAG

altered cDNA sequence snippet

AGCGACTGCAGGACACGCACGGCTGGAAGTCGGAGCTGCAG

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

Problems