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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000217074
Querying Taster for transcript #2: ENST00000217073
Querying Taster for transcript #3: ENST00000255136
Querying Taster for transcript #4: ENST00000537323
MT speed 3.69 s - this script 4.972896 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PABPC1L	polymorphism_automatic	0.709589151344798	simple_aae		affected		S212A	single base exchange	rs2075960		show file
PABPC1L	polymorphism_automatic	0.709589151344798	simple_aae		affected		S212A	single base exchange	rs2075960		show file
PABPC1L	polymorphism_automatic	0.709589151344798	simple_aae		affected		S212A	single base exchange	rs2075960		show file
PABPC1L	polymorphism_automatic	0.709589151344798	simple_aae		affected		S212A	single base exchange	rs2075960		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.290410848655202 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43547677T>GN/A show variant in all transcripts IGV

HGNC symbol

PABPC1L

Ensembl transcript ID

ENST00000217074

Genbank transcript ID

N/A

UniProt peptide

Q4VXU2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.634T>G
cDNA.716T>G
g.8975T>G

AA changes

S212A Score: 99 explain score(s)

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

212

frameshift

known variant

Reference ID: rs2075960

database	homozygous (G/G)	heterozygous	allele carriers
1000G	144	871	1015
ExAC	3769	21693	25462

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.537	1
	0.461	0.997
(flanking)	1.647	0.997

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
Acc decreased	8983	wt: 0.96 / mu: 0.82	wt: CAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTCCCCAAGGG mu: CAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTCCCCAAGGG	gttt\|GGTG
Donor increased	8979	wt: 0.36 / mu: 0.46	wt: CTCCCAGTTTGGTGG mu: CGCCCAGTTTGGTGG	CCCA\|gttt
Donor gained	8974	0.96	mu: CTCTTCGCCCAGTTT	CTTC\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

212

mutated

all conserved

212

Ptroglodytes

all identical

ENSPTRG00000013531

212

Mmulatta

all identical

ENSMMUG00000013209

212

Fcatus

not conserved

ENSFCAG00000011692

212

Mmusculus

all identical

ENSMUSG00000054582

212

Ggallus

all identical

ENSGALG00000004123

212

Trubripes

all conserved

ENSTRUG00000011085

212

Drerio

all conserved

ENSDARG00000002597

212

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022831

212

protein features

start (aa)	end (aa)	feature	details
191	268	DOMAIN	RRM 3.	lost
294	370	DOMAIN	RRM 4.	might get lost (downstream of altered splice site)
409	458	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
528	605	DOMAIN	PABC.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

993 / 993

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

331 / 331

position of stopcodon in wt / mu cDNA

1075 / 1075

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

83 / 83

chromosome

strand

last intron/exon boundary

1055

theoretical NMD boundary in CDS

922

length of CDS

993

coding sequence (CDS) position

634

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

716

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

8975

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

43547677

original gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTC

altered gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTC

original cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGGAAAATGCTG

altered cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGGAAAATGCTG

wildtype AA sequence

mutated AA sequence

speed

0.91 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: 0.290410848655202 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43547677T>GN/A show variant in all transcripts IGV

HGNC symbol

PABPC1L

Ensembl transcript ID

ENST00000217073

Genbank transcript ID

N/A

UniProt peptide

Q4VXU2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.634T>G
cDNA.634T>G
g.8975T>G

AA changes

S212A Score: 99 explain score(s)

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

212

frameshift

known variant

Reference ID: rs2075960

database	homozygous (G/G)	heterozygous	allele carriers
1000G	144	871	1015
ExAC	3769	21693	25462

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.537	1
	0.461	0.997
(flanking)	1.647	0.997

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
Acc decreased	8983	wt: 0.96 / mu: 0.82	wt: CAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTCCCCAAGGG mu: CAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTCCCCAAGGG	gttt\|GGTG
Donor increased	8979	wt: 0.36 / mu: 0.46	wt: CTCCCAGTTTGGTGG mu: CGCCCAGTTTGGTGG	CCCA\|gttt
Donor gained	8974	0.96	mu: CTCTTCGCCCAGTTT	CTTC\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

212

mutated

all conserved

212

Ptroglodytes

all identical

ENSPTRG00000013531

212

Mmulatta

all identical

ENSMMUG00000013209

212

Fcatus

not conserved

ENSFCAG00000011692

212

Mmusculus

all identical

ENSMUSG00000054582

212

Ggallus

all identical

ENSGALG00000004123

212

Trubripes

all conserved

ENSTRUG00000011085

212

Drerio

all conserved

ENSDARG00000002597

212

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022831

212

protein features

start (aa)	end (aa)	feature	details
191	268	DOMAIN	RRM 3.	lost
294	370	DOMAIN	RRM 4.	might get lost (downstream of altered splice site)
409	458	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
528	605	DOMAIN	PABC.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1845 / 1845

