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: ENST00000297534
Querying Taster for transcript #2: ENST00000541515
Querying Taster for transcript #3: ENST00000541170
MT speed 0 s - this script 3.330395 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FMC1	polymorphism_automatic	2.95466495714436e-09	simple_aae				S8A	single base exchange	rs10265		show file
LUC7L2	polymorphism_automatic	2.59756827603042e-06	simple_aae				S8A	single base exchange	rs10265		show file
LUC7L2	polymorphism_automatic	0.999999999505957	without_aae					single base exchange	rs10265		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999997045335 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:139026152T>GN/A show variant in all transcripts IGV

HGNC symbol

FMC1

Ensembl transcript ID

ENST00000297534

Genbank transcript ID

NM_197964

UniProt peptide

Q96HJ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.22T>G
cDNA.275T>G
g.1950T>G

AA changes

S8A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs10265

database	homozygous (G/G)	heterozygous	allele carriers
1000G	638	813	1451
ExAC	6445	19877	26322

regulatory features

Ini1, Transcription Factor, Ini1 Transcription Factor Binding
p300, Transcription Factor, p300 Transcription Factor Binding
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
GTF2B, Transcription Factor, GTF2B Transcription Factor Binding
H2BK12ac, Histone, Histone 2B Lysine 12 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
Jund, Transcription Factor, Jund TF binding
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolIII Transcription Associated, Regulatory Feature, PolIII transcribed RNA gene associated regulatory feature
Znf263, Transcription Factor, Znf263 TF binding
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
TFIIIC-110, Transcription Factor, TFIIIC-110 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.185	1
	0.364	0.999
(flanking)	1.015	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

117

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000019754

Mmulatta

all conserved

ENSMMUG00000006769

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000019689

Ggallus

not conserved

ENSGALG00000011856

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000074266

Dmelanogaster

no alignment

FBgn0083953

n/a

Celegans

no alignment

C29E4.12

n/a

Xtropicalis

not conserved

ENSXETG00000032301

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

342 / 342

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

114 / 114

position of stopcodon in wt / mu cDNA

595 / 595

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

254 / 254

chromosome

strand

last intron/exon boundary

392

theoretical NMD boundary in CDS

length of CDS

342

coding sequence (CDS) position

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

275

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

1950

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

139026152

original gDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGTCGCACACTTTTCGAGGACTT

altered gDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGGCGCACACTTTTCGAGGACTT

original cDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGTCGCACACTTTTCGAGGACTT

altered cDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGGCGCACACTTTTCGAGGACTT

wildtype AA sequence

MAALGSPSHT FRGLLRELRY LSAATGRPYR DTAAYRYLVK AFRAHRVTSE KLCRAQHELH
FQAATYLCLL RSIRKHVALH QEFHGKGERS VEESAGLVGL KLPHQPGGKG WEP*

mutated AA sequence

MAALGSPAHT FRGLLRELRY LSAATGRPYR DTAAYRYLVK AFRAHRVTSE KLCRAQHELH
FQAATYLCLL RSIRKHVALH QEFHGKGERS VEESAGLVGL KLPHQPGGKG WEP*

speed

0.35 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: 0.999997402431724 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:139026152T>GN/A show variant in all transcripts IGV

HGNC symbol

LUC7L2

Ensembl transcript ID

ENST00000541515

Genbank transcript ID

N/A

UniProt peptide

Q9Y383

alteration type

single base exchange

alteration region

CDS

DNA changes

c.22T>G
cDNA.47T>G
g.1048T>G

AA changes

S8A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs10265

database	homozygous (G/G)	heterozygous	allele carriers
1000G	638	813	1451
ExAC	6445	19877	26322

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.185	1
	0.364	0.999
(flanking)	1.015	1

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

splice sites

no abrogation of potential splice sites

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

no alignment

ENSPTRG00000019755

n/a

Mmulatta

no alignment

ENSMMUG00000006770

n/a

Fcatus

no alignment

ENSFCAG00000010563

n/a

Mmusculus

no alignment

ENSMUSG00000029823

n/a

Ggallus

no alignment

ENSGALG00000011857

n/a

Trubripes

no alignment

ENSTRUG00000000039

n/a

Drerio

no alignment

ENSDARG00000019765

n/a

Dmelanogaster

no alignment

FBgn0036734

n/a

Celegans

no alignment

B0495.8

n/a

Xtropicalis

no alignment

ENSXETG00000000229

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1377 / 1377

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

459 / 459

position of stopcodon in wt / mu cDNA

1402 / 1402

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

26 / 26

chromosome

strand

last intron/exon boundary

1225

theoretical NMD boundary in CDS

1149

length of CDS

1377

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)

