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: ENST00000404685
Querying Taster for transcript #2: ENST00000405511
Querying Taster for transcript #3: ENST00000429038
Querying Taster for transcript #4: ENST00000352371
Querying Taster for transcript #5: ENST00000332987
MT speed 0 s - this script 6.149828 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
APOL4	polymorphism_automatic	2.15194528863094e-12	simple_aae		affected		A318E	single base exchange	rs6000173		show file
APOL4	polymorphism_automatic	2.15194528863094e-12	simple_aae		affected		A315E	single base exchange	rs6000173		show file
APOL4	polymorphism_automatic	2.47152463050959e-07	without_aae		affected			single base exchange	rs6000173		show file
APOL4	polymorphism_automatic	2.47152463050959e-07	without_aae		affected			single base exchange	rs6000173		show file
APOL4	polymorphism_automatic	2.47152463050959e-07	without_aae		affected			single base exchange	rs6000173		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997848 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:36587223G>TN/A show variant in all transcripts IGV

HGNC symbol

APOL4

Ensembl transcript ID

ENST00000352371

Genbank transcript ID

N/A

UniProt peptide

Q9BPW4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.953C>A
cDNA.1178C>A
g.13664C>A

AA changes

A318E Score: 107 explain score(s)

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

318

frameshift

known variant

Reference ID: rs6000173

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1087	1067	2154
ExAC	17528	-2289	15239

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.475	0.001
	0.49	0.002
(flanking)	0.458	0.002

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	13661	wt: 0.5388 / mu: 0.5702 (marginal change - not scored)	wt: CAAGGGGGCAAAATC mu: CAAGGGGGAAAAATC	AGGG\|ggca
Donor gained	13660	0.84	mu: ACAAGGGGGAAAAAT	AAGG\|ggga
Donor gained	13659	0.47	mu: CACAAGGGGGAAAAA	CAAG\|gggg

distance from splice site

101

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

318

mutated

not conserved

318

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000057346

284

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

1053 / 1053

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

351 / 351

position of stopcodon in wt / mu cDNA

1278 / 1278

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

226 / 226

chromosome

strand

-1

last intron/exon boundary

556

theoretical NMD boundary in CDS

280

length of CDS

1053

coding sequence (CDS) position

953

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

1178

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

13664

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

36587223

original gDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered gDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

original cDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered cDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

wildtype AA sequence

MEGAALLKIF VVCIWVQQNH PGWTVAGQFQ EKKRFTEEVI EYFQKKVSPV HLKILLTSDE
AWKRFVRVAE LPREEADALY EALKNLTPYV AIEDKDMQQK EQQFREWFLK FPQIRWKIQE
SIERLRVIAN EIEKVHRGCV IANVVSGSTG ILSVIGVMLA PFTAGLSLSI TAAGVGLGIA
SATAGIASSI VENTYTRSAE LTASRLTATS TDQLEALRDI LRDITPNVLS FALDFDEATK
MIANDVHTLR RSKATVGRPL IAWRYVPINV VETLRTRGAP TRIVRKVARN LGKATSGVLV
VLDVVNLVQD SLDLHKGAKS ESAESLRQWA QELEENLNEL THIHQSLKAG *

mutated AA sequence

speed

0.42 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: 0.999999999997848 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:36587223G>TN/A show variant in all transcripts IGV

HGNC symbol

APOL4

Ensembl transcript ID

ENST00000332987

Genbank transcript ID

N/A

UniProt peptide

Q9BPW4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.944C>A
cDNA.1367C>A
g.13664C>A

AA changes

A315E Score: 107 explain score(s)

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

315

frameshift

known variant

Reference ID: rs6000173

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1087	1067	2154
ExAC	17528	-2289	15239

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.475	0.001
	0.49	0.002
(flanking)	0.458	0.002

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	13661	wt: 0.5388 / mu: 0.5702 (marginal change - not scored)	wt: CAAGGGGGCAAAATC mu: CAAGGGGGAAAAATC	AGGG\|ggca
Donor gained	13660	0.84	mu: ACAAGGGGGAAAAAT	AAGG\|ggga
Donor gained	13659	0.47	mu: CACAAGGGGGAAAAA	CAAG\|gggg

distance from splice site

101

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

315

mutated

not conserved

315

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000057346

284

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

1044 / 1044

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

348 / 348

position of stopcodon in wt / mu cDNA

1467 / 1467

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

424 / 424

chromosome

strand

-1

last intron/exon boundary

745

theoretical NMD boundary in CDS

271

length of CDS

1044

coding sequence (CDS) position

944

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

1367

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

13664

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

36587223

original gDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered gDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

original cDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered cDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

wildtype AA sequence

MGSWVQLITS VGVQQNHPGW TVAGQFQEKK RFTEEVIEYF QKKVSPVHLK ILLTSDEAWK
RFVRVAELPR EEADALYEAL KNLTPYVAIE DKDMQQKEQQ FREWFLKFPQ IRWKIQESIE
RLRVIANEIE KVHRGCVIAN VVSGSTGILS VIGVMLAPFT AGLSLSITAA GVGLGIASAT
AGIASSIVEN TYTRSAELTA SRLTATSTDQ LEALRDILRD ITPNVLSFAL DFDEATKMIA
NDVHTLRRSK ATVGRPLIAW RYVPINVVET LRTRGAPTRI VRKVARNLGK ATSGVLVVLD
VVNLVQDSLD LHKGAKSESA ESLRQWAQEL EENLNELTHI HQSLKAG*

mutated AA sequence

speed

1.40 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999752847537 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:36587223G>TN/A show variant in all transcripts IGV

HGNC symbol

APOL4

Ensembl transcript ID

ENST00000405511

Genbank transcript ID

NM_030643

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1368C>A
g.13664C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6000173

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1087	1067	2154
ExAC	17528	-2289	15239

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.475	0.001
	0.49	0.002
(flanking)	0.458	0.002

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

splice sites

splice site change occurs after stopcodon (at aa 314)

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	13661	wt: 0.5388 / mu: 0.5702 (marginal change - not scored)	wt: CAAGGGGGCAAAATC mu: CAAGGGGGAAAAATC	AGGG\|ggca
Donor gained	13660	0.84	mu: ACAAGGGGGAAAAAT	AAGG\|ggga
Donor gained	13659	0.47	mu: CACAAGGGGGAAAAA	CAAG\|gggg

distance from splice site

736

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

424 / 424

chromosome

strand

-1

last intron/exon boundary

633

theoretical NMD boundary in CDS

159

length of CDS

384

coding sequence (CDS) position

N/A

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

1368

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

13664

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

36587223

original gDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered gDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

original cDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered cDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

wildtype AA sequence

MGSWVQLITS VGVQQNHPGW TVAGQFQEKK RFTEEVIEYF QKKVSPVHLK ILLTSDEAWK
RFVRVAELPR EEADALYEAL KNLTPYVAIE DKDMQQKEQQ FREWFLKVSS NQMEDSGVHR
KASCHCK*

mutated AA sequence

N/A

speed

1.33 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999752847537 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:36587223G>TN/A show variant in all transcripts IGV

HGNC symbol

APOL4

Ensembl transcript ID

ENST00000404685

Genbank transcript ID

NM_145660

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1179C>A
g.13664C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6000173

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1087	1067	2154
ExAC	17528	-2289	15239

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.475	0.001
	0.49	0.002
(flanking)	0.458	0.002

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

splice sites

splice site change occurs after stopcodon (at aa 317)

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	13661	wt: 0.5388 / mu: 0.5702 (marginal change - not scored)	wt: CAAGGGGGCAAAATC mu: CAAGGGGGAAAAATC	AGGG\|ggca
Donor gained	13660	0.84	mu: ACAAGGGGGAAAAAT	AAGG\|ggga
Donor gained	13659	0.47	mu: CACAAGGGGGAAAAA	CAAG\|gggg

distance from splice site

736

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

226 / 226

chromosome

strand

-1

last intron/exon boundary

444

theoretical NMD boundary in CDS

168

length of CDS

393

coding sequence (CDS) position

N/A

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

1179

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

13664

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

36587223

original gDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered gDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

original cDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered cDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

wildtype AA sequence

MEGAALLKIF VVCIWVQQNH PGWTVAGQFQ EKKRFTEEVI EYFQKKVSPV HLKILLTSDE
AWKRFVRVAE LPREEADALY EALKNLTPYV AIEDKDMQQK EQQFREWFLK VSSNQMEDSG
VHRKASCHCK *

mutated AA sequence

N/A

speed

0.43 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999752847537 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:36587223G>TN/A show variant in all transcripts IGV

HGNC symbol

APOL4

Ensembl transcript ID

ENST00000429038

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1445C>A
g.13664C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6000173

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1087	1067	2154
ExAC	17528	-2289	15239

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.475	0.001
	0.49	0.002
(flanking)	0.458	0.002

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

splice sites

splice site change occurs after stopcodon (at aa 314)

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	13661	wt: 0.5388 / mu: 0.5702 (marginal change - not scored)	wt: CAAGGGGGCAAAATC mu: CAAGGGGGAAAAATC	AGGG\|ggca
Donor gained	13660	0.84	mu: ACAAGGGGGAAAAAT	AAGG\|ggga
Donor gained	13659	0.47	mu: CACAAGGGGGAAAAA	CAAG\|gggg

distance from splice site

379

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

501 / 501

chromosome

strand

-1

last intron/exon boundary

710

theoretical NMD boundary in CDS

159

length of CDS

384

coding sequence (CDS) position

N/A

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

1445

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

13664

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

36587223

original gDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered gDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

original cDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered cDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

wildtype AA sequence

MGSWVQLITS VGVQQNHPGW TVAGQFQEKK RFTEEVIEYF QKKVSPVHLK ILLTSDEAWK
RFVRVAELPR EEADALYEAL KNLTPYVAIE DKDMQQKEQQ FREWFLKVSS NQMEDSGVHR
KASCHCK*

mutated AA sequence

N/A

speed

1.38 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