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

615 / 615

position of stopcodon in wt / mu cDNA

1845 / 1845

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

1 / 1

chromosome

strand

last intron/exon boundary

1777

theoretical NMD boundary in CDS

1726

length of CDS

1845

coding sequence (CDS) position

634

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

634

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

8975

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

43547677

original gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTC

altered gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTC

original cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGGAAAATGCTG

altered cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGGAAAATGCTG

wildtype AA sequence

MNASGSGYPL ASLYVGDLHP DVTEAMLYEK FSPAGPILSI RVCRDVATRR SLGYAYINFQ
QPADAERALD TMNFEMLKGQ PIRIMWSQRD PGLRKSGVGN IFIKNLEDSI DNKALYDTFS
TFGNILSCKV ACDEHGSRGF GFVHFETHEA AQQAINTMNG MLLNDRKVFV GHFKSRRERE
AELGARALEF TNIYVKNLPV DVDEQGLQDL FSQFGKMLSV KVMRDNSGHS RCFGFVNFEK
HEEAQKAVVH MNGKEVSGRL LYAGRAQKRV ERQNELKRRF EQMKQDRLRR YQGVNLYVKN
LDDSIDDDKL RKEFSPYGVI TSAKVMTEGG HSKGFGFVCF SSPEEATKAV TEMNGRIVGT
KPLYVALAQR KEERKAILTN QYMQRLSTMR TLSNPLLGSF QQPSSYFLPA MPQPPAQAAY
YGCGPVTPTQ PAPRWTSQPP RPSCASMVRP PVVPRRPPAH ISSVRQASTQ VPRTVPHTQR
VANIGTQTTG PSGVGCCTPG RPLLPCKCSS AAHSTYRVQE PAVHIPGQEP LTASMLAAAP
LHEQKQMIGE RLYPLIHDVH TQLAGKITGM LLEIDNSELL LMLESPESLH AKIDEAVAVL
QAHQAMEQPK AYMH*

mutated AA sequence

MNASGSGYPL ASLYVGDLHP DVTEAMLYEK FSPAGPILSI RVCRDVATRR SLGYAYINFQ
QPADAERALD TMNFEMLKGQ PIRIMWSQRD PGLRKSGVGN IFIKNLEDSI DNKALYDTFS
TFGNILSCKV ACDEHGSRGF GFVHFETHEA AQQAINTMNG MLLNDRKVFV GHFKSRRERE
AELGARALEF TNIYVKNLPV DVDEQGLQDL FAQFGKMLSV KVMRDNSGHS RCFGFVNFEK
HEEAQKAVVH MNGKEVSGRL LYAGRAQKRV ERQNELKRRF EQMKQDRLRR YQGVNLYVKN
LDDSIDDDKL RKEFSPYGVI TSAKVMTEGG HSKGFGFVCF SSPEEATKAV TEMNGRIVGT
KPLYVALAQR KEERKAILTN QYMQRLSTMR TLSNPLLGSF QQPSSYFLPA MPQPPAQAAY
YGCGPVTPTQ PAPRWTSQPP RPSCASMVRP PVVPRRPPAH ISSVRQASTQ VPRTVPHTQR
VANIGTQTTG PSGVGCCTPG RPLLPCKCSS AAHSTYRVQE PAVHIPGQEP LTASMLAAAP
LHEQKQMIGE RLYPLIHDVH TQLAGKITGM LLEIDNSELL LMLESPESLH AKIDEAVAVL
QAHQAMEQPK AYMH*

speed

0.79 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.290410848655202 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43547677T>GN/A show variant in all transcripts IGV

HGNC symbol

PABPC1L

Ensembl transcript ID

ENST00000255136

Genbank transcript ID

NM_001124756

UniProt peptide

Q4VXU2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.634T>G
cDNA.716T>G
g.8975T>G

AA changes

S212A Score: 99 explain score(s)

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

212

frameshift

known variant

Reference ID: rs2075960

database	homozygous (G/G)	heterozygous	allele carriers
1000G	144	871	1015
ExAC	3769	21693	25462

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.537	1
	0.461	0.997
(flanking)	1.647	0.997

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
Acc decreased	8983	wt: 0.96 / mu: 0.82	wt: CAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTCCCCAAGGG mu: CAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTCCCCAAGGG	gttt\|GGTG
Donor increased	8979	wt: 0.36 / mu: 0.46	wt: CTCCCAGTTTGGTGG mu: CGCCCAGTTTGGTGG	CCCA\|gttt
Donor gained	8974	0.96	mu: CTCTTCGCCCAGTTT	CTTC\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

