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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000246015
Querying Taster for transcript #2: ENST00000335877
Querying Taster for transcript #3: ENST00000438768
Querying Taster for transcript #4: ENST00000333082
Querying Taster for transcript #5: ENST00000381898
MT speed 0 s - this script 4.231634 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PSMF1	polymorphism_automatic	0.00882846509409896	simple_aae		affected		H174R	single base exchange	rs2235587		show file
PSMF1	polymorphism_automatic	0.00882846509409896	simple_aae		affected		H174R	single base exchange	rs2235587		show file
PSMF1	polymorphism_automatic	0.00882846509409896	simple_aae		affected		H174R	single base exchange	rs2235587		show file
PSMF1	polymorphism_automatic	0.034483127883369	simple_aae		affected		H86R	single base exchange	rs2235587		show file
PSMF1	polymorphism_automatic	0.999999999924684	without_aae		affected			single base exchange	rs2235587		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.991171534905901 (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)

chr20:1115919A>GN/A show variant in all transcripts IGV

HGNC symbol

PSMF1

Ensembl transcript ID

ENST00000246015

Genbank transcript ID

N/A

UniProt peptide

Q92530

alteration type

single base exchange

alteration region

CDS

DNA changes

c.521A>G
cDNA.697A>G
g.22014A>G

AA changes

H174R Score: 29 explain score(s)

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

174

frameshift

known variant

Reference ID: rs2235587

database	homozygous (G/G)	heterozygous	allele carriers
1000G	180	650	830
ExAC	2500	16400	18900

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.424	0.915
	0.462	0.91
(flanking)	-0.129	0.906

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 increased	22024	wt: 0.23 / mu: 0.37	wt: ATTCCTCCACACCACCCACACACCAGTCGGCAGCCTCCCTG mu: ATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTCCCTG	acac\|ACCA
Acc marginally increased	22015	wt: 0.9313 / mu: 0.9396 (marginal change - not scored)	wt: CCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGCA mu: CCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGCA	acac\|CACC
Acc increased	22020	wt: 0.41 / mu: 0.46	wt: CCGGATTCCTCCACACCACCCACACACCAGTCGGCAGCCTC mu: CCGGATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTC	accc\|ACAC
Donor gained	22008	0.41	mu: GATTCCTCCACGCCA	TTCC\|tcca
Donor gained	22013	0.85	mu: CTCCACGCCACCCAC	CCAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

174

mutated

not conserved

174

Ptroglodytes

all identical

ENSPTRG00000013155

174

Mmulatta

all identical

ENSMMUG00000004709

174

Fcatus

not conserved

ENSFCAG00000010927

174

Mmusculus

all identical

ENSMUSG00000032869

174

Ggallus

not conserved

ENSGALG00000000259

174

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000022652

144

Dmelanogaster

not conserved

FBgn0033669

185

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000030118

n/a

protein features

start (aa)	end (aa)	feature	details
154	271	COMPBIAS	Pro-rich.	lost
251	251	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
252	252	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

792 / 792

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

264 / 264

position of stopcodon in wt / mu cDNA

968 / 968

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

177 / 177

chromosome

strand

last intron/exon boundary

941

theoretical NMD boundary in CDS

714

length of CDS

792

coding sequence (CDS) position

521

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

697

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

22014

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

1115919

original gDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered gDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

original cDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered cDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

wildtype AA sequence

MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRTYKNSEEL RSRIVSGIIT PIHEQWEKAN VSSPHREFPP ATAREVDPLR IPPHHPHTSR
QPPWCDPLGP FVVGGEDLDP FGPRRGGMIV DPLRSGFPRA LIDPSSGLPN RLPPGAVPPG
ARFDPFGPIG TSPPGPRPDR RGQ*

