MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 9 transcript(s)...
Querying Taster for transcript #1: ENST00000411589
Querying Taster for transcript #2: ENST00000442938
Querying Taster for transcript #3: ENST00000354284
Querying Taster for transcript #4: ENST00000354064
Querying Taster for transcript #5: ENST00000533102
Querying Taster for transcript #6: ENST00000313236
Querying Taster for transcript #7: ENST00000524725
Querying Taster for transcript #8: ENST00000359862
Querying Taster for transcript #9: ENST00000544878
MT speed 0 s - this script 8.083028 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TMEM25	polymorphism_automatic	1.60871752030722e-07	simple_aae		affected		Q298R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	1.60871752030722e-07	simple_aae		affected		Q194R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	1.60871752030722e-07	simple_aae		affected		Q342R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	1.60871752030722e-07	simple_aae		affected		Q298R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	1.60871752030722e-07	simple_aae		affected		Q298R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	1.80476439015642e-07	simple_aae		affected		Q297R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	1.80476439015642e-07	simple_aae		affected		Q342R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	1.80476439015642e-07	simple_aae		affected		Q341R	single base exchange	rs12289253		show file
TMEM25	polymorphism_automatic	2.83248597021668e-07	simple_aae		affected		Q245R	single base exchange	rs12289253		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999839128248 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000411589

Genbank transcript ID

NM_001144035

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.893A>G
cDNA.1111A>G
g.3313A>G

AA changes

Q298R Score: 43 explain score(s)

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

298

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

298

mutated

all conserved

298

Ptroglodytes

all conserved

ENSPTRG00000004347

343

Mmulatta

all conserved

ENSMMUG00000005492

342

Fcatus

all conserved

ENSFCAG00000011792

342

Mmusculus

all conserved

ENSMUSG00000002032

342

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

316

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032181

248

protein features

start (aa)	end (aa)	feature	details
254	366	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

969 / 969

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

323 / 323

position of stopcodon in wt / mu cDNA

1187 / 1187

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

219 / 219

chromosome

strand

last intron/exon boundary

1114

theoretical NMD boundary in CDS

845

length of CDS

969

coding sequence (CDS) position

893

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

1111

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTTTCATCCGCCTCCCAG

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTTTCATCCGCCTCCCAG

wildtype AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQFKP EIAQVGAKYQ EAQGPGLLVV LFALVRANPP ANVTWIDQDG PVTVNTSDFL
VLDAQNYPWL TNHTVQLQLR SLAHNLSVVA TNDVGVTSAS LPAPGPSRHP SLISSDSNNL
KLNNVRLPRE NMSLPSNLQL NDLTPDSRAV KPADRQMAQN NSRPELLDPE PGGLLTSQGF
IRLPVLGYIY RVSSVSSDEI WL*

mutated AA sequence

speed

1.33 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: 0.999999839128248 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000354064

Genbank transcript ID

NM_001144036

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.581A>G
cDNA.641A>G
g.3313A>G

AA changes

Q194R Score: 43 explain score(s)

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

194

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

194

mutated

all conserved

194

Ptroglodytes

all conserved

ENSPTRG00000004347

343

Mmulatta

all conserved

ENSMMUG00000005492

342

Fcatus

all conserved

ENSFCAG00000011792

342

Mmusculus

all conserved

ENSMUSG00000002032

342

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

321

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032181

245

protein features

start (aa)	end (aa)	feature	details
27	232	TOPO_DOM	Extracellular (Potential).	lost
205	205	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
233	253	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
254	366	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

657 / 657

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

219 / 219

position of stopcodon in wt / mu cDNA

717 / 717

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

61 / 61

chromosome

strand

last intron/exon boundary

644

theoretical NMD boundary in CDS

533

length of CDS

657

coding sequence (CDS) position

581

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

641

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTTTCATCCGCCTCCCAG

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTTTCATCCGCCTCCCAG

wildtype AA sequence

MALPPGPAAL RHTLLLLPAL LSSVKPEIAQ VGAKYQEAQG PGLLVVLFAL VRANPPANVT
WIDQDGPVTV NTSDFLVLDA QNYPWLTNHT VQLQLRSLAH NLSVVATNDV GVTSASLPAP
GPSRHPSLIS SDSNNLKLNN VRLPRENMSL PSNLQLNDLT PDSRAVKPAD RQMAQNNSRP
ELLDPEPGGL LTSQGFIRLP VLGYIYRVSS VSSDEIWL*

mutated AA sequence

speed

1.19 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999839128248 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000313236

Genbank transcript ID

NM_032780

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1025A>G
cDNA.1078A>G
g.3313A>G

AA changes

Q342R Score: 43 explain score(s)

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

342

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

342

mutated

all conserved

342

Ptroglodytes

all conserved

ENSPTRG00000004347

343

Mmulatta

all conserved

ENSMMUG00000005492

342

Fcatus

all conserved

ENSFCAG00000011792

342

Mmusculus

all conserved

ENSMUSG00000002032

342

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

316

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032181

248

protein features

start (aa)	end (aa)	feature	details
254	366	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1101 / 1101

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

367 / 367

position of stopcodon in wt / mu cDNA

1154 / 1154

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

54 / 54

chromosome

strand

last intron/exon boundary

1081

theoretical NMD boundary in CDS

977

length of CDS

1101

coding sequence (CDS) position

1025

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

1078

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTTTCATCCGCCTCCCAG

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTTTCATCCGCCTCCCAG

wildtype AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQFKP EIAQVGAKYQ EAQGPGLLVV LFALVRANPP ANVTWIDQDG PVTVNTSDFL
VLDAQNYPWL TNHTVQLQLR SLAHNLSVVA TNDVGVTSAS LPAPGLLATR VEVPLLGIVV
AAGLALGTLV GFSTLVACLV CRKEKKTKGP SRHPSLISSD SNNLKLNNVR LPRENMSLPS
NLQLNDLTPD SRAVKPADRQ MAQNNSRPEL LDPEPGGLLT SQGFIRLPVL GYIYRVSSVS
SDEIWL*

mutated AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQFKP EIAQVGAKYQ EAQGPGLLVV LFALVRANPP ANVTWIDQDG PVTVNTSDFL
VLDAQNYPWL TNHTVQLQLR SLAHNLSVVA TNDVGVTSAS LPAPGLLATR VEVPLLGIVV
AAGLALGTLV GFSTLVACLV CRKEKKTKGP SRHPSLISSD SNNLKLNNVR LPRENMSLPS
NLQLNDLTPD SRAVKPADRQ MAQNNSRPEL LDPEPGGLLT SRGFIRLPVL GYIYRVSSVS
SDEIWL*

speed

1.22 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999839128248 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000524725

Genbank transcript ID

N/A

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.893A>G
cDNA.1305A>G
g.3313A>G

AA changes

Q298R Score: 43 explain score(s)

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

298

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

298

mutated

all conserved

298

Ptroglodytes

all conserved

ENSPTRG00000004347

343

Mmulatta

all conserved

ENSMMUG00000005492

342

Fcatus

all conserved

ENSFCAG00000011792

342

Mmusculus

all conserved

ENSMUSG00000002032

342

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

316

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032181

248

protein features

start (aa)	end (aa)	feature	details
254	366	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

969 / 969

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

323 / 323

position of stopcodon in wt / mu cDNA

1381 / 1381

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

413 / 413

chromosome

strand

last intron/exon boundary

1308

theoretical NMD boundary in CDS

845

length of CDS

969

coding sequence (CDS) position

893

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

1305

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTTTCATCCGCCTCCCAG

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTTTCATCCGCCTCCCAG

wildtype AA sequence

mutated AA sequence

speed

0.60 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999839128248 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000359862

Genbank transcript ID

NM_001144034

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.893A>G
cDNA.1067A>G
g.3313A>G

AA changes

Q298R Score: 43 explain score(s)

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

298

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

298

mutated

all conserved

298

Ptroglodytes

all conserved

ENSPTRG00000004347

343

Mmulatta

all conserved

ENSMMUG00000005492

342

Fcatus

all conserved

ENSFCAG00000011792

342

Mmusculus

all conserved

ENSMUSG00000002032

342

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

316

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032181

248

protein features

start (aa)	end (aa)	feature	details
254	366	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

969 / 969

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

323 / 323

position of stopcodon in wt / mu cDNA

1143 / 1143

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

1070

theoretical NMD boundary in CDS

845

length of CDS

969

coding sequence (CDS) position

893

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

1067

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTTTCATCCGCCTCCCAG

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTTTCATCCGCCTCCCAG

wildtype AA sequence

mutated AA sequence

speed

1.19 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999819523561 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000442938