1048

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

139026152

original gDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGTCGCACACTTTTCGAGGACTT

altered gDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGGCGCACACTTTTCGAGGACTT

original cDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGTCGCACACTTTTCGAGGACTT

altered cDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGGCGCACACTTTTCGAGGACTT

wildtype AA sequence

MAALGSPSHT FRGLLRELRY LSAATGRPYR DTAAYRYLVK AFRAHRVTSE KLCRAQHELH
FQAATYLCLL RSIRKHVALH QEFHGKGDTT RQRIKFSDDR VCKSHLLNCC PHDVLSGTRM
DLGECLKVHD LALRADYEIA SKEQDFFFEL DAMDHLQSFI ADCDRRTEVA KKRLAETQEE
ISAEVAAKAE RVHELNEEIG KLLAKVEQLG AEGNVEESQK VMDEVEKARA KKREAEEVYR
NSMPASSFQQ QKLRVCEVCS AYLGLHDNDR RLADHFGGKL HLGFIEIREK LEELKRVVAE
KQEKRNQERL KRREEREREE REKLRRSRSH SKNPKRSRSR EHRRHRSRSM SRERKRRTRS
KSREKRHRHR SRSSSRSRSR SHQRSRHSSR DRSRERSKRR SSKERFRDQD LASCDRDRSS
RDRSPRDRDR KDKKRSYESA NGRSEDRRSS EEREAGEI*

mutated AA sequence

MAALGSPAHT FRGLLRELRY LSAATGRPYR DTAAYRYLVK AFRAHRVTSE KLCRAQHELH
FQAATYLCLL RSIRKHVALH QEFHGKGDTT RQRIKFSDDR VCKSHLLNCC PHDVLSGTRM
DLGECLKVHD LALRADYEIA SKEQDFFFEL DAMDHLQSFI ADCDRRTEVA KKRLAETQEE
ISAEVAAKAE RVHELNEEIG KLLAKVEQLG AEGNVEESQK VMDEVEKARA KKREAEEVYR
NSMPASSFQQ QKLRVCEVCS AYLGLHDNDR RLADHFGGKL HLGFIEIREK LEELKRVVAE
KQEKRNQERL KRREEREREE REKLRRSRSH SKNPKRSRSR EHRRHRSRSM SRERKRRTRS
KSREKRHRHR SRSSSRSRSR SHQRSRHSSR DRSRERSKRR SSKERFRDQD LASCDRDRSS
RDRSPRDRDR KDKKRSYESA NGRSEDRRSS EEREAGEI*

speed

0.42 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.9404332948582e-10 (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)

chr7:139026152T>GN/A show variant in all transcripts IGV

HGNC symbol

LUC7L2

Ensembl transcript ID

ENST00000541170

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.1048T>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs10265

database	homozygous (G/G)	heterozygous	allele carriers
1000G	638	813	1451
ExAC	6445	19877	26322

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.185	1
	0.364	0.999
(flanking)	1.015	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

889

Kozak consensus sequence altered?

N/A

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

185 / 185

chromosome

strand

last intron/exon boundary

1177

theoretical NMD boundary in CDS

942

length of CDS

1170

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)

1048

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

139026152

original gDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGTCGCACACTTTTCGAGGACTT

altered gDNA sequence snippet

TGGCGGCCTTAGGGTCCCCGGCGCACACTTTTCGAGGACTT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVIHSQLKKI QGASERMGDT TRQRIKFSDD RVCKSHLLNC CPHDVLSGTR MDLGECLKVH
DLALRADYEI ASKEQDFFFE LDAMDHLQSF IADCDRRTEV AKKRLAETQE EISAEVAAKA
ERVHELNEEI GKLLAKVEQL GAEGNVEESQ KVMDEVEKAR AKKREAEEVY RNSMPASSFQ
QQKLRVCEVC SAYLGLHDND RRLADHFGGK LHLGFIEIRE KLEELKRVVA EKQEKRNQER
LKRREERERE EREKLRRSRS HSKNPKRSRS REHRRHRSRS MSRERKRRTR SKSREKRHRH
RSRSSSRSRS RSHQRSRHSS RDRSRERSKR RSSKERFRDQ DLASCDRDRS SRDRSPRDRD
RKDKKRSYES ANGRSEDRRS SEEREAGEI*

mutated AA sequence

N/A

speed

0.92 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