MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000231751
Querying Taster for transcript #2: ENST00000417439
Querying Taster for transcript #3: ENST00000426532
MT speed 0 s - this script 3.323714 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LTF	polymorphism_automatic	5.55919754674505e-11	simple_aae				A29T	single base exchange	rs1126477		show file
LTF	polymorphism_automatic	5.55919754674505e-11	simple_aae				A29T	single base exchange	rs1126477		show file
LTF	polymorphism_automatic	2.42637797798206e-06	without_aae					single base exchange	rs1126477		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999944408 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:46501268C>TN/A show variant in all transcripts IGV

HGNC symbol

LTF

Ensembl transcript ID

ENST00000231751

Genbank transcript ID

NM_002343

UniProt peptide

P02788

alteration type

single base exchange

alteration region

CDS

DNA changes

c.85G>A
cDNA.381G>A
g.25457G>A

AA changes

A29T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs1126477

database	homozygous (T/T)	heterozygous	allele carriers
1000G	648	1056	1704
ExAC	7529	17709	25238

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.693	0.001
	-1.456	0
(flanking)	-0.894	0.004

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 marginally increased	25449	wt: 0.9866 / mu: 0.9957 (marginal change - not scored)	wt: TGTTCAGTGGTGCGC mu: TGTTCAGTGGTGCAC	TTCA\|gtgg

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

not conserved

ENSPTRG00000014850

Mmulatta

all identical

ENSMMUG00000014261

Fcatus

not conserved

ENSFCAG00000014504

Mmusculus

all identical

ENSMUSG00000032496

Ggallus

not conserved

ENSGALG00000006453

Trubripes

not conserved

ENSTRUG00000005493

Drerio

not conserved

ENSDARG00000016771

Dmelanogaster

not conserved

FBgn0036299

454

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000011814

protein features

start (aa)	end (aa)	feature	details
24	31	STRAND		lost
25	352	DOMAIN	Transferrin-like 1.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2133 / 2133

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

711 / 711

position of stopcodon in wt / mu cDNA

2429 / 2429

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

297 / 297

chromosome

strand

-1

last intron/exon boundary

2395

theoretical NMD boundary in CDS

2048

length of CDS

2133

coding sequence (CDS) position

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

381

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

25457

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

46501268

original gDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC

altered gDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC

original cDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC

altered cDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC

wildtype AA sequence

MKLVFLVLLF LGALGLCLAG RRRSVQWCAV SQPEATKCFQ WQRNMRKVRG PPVSCIKRDS
PIQCIQAIAE NRADAVTLDG GFIYEAGLAP YKLRPVAAEV YGTERQPRTH YYAVAVVKKG
GSFQLNELQG LKSCHTGLRR TAGWNVPIGT LRPFLNWTGP PEPIEAAVAR FFSASCVPGA
DKGQFPNLCR LCAGTGENKC AFSSQEPYFS YSGAFKCLRD GAGDVAFIRE STVFEDLSDE
AERDEYELLC PDNTRKPVDK FKDCHLARVP SHAVVARSVN GKEDAIWNLL RQAQEKFGKD
KSPKFQLFGS PSGQKDLLFK DSAIGFSRVP PRIDSGLYLG SGYFTAIQNL RKSEEEVAAR
RARVVWCAVG EQELRKCNQW SGLSEGSVTC SSASTTEDCI ALVLKGEADA MSLDGGYVYT
AGKCGLVPVL AENYKSQQSS DPDPNCVDRP VEGYLAVAVV RRSDTSLTWN SVKGKKSCHT
AVDRTAGWNI PMGLLFNQTG SCKFDEYFSQ SCAPGSDPRS NLCALCIGDE QGENKCVPNS
NERYYGYTGA FRCLAENAGD VAFVKDVTVL QNTDGNNNEA WAKDLKLADF ALLCLDGKRK
PVTEARSCHL AMAPNHAVVS RMDKVERLKQ VLLHQQAKFG RNGSDCPDKF CLFQSETKNL
LFNDNTECLA RLHGKTTYEK YLGPQYVAGI TNLKKCSTSP LLEACEFLRK *

mutated AA sequence

MKLVFLVLLF LGALGLCLAG RRRSVQWCTV SQPEATKCFQ WQRNMRKVRG PPVSCIKRDS
PIQCIQAIAE NRADAVTLDG GFIYEAGLAP YKLRPVAAEV YGTERQPRTH YYAVAVVKKG
GSFQLNELQG LKSCHTGLRR TAGWNVPIGT LRPFLNWTGP PEPIEAAVAR FFSASCVPGA
DKGQFPNLCR LCAGTGENKC AFSSQEPYFS YSGAFKCLRD GAGDVAFIRE STVFEDLSDE
AERDEYELLC PDNTRKPVDK FKDCHLARVP SHAVVARSVN GKEDAIWNLL RQAQEKFGKD
KSPKFQLFGS PSGQKDLLFK DSAIGFSRVP PRIDSGLYLG SGYFTAIQNL RKSEEEVAAR
RARVVWCAVG EQELRKCNQW SGLSEGSVTC SSASTTEDCI ALVLKGEADA MSLDGGYVYT
AGKCGLVPVL AENYKSQQSS DPDPNCVDRP VEGYLAVAVV RRSDTSLTWN SVKGKKSCHT
AVDRTAGWNI PMGLLFNQTG SCKFDEYFSQ SCAPGSDPRS NLCALCIGDE QGENKCVPNS
NERYYGYTGA FRCLAENAGD VAFVKDVTVL QNTDGNNNEA WAKDLKLADF ALLCLDGKRK
PVTEARSCHL AMAPNHAVVS RMDKVERLKQ VLLHQQAKFG RNGSDCPDKF CLFQSETKNL
LFNDNTECLA RLHGKTTYEK YLGPQYVAGI TNLKKCSTSP LLEACEFLRK *

speed

0.77 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: 0.999999999944408 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:46501268C>TN/A show variant in all transcripts IGV

HGNC symbol

LTF

Ensembl transcript ID

ENST00000417439

Genbank transcript ID

N/A

UniProt peptide

P02788

alteration type

single base exchange

alteration region

CDS

DNA changes

c.85G>A
cDNA.86G>A
g.25457G>A

AA changes

A29T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs1126477

database	homozygous (T/T)	heterozygous	allele carriers
1000G	648	1056	1704
ExAC	7529	17709	25238

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.693	0.001
	-1.456	0
(flanking)	-0.894	0.004

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 marginally increased	25449	wt: 0.9866 / mu: 0.9957 (marginal change - not scored)	wt: TGTTCAGTGGTGCGC mu: TGTTCAGTGGTGCAC	TTCA\|gtgg

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

not conserved

ENSPTRG00000014850

Mmulatta

all identical

ENSMMUG00000014261

Fcatus

not conserved

ENSFCAG00000014504

Mmusculus

all identical

ENSMUSG00000032496

Ggallus

not conserved

ENSGALG00000006453

Trubripes

not conserved

ENSTRUG00000005493

Drerio

not conserved

ENSDARG00000016771

Dmelanogaster

not conserved

FBgn0036299

454

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000011814

protein features

start (aa)	end (aa)	feature	details
24	31	STRAND		lost
25	352	DOMAIN	Transferrin-like 1.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2127 / 2127

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

709 / 709

position of stopcodon in wt / mu cDNA

2128 / 2128

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

2 / 2

chromosome

strand

-1

last intron/exon boundary

2094

theoretical NMD boundary in CDS

2042

length of CDS

2127

coding sequence (CDS) position

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

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

25457

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

46501268

original gDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC

altered gDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC

original cDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC

altered cDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC

wildtype AA sequence

MKLVFLVLLF LGALGLCLAG RRRSVQWCAV SQPEATKCFQ WQRNMRKVRG PPVSCIKRDS
PIQCIQAIAE NRADAVTLDG GFIYEAGLAP YKLRPVAAEV YGTERQPRTH YYAVAVVKKG
GSFQLNELQG LKSCHTGLRR TAGWNVPIGT LRPFLNWTGP PEPIEAAVAR FFSASCVPGA
DKGQFPNLCR LCAGTGENKC AFSSQEPYFS YSGAFKCLRD GAGDVAFIRE STVFEDLSDE
AERDEYELLC PDNTRKPVDK FKDCHLARVP SHAVVARSVN GKEDAIWNLL RQAQEKFGKD
KSPKFQLFGS PSGQKDLLFK DSAIGFSRVP PRIDSGLYLG SGYFTAIQNL RKSEEEVAAR
RARVVWCAVG EQELRKCNQW SGLSEGSVTC SSASTTEDCI ALKGEADAMS LDGGYVYTAG
KCGLVPVLAE NYKSQQSSDP DPNCVDRPVE GYLAVAVVRR SDTSLTWNSV KGKKSCHTAV
DRTAGWNIPM GLLFNQTGSC KFDEYFSQSC APGSDPRSNL CALCIGDEQG ENKCVPNSNE
RYYGYTGAFR CLAENAGDVA FVKDVTVLQN TDGNNNEAWA KDLKLADFAL LCLDGKRKPV
TEARSCHLAM APNHAVVSRM DKVERLKQVL LHQQAKFGRN GSDCPDKFCL FQSETKNLLF
NDNTECLARL HGKTTYEKYL GPQYVAGITN LKKCSTSPLL EACEFLRK*