Genbank transcript ID

NM_001144038

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.890A>G
cDNA.1064A>G
g.3313A>G

AA changes

Q297R Score: 43 explain score(s)

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

297

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

297

mutated

all conserved

297

Ptroglodytes

all conserved

ENSPTRG00000004347

342

Mmulatta

all conserved

ENSMMUG00000005492

341

Fcatus

all conserved

ENSFCAG00000011792

341

Mmusculus

all conserved

ENSMUSG00000002032

341

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

319

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032181

n/a

protein features

start (aa)	end (aa)	feature	details
254	366	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

921 / 921

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

307 / 307

position of stopcodon in wt / mu cDNA

1095 / 1095

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

1067

theoretical NMD boundary in CDS

842

length of CDS

921

coding sequence (CDS) position

890

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

1064

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGAAGAAGAAATCAGGACA

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGAAGAAGAAATCAGGACA

wildtype AA sequence

mutated AA sequence

speed

1.46 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999819523561 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000354284

Genbank transcript ID

NM_001144037

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1025A>G
cDNA.1088A>G
g.3313A>G

AA changes

Q342R Score: 43 explain score(s)

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

342

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

342

mutated

all conserved

342

Ptroglodytes

all conserved

ENSPTRG00000004347

343

Mmulatta

all conserved

ENSMMUG00000005492

342

Fcatus

all conserved

ENSFCAG00000011792

342

Mmusculus

all conserved

ENSMUSG00000002032

342

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

316

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032181

n/a

protein features

start (aa)	end (aa)	feature	details
254	366	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1056 / 1056

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

352 / 352

position of stopcodon in wt / mu cDNA

1119 / 1119

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

64 / 64

chromosome

strand

last intron/exon boundary

1091

theoretical NMD boundary in CDS

977

length of CDS

1056

coding sequence (CDS) position

1025

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

1088

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGAAGAAGAAATCAGGACA

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGAAGAAGAAATCAGGACA

wildtype AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQFKP EIAQVGAKYQ EAQGPGLLVV LFALVRANPP ANVTWIDQDG PVTVNTSDFL
VLDAQNYPWL TNHTVQLQLR SLAHNLSVVA TNDVGVTSAS LPAPGLLATR VEVPLLGIVV
AAGLALGTLV GFSTLVACLV CRKEKKTKGP SRHPSLISSD SNNLKLNNVR LPRENMSLPS
NLQLNDLTPD SRAVKPADRQ MAQNNSRPEL LDPEPGGLLT SQGRRNQDKD A*

mutated AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQFKP EIAQVGAKYQ EAQGPGLLVV LFALVRANPP ANVTWIDQDG PVTVNTSDFL
VLDAQNYPWL TNHTVQLQLR SLAHNLSVVA TNDVGVTSAS LPAPGLLATR VEVPLLGIVV
AAGLALGTLV GFSTLVACLV CRKEKKTKGP SRHPSLISSD SNNLKLNNVR LPRENMSLPS
NLQLNDLTPD SRAVKPADRQ MAQNNSRPEL LDPEPGGLLT SRGRRNQDKD A*

speed

1.17 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999819523561 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000533102

Genbank transcript ID

N/A

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1022A>G
cDNA.1082A>G
g.3313A>G

AA changes

Q341R Score: 43 explain score(s)

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

341

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

341

mutated

all conserved

341

Ptroglodytes

all conserved

ENSPTRG00000004347

342

Mmulatta

all conserved

ENSMMUG00000005492

341

Fcatus

all conserved

ENSFCAG00000011792

341

Mmusculus

all conserved

ENSMUSG00000002032

341

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

320

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032181

n/a

protein features

start (aa)	end (aa)	feature	details
254	366	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1146 / 1146