mutated AA sequence

MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRTYKNSEEL RSRIVSGIIT PIHEQWEKAN VSSPHREFPP ATAREVDPLR IPPRHPHTSR
QPPWCDPLGP FVVGGEDLDP FGPRRGGMIV DPLRSGFPRA LIDPSSGLPN RLPPGAVPPG
ARFDPFGPIG TSPPGPRPDR RGQ*

speed

0.93 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: 0.991171534905901 (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)

chr20:1115919A>GN/A show variant in all transcripts IGV

HGNC symbol

PSMF1

Ensembl transcript ID

ENST00000335877

Genbank transcript ID

NM_006814

UniProt peptide

Q92530

alteration type

single base exchange

alteration region

CDS

DNA changes

c.521A>G
cDNA.697A>G
g.22014A>G

AA changes

H174R Score: 29 explain score(s)

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

174

frameshift

known variant

Reference ID: rs2235587

database	homozygous (G/G)	heterozygous	allele carriers
1000G	180	650	830
ExAC	2500	16400	18900

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.424	0.915
	0.462	0.91
(flanking)	-0.129	0.906

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 increased	22024	wt: 0.23 / mu: 0.37	wt: ATTCCTCCACACCACCCACACACCAGTCGGCAGCCTCCCTG mu: ATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTCCCTG	acac\|ACCA
Acc marginally increased	22015	wt: 0.9313 / mu: 0.9396 (marginal change - not scored)	wt: CCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGCA mu: CCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGCA	acac\|CACC
Acc increased	22020	wt: 0.41 / mu: 0.46	wt: CCGGATTCCTCCACACCACCCACACACCAGTCGGCAGCCTC mu: CCGGATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTC	accc\|ACAC
Donor gained	22008	0.41	mu: GATTCCTCCACGCCA	TTCC\|tcca
Donor gained	22013	0.85	mu: CTCCACGCCACCCAC	CCAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

174

mutated

not conserved

174

Ptroglodytes

all identical

ENSPTRG00000013155

174

Mmulatta

all identical

ENSMMUG00000004709

174

Fcatus

not conserved

ENSFCAG00000010927

174

Mmusculus

all identical

ENSMUSG00000032869

174

Ggallus

not conserved

ENSGALG00000000259

174

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000022652

144

Dmelanogaster

not conserved

FBgn0033669

185

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000030118

n/a

protein features

start (aa)	end (aa)	feature	details
154	271	COMPBIAS	Pro-rich.	lost
251	251	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
252	252	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

816 / 816

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

272 / 272

position of stopcodon in wt / mu cDNA

992 / 992

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

177 / 177

chromosome

strand

last intron/exon boundary

941

theoretical NMD boundary in CDS

714

length of CDS

816

coding sequence (CDS) position

521

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

697

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

22014

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

1115919

original gDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered gDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

original cDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered cDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

wildtype AA sequence

mutated AA sequence

MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRTYKNSEEL RSRIVSGIIT PIHEQWEKAN VSSPHREFPP ATAREVDPLR IPPRHPHTSR
QPPWCDPLGP FVVGGEDLDP FGPRRGGMIV DPLRSGFPRA LIDPSSGLPN RLPPGAVPPG
ARFDPFGPIG TSPPGPNPDH LPPPGYDDMY L*

speed

0.64 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.991171534905901 (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)

chr20:1115919A>GN/A show variant in all transcripts IGV

HGNC symbol

PSMF1

Ensembl transcript ID

ENST00000333082

Genbank transcript ID

NM_178578

UniProt peptide

Q92530

alteration type

single base exchange

alteration region

CDS

DNA changes

c.521A>G
cDNA.689A>G
g.22014A>G

AA changes

H174R Score: 29 explain score(s)

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

174

frameshift

known variant

Reference ID: rs2235587

database	homozygous (G/G)	heterozygous	allele carriers
1000G	180	650	830
ExAC	2500	16400	18900

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.424	0.915
	0.462	0.91
(flanking)	-0.129	0.906

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 increased	22024	wt: 0.23 / mu: 0.37	wt: ATTCCTCCACACCACCCACACACCAGTCGGCAGCCTCCCTG mu: ATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTCCCTG	acac\|ACCA
Acc marginally increased	22015	wt: 0.9313 / mu: 0.9396 (marginal change - not scored)	wt: CCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGCA mu: CCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGCA	acac\|CACC
Acc increased	22020	wt: 0.41 / mu: 0.46	wt: CCGGATTCCTCCACACCACCCACACACCAGTCGGCAGCCTC mu: CCGGATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTC	accc\|ACAC
Donor gained	22008	0.41	mu: GATTCCTCCACGCCA	TTCC\|tcca
Donor gained	22013	0.85	mu: CTCCACGCCACCCAC	CCAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

174

mutated

not conserved

174

Ptroglodytes

all identical

ENSPTRG00000013155

174

Mmulatta

all identical

ENSMMUG00000004709

174

Fcatus

not conserved

ENSFCAG00000010927

174

Mmusculus

all identical

ENSMUSG00000032869

174

Ggallus

not conserved

ENSGALG00000000259

174

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000022652

144

Dmelanogaster

not conserved

FBgn0033669

185

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000030118

n/a

protein features

start (aa)	end (aa)	feature	details
154	271	COMPBIAS	Pro-rich.	lost
251	251	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
252	252	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

816 / 816

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

272 / 272

position of stopcodon in wt / mu cDNA

984 / 984

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

169 / 169

chromosome

strand

last intron/exon boundary

933

theoretical NMD boundary in CDS

714

length of CDS

816

coding sequence (CDS) position

521

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

689

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

22014

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

1115919

original gDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered gDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

original cDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered cDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

wildtype AA sequence

mutated AA sequence

MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRTYKNSEEL RSRIVSGIIT PIHEQWEKAN VSSPHREFPP ATAREVDPLR IPPRHPHTSR
QPPWCDPLGP FVVGGEDLDP FGPRRGGMIV DPLRSGFPRA LIDPSSGLPN RLPPGAVPPG
ARFDPFGPIG TSPPGPNPDH LPPPGYDDMY L*

speed

0.88 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.965516872116631 (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)

chr20:1115919A>GN/A show variant in all transcripts IGV

HGNC symbol

PSMF1

Ensembl transcript ID

ENST00000381898

Genbank transcript ID

N/A

UniProt peptide

Q92530

alteration type

single base exchange

alteration region

CDS

DNA changes

c.257A>G
cDNA.539A>G
g.22014A>G

AA changes

H86R Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs2235587

database	homozygous (G/G)	heterozygous	allele carriers
1000G	180	650	830
ExAC	2500	16400	18900

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.424	0.915
	0.462	0.91
(flanking)	-0.129	0.906

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 increased	22024	wt: 0.23 / mu: 0.37	wt: ATTCCTCCACACCACCCACACACCAGTCGGCAGCCTCCCTG mu: ATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTCCCTG	acac\|ACCA
Acc marginally increased	22015	wt: 0.9313 / mu: 0.9396 (marginal change - not scored)	wt: CCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGCA mu: CCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGCA	acac\|CACC
Acc increased	22020	wt: 0.41 / mu: 0.46	wt: CCGGATTCCTCCACACCACCCACACACCAGTCGGCAGCCTC mu: CCGGATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTC	accc\|ACAC
Donor gained	22008	0.41	mu: GATTCCTCCACGCCA	TTCC\|tcca
Donor gained	22013	0.85	mu: CTCCACGCCACCCAC	CCAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000013155

174

Mmulatta

all identical

ENSMMUG00000004709

174

Fcatus

not conserved

ENSFCAG00000010927

174

Mmusculus

all identical

ENSMUSG00000032869

174

Ggallus

not conserved

ENSGALG00000000259

174

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000022652

145

Dmelanogaster

not conserved

FBgn0033669

184

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000030118

n/a

protein features

start (aa)	end (aa)	feature	details
77	85	STRAND		might get lost (downstream of altered splice site)
88	95	STRAND		might get lost (downstream of altered splice site)
96	99	TURN		might get lost (downstream of altered splice site)
100	107	STRAND		might get lost (downstream of altered splice site)
108	111	HELIX		might get lost (downstream of altered splice site)
120	123	HELIX		might get lost (downstream of altered splice site)
127	137	HELIX		might get lost (downstream of altered splice site)
153	153	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
154	271	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
251	251	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
252	252	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

528 / 528

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

176 / 176

position of stopcodon in wt / mu cDNA

810 / 810

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

283 / 283

chromosome

strand

last intron/exon boundary

783

theoretical NMD boundary in CDS

450

length of CDS

528

coding sequence (CDS) position

257

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

539

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

22014

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

1115919

original gDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered gDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

original cDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered cDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

wildtype AA sequence

MILNVLEYGS QQVADLTLNL DDYIDAEHLG DFHRTYKNSE ELRSRIVSGI ITPIHEQWEK
ANVSSPHREF PPATAREVDP LRIPPHHPHT SRQPPWCDPL GPFVVGGEDL DPFGPRRGGM
IVDPLRSGFP RALIDPSSGL PNRLPPGAVP PGARFDPFGP IGTSPPGPRP DRRGQ*

mutated AA sequence

MILNVLEYGS QQVADLTLNL DDYIDAEHLG DFHRTYKNSE ELRSRIVSGI ITPIHEQWEK
ANVSSPHREF PPATAREVDP LRIPPRHPHT SRQPPWCDPL GPFVVGGEDL DPFGPRRGGM
IVDPLRSGFP RALIDPSSGL PNRLPPGAVP PGARFDPFGP IGTSPPGPRP DRRGQ*

speed

0.49 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 7.5315862940123e-11 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr20:1115919A>GN/A show variant in all transcripts IGV

HGNC symbol

PSMF1

Ensembl transcript ID

ENST00000438768

Genbank transcript ID

N/A

UniProt peptide

Q92530

alteration type

single base exchange

alteration region

intron

DNA changes

g.22014A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2235587

database	homozygous (G/G)	heterozygous	allele carriers
1000G	180	650	830
ExAC	2500	16400	18900

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.424	0.915
	0.462	0.91
(flanking)	-0.129	0.906

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 increased	22024	wt: 0.23 / mu: 0.37	wt: ATTCCTCCACACCACCCACACACCAGTCGGCAGCCTCCCTG mu: ATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTCCCTG	acac\|ACCA
Acc marginally increased	22015	wt: 0.9313 / mu: 0.9396 (marginal change - not scored)	wt: CCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGCA mu: CCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGCA	acac\|CACC
Acc increased	22020	wt: 0.41 / mu: 0.46	wt: CCGGATTCCTCCACACCACCCACACACCAGTCGGCAGCCTC mu: CCGGATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTC	accc\|ACAC
Donor gained	22008	0.41	mu: GATTCCTCCACGCCA	TTCC\|tcca
Donor gained	22013	0.85	mu: CTCCACGCCACCCAC	CCAC\|gcca

distance from splice site

7768

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
120	123	HELIX		might get lost (downstream of altered splice site)
127	137	HELIX		might get lost (downstream of altered splice site)
153	153	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
154	271	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
251	251	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
252	252	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

716

theoretical NMD boundary in CDS

528

length of CDS

606

coding sequence (CDS) position

N/A

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

N/A

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

22014

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

1115919

original gDNA sequence snippet

CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC

altered gDNA sequence snippet

CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRCDPLGPFV VGGEDLDPFG PRRGGMIVDP LRSGFPRALI DPSSGLPNRL PPGAVPPGAR
FDPFGPIGTS PPGPRPDRRG Q*

mutated AA sequence

N/A

speed

0.44 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

Problems