mutated AA sequence

MKLVFLVLLF LGALGLCLAG RRRSVQWCTV SQPEATKCFQ WQRNMRKVRG PPVSCIKRDS
PIQCIQAIAE NRADAVTLDG GFIYEAGLAP YKLRPVAAEV YGTERQPRTH YYAVAVVKKG
GSFQLNELQG LKSCHTGLRR TAGWNVPIGT LRPFLNWTGP PEPIEAAVAR FFSASCVPGA
DKGQFPNLCR LCAGTGENKC AFSSQEPYFS YSGAFKCLRD GAGDVAFIRE STVFEDLSDE
AERDEYELLC PDNTRKPVDK FKDCHLARVP SHAVVARSVN GKEDAIWNLL RQAQEKFGKD
KSPKFQLFGS PSGQKDLLFK DSAIGFSRVP PRIDSGLYLG SGYFTAIQNL RKSEEEVAAR
RARVVWCAVG EQELRKCNQW SGLSEGSVTC SSASTTEDCI ALKGEADAMS LDGGYVYTAG
KCGLVPVLAE NYKSQQSSDP DPNCVDRPVE GYLAVAVVRR SDTSLTWNSV KGKKSCHTAV
DRTAGWNIPM GLLFNQTGSC KFDEYFSQSC APGSDPRSNL CALCIGDEQG ENKCVPNSNE
RYYGYTGAFR CLAENAGDVA FVKDVTVLQN TDGNNNEAWA KDLKLADFAL LCLDGKRKPV
TEARSCHLAM APNHAVVSRM DKVERLKQVL LHQQAKFGRN GSDCPDKFCL FQSETKNLLF
NDNTECLARL HGKTTYEKYL GPQYVAGITN LKKCSTSPLL EACEFLRK*

speed

0.33 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999997573622022 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:46501268C>TN/A show variant in all transcripts IGV

HGNC symbol

LTF

Ensembl transcript ID

ENST00000426532

Genbank transcript ID

NM_001199149

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.270G>A
g.25457G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1126477

database	homozygous (T/T)	heterozygous	allele carriers
1000G	648	1056	1704
ExAC	7529	17709	25238

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.693	0.001
	-1.456	0
(flanking)	-0.894	0.004

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 marginally increased	25449	wt: 0.9866 / mu: 0.9957 (marginal change - not scored)	wt: TGTTCAGTGGTGCGC mu: TGTTCAGTGGTGCAC	TTCA\|gtgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

318 / 318

chromosome

strand

-1

last intron/exon boundary

2284

theoretical NMD boundary in CDS

1916

length of CDS

2001

coding sequence (CDS) position

N/A

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

270

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

25457

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

46501268

original gDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC

altered gDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC

original cDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC

altered cDNA sequence snippet

GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC

wildtype AA sequence

MRKVRGPPVS CIKRDSPIQC IQAIAENRAD AVTLDGGFIY EAGLAPYKLR PVAAEVYGTE
RQPRTHYYAV AVVKKGGSFQ LNELQGLKSC HTGLRRTAGW NVPIGTLRPF LNWTGPPEPI
EAAVARFFSA SCVPGADKGQ FPNLCRLCAG TGENKCAFSS QEPYFSYSGA FKCLRDGAGD
VAFIRESTVF EDLSDEAERD EYELLCPDNT RKPVDKFKDC HLARVPSHAV VARSVNGKED
AIWNLLRQAQ EKFGKDKSPK FQLFGSPSGQ KDLLFKDSAI GFSRVPPRID SGLYLGSGYF
TAIQNLRKSE EEVAARRARV VWCAVGEQEL RKCNQWSGLS EGSVTCSSAS TTEDCIALVL
KGEADAMSLD GGYVYTAGKC GLVPVLAENY KSQQSSDPDP NCVDRPVEGY LAVAVVRRSD
TSLTWNSVKG KKSCHTAVDR TAGWNIPMGL LFNQTGSCKF DEYFSQSCAP GSDPRSNLCA
LCIGDEQGEN KCVPNSNERY YGYTGAFRCL AENAGDVAFV KDVTVLQNTD GNNNEAWAKD
LKLADFALLC LDGKRKPVTE ARSCHLAMAP NHAVVSRMDK VERLKQVLLH QQAKFGRNGS
DCPDKFCLFQ SETKNLLFND NTECLARLHG KTTYEKYLGP QYVAGITNLK KCSTSPLLEA
CEFLRK*

mutated AA sequence

N/A

speed

0.60 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