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

382 / 382

position of stopcodon in wt / mu cDNA

1206 / 1206

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

61 / 61

chromosome

strand

last intron/exon boundary

1085

theoretical NMD boundary in CDS

974

length of CDS

1146

coding sequence (CDS) position

1022

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

1082

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGCATGTCTCCTCCACCACG

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGCATGTCTCCTCCACCACG

wildtype AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQFKP EIAQVGAKYQ EAQGPGLLVV LFALVRANPP ANVTWIDQDG PVTVNTSDFL
VLDAQNYPWL TNHTVQLQLR SLAHNLSVVA TNDVGVTSAS LPAPGLLATR VEVPLLGIVV
AAGLALGTLV GFSTLVACLV CRKEKKTKGP SRHPSLISSD SNNLKLNNVR LPRENMSLPS
NLQLNDLTPD SRVKPADRQM AQNNSRPELL DPEPGGLLTS QACLLHHGTP ALTNPWLPHQ
QEGALPGGWS PQAHNSTVWK L*

mutated AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQFKP EIAQVGAKYQ EAQGPGLLVV LFALVRANPP ANVTWIDQDG PVTVNTSDFL
VLDAQNYPWL TNHTVQLQLR SLAHNLSVVA TNDVGVTSAS LPAPGLLATR VEVPLLGIVV
AAGLALGTLV GFSTLVACLV CRKEKKTKGP SRHPSLISSD SNNLKLNNVR LPRENMSLPS
NLQLNDLTPD SRVKPADRQM AQNNSRPELL DPEPGGLLTS RACLLHHGTP ALTNPWLPHQ
QEGALPGGWS PQAHNSTVWK L*

speed

0.60 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999716751403 (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)

chr11:118405068A>GN/A show variant in all transcripts IGV

HGNC symbol

TMEM25

Ensembl transcript ID

ENST00000544878

Genbank transcript ID

N/A

UniProt peptide

Q86YD3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.734A>G
cDNA.804A>G
g.3313A>G

AA changes

Q245R Score: 43 explain score(s)

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

245

frameshift

known variant

Reference ID: rs12289253

database	homozygous (G/G)	heterozygous	allele carriers
1000G	300	898	1198
ExAC	3125	17167	20292

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.632	0.999
	0.288	0.999
(flanking)	2.776	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	3314	sequence motif lost	-	wt: CAAG\|gtac mu: CGAG.gtac
Acc marginally increased	3309	wt: 0.8363 / mu: 0.9140 (marginal change - not scored)	wt: AGCCCGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGG mu: AGCCCGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGG	acca\|GCCA
Donor marginally decreased	3314	wt: 0.8633 / mu: 0.7911 (marginal change - not scored)	wt: AGCCAAGGTACTGGG mu: AGCCGAGGTACTGGG	CCAA\|ggta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

245

mutated

all conserved

245

Ptroglodytes

all conserved

ENSPTRG00000004347

343

Mmulatta

all conserved

ENSMMUG00000005492

342

Fcatus

all conserved

ENSFCAG00000011792

342

Mmusculus

all conserved

ENSMUSG00000002032

341

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000003875

316

Drerio

no alignment

ENSDARG00000077203

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032181

248

protein features

start (aa)	end (aa)	feature	details
233	253	TRANSMEM	Helical; (Potential).	lost
254	366	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

810 / 810

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

270 / 270

position of stopcodon in wt / mu cDNA

880 / 880

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

71 / 71

chromosome

strand

last intron/exon boundary

807

theoretical NMD boundary in CDS

686

length of CDS

810

coding sequence (CDS) position

734

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

804

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

3313

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

118405068

original gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTACTGGGGAAGGGGCCT

altered gDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTACTGGGGAAGGGGCCT

original cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCAAGGTTTCATCCGCCTCCCAG

altered cDNA sequence snippet

CGGCGGCCTCCTCACCAGCCGAGGTTTCATCCGCCTCCCAG

wildtype AA sequence

MALPPGPAAL RHTLLLLPAL LSSGWGELEP QIDGQTWAER ALRENERHAF TCRVAGGPGT
PRLAWYLDGQ LQEASTSRLL SVGGEAFSGG TSTFTVTAHR AQHELNCSLQ DPRSGRSANA
SVILNVQWLL ATRVEVPLLG IVVAAGLALG TLVGFSTLVA CLVCRKEKKT KGPSRHPSLI
SSDSNNLKLN NVRLPRENMS LPSNLQLNDL TPDSRAVKPA DRQMAQNNSR PELLDPEPGG
LLTSQGFIRL PVLGYIYRVS SVSSDEIWL*

mutated AA sequence

speed

0.98 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems