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: ENST00000474069
Querying Taster for transcript #2: ENST00000480462
Querying Taster for transcript #3: ENST00000434001
Querying Taster for transcript #4: ENST00000477515
Querying Taster for transcript #5: ENST00000378704
MT speed 0 s - this script 3.78014 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FAM71F2	polymorphism_automatic	0.059293426687465	simple_aae				R127W	single base exchange	rs6467210		show file
FAM71F2	polymorphism_automatic	0.059293426687465	simple_aae				R136W	single base exchange	rs6467210		show file
FAM71F2	polymorphism_automatic	0.059293426687465	simple_aae				R127W	single base exchange	rs6467210		show file
FAM71F2	polymorphism_automatic	0.059293426687465	simple_aae				R127W	single base exchange	rs6467210		show file
FAM71F2	polymorphism_automatic	0.999630923447491	without_aae					single base exchange	rs6467210		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.940706573312535 (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)

chr7:128317658C>TN/A show variant in all transcripts IGV

HGNC symbol

FAM71F2

Ensembl transcript ID

ENST00000474069

Genbank transcript ID

NM_001128926

UniProt peptide

Q6NXP2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.379C>T
cDNA.485C>T
g.5317C>T

AA changes

R127W Score: 101 explain score(s)

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

127

frameshift

known variant

Reference ID: rs6467210

database	homozygous (T/T)	heterozygous	allele carriers
1000G	332	993	1325
ExAC	5936	20895	26831

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.656	0.83
	0.996	0.709
(flanking)	0.283	0.268

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

127

mutated

not conserved

127

Ptroglodytes

all identical

ENSPTRG00000028396

127

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000000950

136

Mmusculus

all identical

ENSMUSG00000079652

126

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

903 / 903

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

301 / 301

position of stopcodon in wt / mu cDNA

1009 / 1009

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

107 / 107

chromosome

strand

last intron/exon boundary

1106

theoretical NMD boundary in CDS

949

length of CDS

903

coding sequence (CDS) position

379

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

485

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

5317

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

128317658

original gDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered gDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

original cDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered cDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

wildtype AA sequence

MSKIRGLPPE VREPGPGVEL GVENGLLCQL IHSPEFNLFS NSVVFESNFI QVTKPGNWRD
VCEGSATVIL GVTSSVPSLP LPNVLLMANV TWPQGPFTTW STPGDAPVIN LSRLLPLKYV
ELRIYDRLQR ILRVRTVTEK IYYLKLHEKH PEIVFQFWVR LVKILQKGLS ITTKDPRIKF
THCLVPKMPT NSTETTPENS LLSSPQPSEP LVLLAAEQTS GSFSQLSGKP QLTADRNNDT
AIEIDNCSSY KIPSPVASPI NLNIPMRAAL SHSLWEQEDW NEHLLQVHIA SYLGEHFLGA
*

mutated AA sequence

MSKIRGLPPE VREPGPGVEL GVENGLLCQL IHSPEFNLFS NSVVFESNFI QVTKPGNWRD
VCEGSATVIL GVTSSVPSLP LPNVLLMANV TWPQGPFTTW STPGDAPVIN LSRLLPLKYV
ELRIYDWLQR ILRVRTVTEK IYYLKLHEKH PEIVFQFWVR LVKILQKGLS ITTKDPRIKF
THCLVPKMPT NSTETTPENS LLSSPQPSEP LVLLAAEQTS GSFSQLSGKP QLTADRNNDT
AIEIDNCSSY KIPSPVASPI NLNIPMRAAL SHSLWEQEDW NEHLLQVHIA SYLGEHFLGA
*

speed

0.83 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: 0.940706573312535 (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)

chr7:128317658C>TN/A show variant in all transcripts IGV

HGNC symbol

FAM71F2

Ensembl transcript ID

ENST00000480462

Genbank transcript ID

NM_001012454

UniProt peptide

Q6NXP2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.406C>T
cDNA.512C>T
g.5317C>T

AA changes

R136W Score: 101 explain score(s)

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

136

frameshift

known variant

Reference ID: rs6467210

database	homozygous (T/T)	heterozygous	allele carriers
1000G	332	993	1325
ExAC	5936	20895	26831

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.656	0.83
	0.996	0.709
(flanking)	0.283	0.268

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

136

mutated

not conserved

136

Ptroglodytes

all identical

ENSPTRG00000028396

127

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000000950

136

Mmusculus

all identical

ENSMUSG00000079652

126

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

930 / 930

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

310 / 310

position of stopcodon in wt / mu cDNA

1036 / 1036

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

107 / 107

chromosome

strand

last intron/exon boundary

841

theoretical NMD boundary in CDS

684

length of CDS

930

coding sequence (CDS) position

406

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

512

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

5317

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

128317658

original gDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered gDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

original cDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered cDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

wildtype AA sequence

MSKIRGLPPE VREPGPGVEL GVENGLLCQL IHSPEFNLFS NSVVFESNFI QTHVPEADFQ
VTKPGNWRDV CEGSATVILG VTSSVPSLPL PNVLLMANVT WPQGPFTTWS TPGDAPVINL
SRLLPLKYVE LRIYDRLQRI LRVRTVTEKI YYLKLHEKHP EIVFQFWVRL VKILQKGLSI
TTKDPRIKFT HCLVPKMPTN STETTPENSL LSSPQPSEPL VLLAAEQTSG SFSQLSGKPQ
LTADRNNDTA IEIDNCSSYK IPSPVASPIN LNIPMRAALS HSLWEQEDWN EHLLQVHIAS
YLGEHFLGA*

mutated AA sequence

MSKIRGLPPE VREPGPGVEL GVENGLLCQL IHSPEFNLFS NSVVFESNFI QTHVPEADFQ
VTKPGNWRDV CEGSATVILG VTSSVPSLPL PNVLLMANVT WPQGPFTTWS TPGDAPVINL
SRLLPLKYVE LRIYDWLQRI LRVRTVTEKI YYLKLHEKHP EIVFQFWVRL VKILQKGLSI
TTKDPRIKFT HCLVPKMPTN STETTPENSL LSSPQPSEPL VLLAAEQTSG SFSQLSGKPQ
LTADRNNDTA IEIDNCSSYK IPSPVASPIN LNIPMRAALS HSLWEQEDWN EHLLQVHIAS
YLGEHFLGA*

speed

0.61 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.940706573312535 (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)

chr7:128317658C>TN/A show variant in all transcripts IGV

HGNC symbol

FAM71F2

Ensembl transcript ID

ENST00000434001

Genbank transcript ID

N/A

UniProt peptide

Q6NXP2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.379C>T
cDNA.484C>T
g.5317C>T

AA changes

R127W Score: 101 explain score(s)

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

127

frameshift

known variant

Reference ID: rs6467210

database	homozygous (T/T)	heterozygous	allele carriers
1000G	332	993	1325
ExAC	5936	20895	26831

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.656	0.83
	0.996	0.709
(flanking)	0.283	0.268

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

127

mutated

not conserved

127

Ptroglodytes

all identical

ENSPTRG00000028396

127

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000000950

136

Mmusculus

all identical

ENSMUSG00000079652

126

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

903 / 903

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

301 / 301

position of stopcodon in wt / mu cDNA

1008 / 1008

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

106 / 106

chromosome

strand

last intron/exon boundary

1159

theoretical NMD boundary in CDS

1003

length of CDS

903

coding sequence (CDS) position

379

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

484

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

5317

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

128317658

original gDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered gDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

original cDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered cDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

wildtype AA sequence

mutated AA sequence

speed

0.54 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.940706573312535 (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)

chr7:128317658C>TN/A show variant in all transcripts IGV

HGNC symbol

FAM71F2

Ensembl transcript ID

ENST00000378704

Genbank transcript ID

NM_001128926

UniProt peptide

Q6NXP2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.379C>T
cDNA.485C>T
g.5317C>T

AA changes

R127W Score: 101 explain score(s)

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

127

frameshift

known variant

Reference ID: rs6467210

database	homozygous (T/T)	heterozygous	allele carriers
1000G	332	993	1325
ExAC	5936	20895	26831

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.656	0.83
	0.996	0.709
(flanking)	0.283	0.268

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

127

mutated

not conserved

127

Ptroglodytes

all identical

ENSPTRG00000028396

127

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000000950

136

Mmusculus

all identical

ENSMUSG00000079652

126

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

903 / 903

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

301 / 301

position of stopcodon in wt / mu cDNA

1009 / 1009

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

107 / 107

chromosome

strand

last intron/exon boundary

814

theoretical NMD boundary in CDS

657

length of CDS

903

coding sequence (CDS) position

379

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

485

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

5317

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

128317658

original gDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered gDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

original cDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered cDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

wildtype AA sequence

mutated AA sequence

speed

0.39 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.000369076552509387 (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)

chr7:128317658C>TN/A show variant in all transcripts IGV

HGNC symbol

FAM71F2

Ensembl transcript ID

ENST00000477515

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.5317C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6467210

database	homozygous (T/T)	heterozygous	allele carriers
1000G	332	993	1325
ExAC	5936	20895	26831

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.656	0.83
	0.996	0.709
(flanking)	0.283	0.268

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

1745

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

100 / 100

chromosome

strand

last intron/exon boundary

584

theoretical NMD boundary in CDS

434

length of CDS

510

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)

5317

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

128317658

original gDNA sequence snippet

TGGAGCTACGAATCTACGACCGGCTCCAGCGCATCCTGAGG

altered gDNA sequence snippet

TGGAGCTACGAATCTACGACTGGCTCCAGCGCATCCTGAGG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSKIRGLPPE VREPGPGVEL GVENGLLCQL IHSPEFNLFS NSVVFESNFI QTHVPEADFQ
VTKPGNWRDV CEGSATVILG VTSSVPSLPL PNVLLMANVT WPQGPFTTWS TPGDAPVINL
SSLKTASCHP PSPASPSCCW RLSRPVAVSH SSQESPSSQQ TGTMTLPLK*

mutated AA sequence

N/A

speed

0.46 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