212

mutated

all conserved

212

Ptroglodytes

all identical

ENSPTRG00000013531

212

Mmulatta

all identical

ENSMMUG00000013209

212

Fcatus

not conserved

ENSFCAG00000011692

212

Mmusculus

all identical

ENSMUSG00000054582

212

Ggallus

all identical

ENSGALG00000004123

212

Trubripes

all conserved

ENSTRUG00000011085

212

Drerio

all conserved

ENSDARG00000002597

212

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022831

212

protein features

start (aa)	end (aa)	feature	details
191	268	DOMAIN	RRM 3.	lost
294	370	DOMAIN	RRM 4.	might get lost (downstream of altered splice site)
409	458	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
528	605	DOMAIN	PABC.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1845 / 1845

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

615 / 615

position of stopcodon in wt / mu cDNA

1927 / 1927

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

83 / 83

chromosome

strand

last intron/exon boundary

1934

theoretical NMD boundary in CDS

1801

length of CDS

1845

coding sequence (CDS) position

634

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

716

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

8975

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

43547677

original gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTC

altered gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTC

original cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGGAAAATGCTG

altered cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGGAAAATGCTG

wildtype AA sequence

mutated AA sequence

MNASGSGYPL ASLYVGDLHP DVTEAMLYEK FSPAGPILSI RVCRDVATRR SLGYAYINFQ
QPADAERALD TMNFEMLKGQ PIRIMWSQRD PGLRKSGVGN IFIKNLEDSI DNKALYDTFS
TFGNILSCKV ACDEHGSRGF GFVHFETHEA AQQAINTMNG MLLNDRKVFV GHFKSRRERE
AELGARALEF TNIYVKNLPV DVDEQGLQDL FAQFGKMLSV KVMRDNSGHS RCFGFVNFEK
HEEAQKAVVH MNGKEVSGRL LYAGRAQKRV ERQNELKRRF EQMKQDRLRR YQGVNLYVKN
LDDSIDDDKL RKEFSPYGVI TSAKVMTEGG HSKGFGFVCF SSPEEATKAV TEMNGRIVGT
KPLYVALAQR KEERKAILTN QYMQRLSTMR TLSNPLLGSF QQPSSYFLPA MPQPPAQAAY
YGCGPVTPTQ PAPRWTSQPP RPSCASMVRP PVVPRRPPAH ISSVRQASTQ VPRTVPHTQR
VANIGTQTTG PSGVGCCTPG RPLLPCKCSS AAHSTYRVQE PAVHIPGQEP LTASMLAAAP
LHEQKQMIGE RLYPLIHDVH TQLAGKITGM LLEIDNSELL LMLESPESLH AKIDEAVAVL
QAHQAMEQPK AYMH*

speed

1.05 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.290410848655202 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43547677T>GN/A show variant in all transcripts IGV

HGNC symbol

PABPC1L

Ensembl transcript ID

ENST00000537323

Genbank transcript ID

N/A

UniProt peptide

Q4VXU2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.634T>G
cDNA.654T>G
g.8975T>G

AA changes

S212A Score: 99 explain score(s)

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

212

frameshift

known variant

Reference ID: rs2075960

database	homozygous (G/G)	heterozygous	allele carriers
1000G	144	871	1015
ExAC	3769	21693	25462

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.537	1
	0.461	0.997
(flanking)	1.647	0.997

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
Acc decreased	8983	wt: 0.96 / mu: 0.82	wt: CAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTCCCCAAGGG mu: CAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTCCCCAAGGG	gttt\|GGTG
Donor increased	8979	wt: 0.36 / mu: 0.46	wt: CTCCCAGTTTGGTGG mu: CGCCCAGTTTGGTGG	CCCA\|gttt
Donor gained	8974	0.96	mu: CTCTTCGCCCAGTTT	CTTC\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

212

mutated

all conserved

212

Ptroglodytes

all identical

ENSPTRG00000013531

212

Mmulatta

all identical

ENSMMUG00000013209

212

Fcatus

not conserved

ENSFCAG00000011692

212

Mmusculus

all identical

ENSMUSG00000054582

212

Ggallus

all identical

ENSGALG00000004123

212

Trubripes

all conserved

ENSTRUG00000011085

212

Drerio

all conserved

ENSDARG00000002597

212

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022831

212

protein features

start (aa)	end (aa)	feature	details
191	268	DOMAIN	RRM 3.	lost
294	370	DOMAIN	RRM 4.	might get lost (downstream of altered splice site)
409	458	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
528	605	DOMAIN	PABC.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

993 / 993

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

331 / 331

position of stopcodon in wt / mu cDNA

1013 / 1013

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

21 / 21

chromosome

strand

last intron/exon boundary

1723

theoretical NMD boundary in CDS

1652

length of CDS

993

coding sequence (CDS) position

634

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

654

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

8975

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

43547677

original gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTC

altered gDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTC

original cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGGAAAATGCTG

altered cDNA sequence snippet

AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGGAAAATGCTG

wildtype AA sequence

mutated AA sequence

speed

0.94 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

Problems