MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000375320
Querying Taster for transcript #2: ENST00000359492
Querying Taster for transcript #3: ENST00000375329
Querying Taster for transcript #4: ENST00000375323
Querying Taster for transcript #5: ENST00000236850
MT speed 0 s - this script 3.840132 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
APOA1	disease_causing_automatic	3.49363162539187e-10	simple_aae			0	R34L	single base exchange	rs28929476		show file
APOA1	disease_causing_automatic	3.49363162539187e-10	simple_aae			0	R34L	single base exchange	rs28929476		show file
APOA1	disease_causing_automatic	3.49363162539187e-10	simple_aae			0	R34L	single base exchange	rs28929476		show file
APOA1	disease_causing_automatic	3.49363162539187e-10	simple_aae			0	R34L	single base exchange	rs28929476		show file
APOA1	disease_causing_automatic	1.23145805483743e-06	without_aae			0		single base exchange	rs28929476		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 3.49363162539187e-10 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM900015)
known disease mutation: rs17920 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116707816C>AN/A show variant in all transcripts IGV

HGNC symbol

APOA1

Ensembl transcript ID

ENST00000375320

Genbank transcript ID

N/A

UniProt peptide

P02647

alteration type

single base exchange

alteration region

CDS

DNA changes

c.101G>T
cDNA.180G>T
g.851G>T

AA changes

R34L Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs28929476

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs17920 (pathogenic for APOLIPOPROTEIN A-I (BALTIMORE)) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900015)

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.263	0
	-0.447	0
(flanking)	0.452	0.001

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

not conserved

Ptroglodytes

all identical

ENSPTRG00000004316

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000032083

Ggallus

all identical

ENSGALG00000007114

Trubripes

not conserved

ENSTRUG00000007686

Drerio

not conserved

ENSDARG00000086583

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000003763

protein features

start (aa)	end (aa)	feature	details
33	42	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

position of stopcodon in wt / mu cDNA

883 / 883

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

80 / 80

chromosome

strand

-1

last intron/exon boundary

280

theoretical NMD boundary in CDS

150

length of CDS

804

coding sequence (CDS) position

101

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

180

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

851

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

116707816

original gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

original cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

wildtype AA sequence

MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*

mutated AA sequence

MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDLVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*

speed

0.40 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

disease causing

Model: simple_aae, prob: 3.49363162539187e-10 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM900015)
known disease mutation: rs17920 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116707816C>AN/A show variant in all transcripts IGV

HGNC symbol

APOA1

Ensembl transcript ID

ENST00000359492

Genbank transcript ID

N/A

UniProt peptide

P02647

alteration type

single base exchange

alteration region

CDS

DNA changes

c.101G>T
cDNA.172G>T
g.851G>T

AA changes

R34L Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs28929476

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.263	0
	-0.447	0
(flanking)	0.452	0.001

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

not conserved

Ptroglodytes

all identical

ENSPTRG00000004316

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000032083

Ggallus

all identical

ENSGALG00000007114

Trubripes

not conserved

ENSTRUG00000007686

Drerio

not conserved

ENSDARG00000086583

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000003763

protein features

start (aa)	end (aa)	feature	details
33	42	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

position of stopcodon in wt / mu cDNA

875 / 875

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

72 / 72

chromosome

strand

-1

last intron/exon boundary

272

theoretical NMD boundary in CDS

150

length of CDS

804

coding sequence (CDS) position

101

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

172

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

851

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

116707816

original gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

original cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

wildtype AA sequence

mutated AA sequence

speed

0.31 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 3.49363162539187e-10 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM900015)
known disease mutation: rs17920 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116707816C>AN/A show variant in all transcripts IGV

HGNC symbol

APOA1

Ensembl transcript ID

ENST00000375323

Genbank transcript ID

N/A

UniProt peptide

P02647

alteration type

single base exchange

alteration region

CDS

DNA changes

c.101G>T
cDNA.328G>T
g.851G>T

AA changes

R34L Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs28929476

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.263	0
	-0.447	0
(flanking)	0.452	0.001

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

not conserved

Ptroglodytes

all identical

ENSPTRG00000004316

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000032083

Ggallus

all identical

ENSGALG00000007114

Trubripes

not conserved

ENSTRUG00000007686

Drerio

not conserved

ENSDARG00000086583

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000003763

protein features

start (aa)	end (aa)	feature	details
33	42	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

position of stopcodon in wt / mu cDNA

1031 / 1031

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

228 / 228

chromosome

strand

-1

last intron/exon boundary

428

theoretical NMD boundary in CDS

150

length of CDS

804

coding sequence (CDS) position

101

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

328

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

851

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

116707816

original gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

original cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

wildtype AA sequence

mutated AA sequence

speed

0.76 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 3.49363162539187e-10 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM900015)
known disease mutation: rs17920 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116707816C>AN/A show variant in all transcripts IGV

HGNC symbol

APOA1

Ensembl transcript ID

ENST00000236850

Genbank transcript ID

NM_000039

UniProt peptide

P02647

alteration type

single base exchange

alteration region

CDS

DNA changes

c.101G>T
cDNA.467G>T
g.851G>T

AA changes

R34L Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs28929476

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.263	0
	-0.447	0
(flanking)	0.452	0.001

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

not conserved

Ptroglodytes

all identical

ENSPTRG00000004316

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000032083

Ggallus

all identical

ENSGALG00000007114

Trubripes

not conserved

ENSTRUG00000007686

Drerio

not conserved

ENSDARG00000086583

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000003763

protein features

start (aa)	end (aa)	feature	details
33	42	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

position of stopcodon in wt / mu cDNA

1170 / 1170

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

367 / 367

chromosome

strand

-1

last intron/exon boundary

567

theoretical NMD boundary in CDS

150

length of CDS

804

coding sequence (CDS) position

101

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

467

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

851

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

116707816

original gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

original cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered cDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

wildtype AA sequence

mutated AA sequence

speed

0.29 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1.23145805483743e-06 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM900015)
known disease mutation: rs17920 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116707816C>AN/A show variant in all transcripts IGV

HGNC symbol

APOA1

Ensembl transcript ID

ENST00000375329

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.851G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs28929476

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.263	0
	-0.447	0
(flanking)	0.452	0.001

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

245

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

133 / 133

chromosome

strand

-1

last intron/exon boundary

267

theoretical NMD boundary in CDS

length of CDS

738

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)

851

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

116707816

original gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCGAGTGAAGGACCTGGCCACTG

altered gDNA sequence snippet

CCCCCAGAGCCCCTGGGATCTAGTGAAGGACCTGGCCACTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSGGARGFCM LKAPHSARPF FSSRSPTALQ DESCGADLGR ALPDGLKLLD NWDSVTSTFS
KLREQLGPVT QEFWDNLEKE TEGLRQEMSK DLEEVKAKVQ PYLDDFQKKW QEEMELYRQK
VEPLRAELQE GARQKLHELQ EKLSPLGEEM RDRARAHVDA LRTHLAPYSD ELRQRLAARL
EALKENGGAR LAEYHAKATE HLSTLSEKAK PALEDLRQGL LPVLESFKVS FLSALEEYTK
KLNTQ*

mutated AA sequence

N/A

speed

0.23 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems