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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000326639
Querying Taster for transcript #2: ENST00000512292
Querying Taster for transcript #3: ENST00000264584
Querying Taster for transcript #4: ENST00000441387
Querying Taster for transcript #5: ENST00000427266
Querying Taster for transcript #6: ENST00000354456
MT speed 0 s - this script 5.712145 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LARP1B	polymorphism_automatic	0.993055759201633	simple_aae		affected		P462R	single base exchange	rs12508837		show file
LARP1B	polymorphism_automatic	0.993055759201633	simple_aae		affected		P462R	single base exchange	rs12508837		show file
LARP1B	polymorphism_automatic	0.993055759201633	simple_aae		affected		P462R	single base exchange	rs12508837		show file
LARP1B	polymorphism_automatic	0.993055759201633	simple_aae		affected		P462R	single base exchange	rs12508837		show file
LARP1B	polymorphism_automatic	0.993055759201633	simple_aae		affected		P415R	single base exchange	rs12508837		show file
LARP1B	polymorphism_automatic	1	without_aae		affected			single base exchange	rs12508837		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00694424079836709 (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)

chr4:129043204C>GN/A show variant in all transcripts IGV

HGNC symbol

LARP1B

Ensembl transcript ID

ENST00000512292

Genbank transcript ID

N/A

UniProt peptide

Q659C4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1385C>G
cDNA.1578C>G
g.60782C>G

AA changes

P462R Score: 103 explain score(s)

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

462

frameshift

known variant

Reference ID: rs12508837

database	homozygous (G/G)	heterozygous	allele carriers
1000G	938	1080	2018
ExAC	26429	-20091	6338

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.389	1
	2.543	1
(flanking)	0.036	0.993

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	60773	wt: 0.5189 / mu: 0.5599 (marginal change - not scored)	wt: TGTGAAAAAACATCC mu: TGTGAAAAAACATCG	TGAA\|aaaa
Donor increased	60781	wt: 0.82 / mu: 0.99	wt: AACATCCTGGAGGAG mu: AACATCGTGGAGGAG	CATC\|ctgg
Donor gained	60776	0.49	mu: GAAAAAACATCGTGG	AAAA\|acat

distance from splice site

140

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

462

mutated

not conserved

462

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000021347

462

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000037814

n/a

Ggallus

all identical

ENSGALG00000010207

426

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0261618

1150

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022512

556

protein features

start (aa)	end (aa)	feature	details
473	473	CONFLICT	R -> Q (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
639	639	CONFLICT	T -> A (in Ref. 2; CAD97908).	might get lost (downstream of altered splice site)
671	671	CONFLICT	N -> S (in Ref. 4; AAH62606).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1557 / 1557

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

519 / 519

position of stopcodon in wt / mu cDNA

1750 / 1750

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

194 / 194

chromosome

strand

last intron/exon boundary

1718

theoretical NMD boundary in CDS

1474

length of CDS

1557

coding sequence (CDS) position

1385

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

1578

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

60782

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

129043204

original gDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered gDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

original cDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered cDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

wildtype AA sequence

mutated AA sequence

speed

0.85 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: 0.00694424079836709 (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)

chr4:129043204C>GN/A show variant in all transcripts IGV

HGNC symbol

LARP1B

Ensembl transcript ID

ENST00000326639

Genbank transcript ID

NM_018078

UniProt peptide

Q659C4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1385C>G
cDNA.1596C>G
g.60782C>G

AA changes

P462R Score: 103 explain score(s)

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

462

frameshift

known variant

Reference ID: rs12508837

database	homozygous (G/G)	heterozygous	allele carriers
1000G	938	1080	2018
ExAC	26429	-20091	6338

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.389	1
	2.543	1
(flanking)	0.036	0.993

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	60773	wt: 0.5189 / mu: 0.5599 (marginal change - not scored)	wt: TGTGAAAAAACATCC mu: TGTGAAAAAACATCG	TGAA\|aaaa
Donor increased	60781	wt: 0.82 / mu: 0.99	wt: AACATCCTGGAGGAG mu: AACATCGTGGAGGAG	CATC\|ctgg
Donor gained	60776	0.49	mu: GAAAAAACATCGTGG	AAAA\|acat

distance from splice site

140

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

462

mutated

not conserved

462

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000021347

462

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000037814

n/a

Ggallus

all identical

ENSGALG00000010207

426

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0261618

1150

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022512

556

protein features

start (aa)	end (aa)	feature	details
473	473	CONFLICT	R -> Q (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
639	639	CONFLICT	T -> A (in Ref. 2; CAD97908).	might get lost (downstream of altered splice site)
671	671	CONFLICT	N -> S (in Ref. 4; AAH62606).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2745 / 2745

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

915 / 915

position of stopcodon in wt / mu cDNA

2956 / 2956

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

212 / 212

chromosome

strand

last intron/exon boundary

2759

theoretical NMD boundary in CDS

2497

length of CDS

2745

coding sequence (CDS) position

1385

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

1596

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

60782

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

129043204

original gDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered gDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

original cDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered cDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

wildtype AA sequence

MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRANKHKWVP LHLDVVRSES QERPGSRNSS RCQPEANKPT HNNRRNDTRS
WKRDREKRDD QDDVSSVRSE GGNIRGSFRG RGRGRGRGRG RGRGNPRLNF DYSYGYQEHG
ERTDQPFQTE LNTSMMYYYD DGTGVQVYPV EEALLKEYIK RQIEYYFSVE NLERDFFLRG
KMDEQGFLPI SLIAGFQRVQ ALTTNLNLIL EALKDSTEVE IVDEKMRKKI EPEKWPIPGP
PPRSVPPTDF SQLIDCPEFV PGQAFCSHTE SAPNSPRIGS PLSPKKNSET SILQAMSRGL
STSLPDLDSE PWIEVKKRHQ PAPVKLRESV SVPEGSLNQL CSSEEPEQEE LDFLFDEEIE
QIGRKNTFTD WSDNDSDYEI DDQDLNKILI VTQTPPYVKK HPGGDRTGTH MSRAKITSEL
AKVINDGLYY YEQDLWMEED ENKHTAIKQE VENFKKLNLI SKEQFENLTP ELPFEPNQEV
PVAPSQSRQG GVQGVLHIPK KDLTDELAQK LFDVSEITSA AMVHSLPTAV PESPRIHPTR
TPKTPRTPRL QDPNKTPRFY PVVKEPKAID VKSPRKRKTR HSTNPPLECH VGWVMDSRDR
GPGTSSVSTS NASPSEGAPL AGSYGCTPHS FPKFQHPSHE LLKENGFTQQ VYHKYRRRCL
SERKRLGIGQ SQEMNTLFRF WSFFLRDHFN KKMYEEFRQL AWEDAKENYR YGLECLFRFY
SYGLEKKFRR EIFQDFQEET KKDYESGQLY GLEKFWAYLK YSQSKTQSID PKLQEYLCSF
KRLEDFRVDP PISDEFGRKR HSSTSGEESN RHRLPPNSST KPPNAAKPTS TSELQVPINS
PRRNISPESS DNSH*

mutated AA sequence

MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRANKHKWVP LHLDVVRSES QERPGSRNSS RCQPEANKPT HNNRRNDTRS
WKRDREKRDD QDDVSSVRSE GGNIRGSFRG RGRGRGRGRG RGRGNPRLNF DYSYGYQEHG
ERTDQPFQTE LNTSMMYYYD DGTGVQVYPV EEALLKEYIK RQIEYYFSVE NLERDFFLRG
KMDEQGFLPI SLIAGFQRVQ ALTTNLNLIL EALKDSTEVE IVDEKMRKKI EPEKWPIPGP
PPRSVPPTDF SQLIDCPEFV PGQAFCSHTE SAPNSPRIGS PLSPKKNSET SILQAMSRGL
STSLPDLDSE PWIEVKKRHQ PAPVKLRESV SVPEGSLNQL CSSEEPEQEE LDFLFDEEIE
QIGRKNTFTD WSDNDSDYEI DDQDLNKILI VTQTPPYVKK HRGGDRTGTH MSRAKITSEL
AKVINDGLYY YEQDLWMEED ENKHTAIKQE VENFKKLNLI SKEQFENLTP ELPFEPNQEV
PVAPSQSRQG GVQGVLHIPK KDLTDELAQK LFDVSEITSA AMVHSLPTAV PESPRIHPTR
TPKTPRTPRL QDPNKTPRFY PVVKEPKAID VKSPRKRKTR HSTNPPLECH VGWVMDSRDR
GPGTSSVSTS NASPSEGAPL AGSYGCTPHS FPKFQHPSHE LLKENGFTQQ VYHKYRRRCL
SERKRLGIGQ SQEMNTLFRF WSFFLRDHFN KKMYEEFRQL AWEDAKENYR YGLECLFRFY
SYGLEKKFRR EIFQDFQEET KKDYESGQLY GLEKFWAYLK YSQSKTQSID PKLQEYLCSF
KRLEDFRVDP PISDEFGRKR HSSTSGEESN RHRLPPNSST KPPNAAKPTS TSELQVPINS
PRRNISPESS DNSH*

speed

1.32 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00694424079836709 (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)

chr4:129043204C>GN/A show variant in all transcripts IGV

HGNC symbol

LARP1B

Ensembl transcript ID

ENST00000441387

Genbank transcript ID

N/A

UniProt peptide

Q659C4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1385C>G
cDNA.1516C>G
g.60782C>G

AA changes

P462R Score: 103 explain score(s)

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

462

frameshift

known variant

Reference ID: rs12508837

database	homozygous (G/G)	heterozygous	allele carriers
1000G	938	1080	2018
ExAC	26429	-20091	6338

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.389	1
	2.543	1
(flanking)	0.036	0.993

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	60773	wt: 0.5189 / mu: 0.5599 (marginal change - not scored)	wt: TGTGAAAAAACATCC mu: TGTGAAAAAACATCG	TGAA\|aaaa
Donor increased	60781	wt: 0.82 / mu: 0.99	wt: AACATCCTGGAGGAG mu: AACATCGTGGAGGAG	CATC\|ctgg
Donor gained	60776	0.49	mu: GAAAAAACATCGTGG	AAAA\|acat

distance from splice site

140

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

462

mutated

not conserved

462

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000021347

462

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000037814

n/a

Ggallus

all identical

ENSGALG00000010207

426

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0261618

1150

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022512

556

protein features

start (aa)	end (aa)	feature	details
473	473	CONFLICT	R -> Q (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
639	639	CONFLICT	T -> A (in Ref. 2; CAD97908).	might get lost (downstream of altered splice site)
671	671	CONFLICT	N -> S (in Ref. 4; AAH62606).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2364 / 2364

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

788 / 788

position of stopcodon in wt / mu cDNA

2495 / 2495

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

132 / 132

chromosome

strand

last intron/exon boundary

2569

theoretical NMD boundary in CDS

2387

length of CDS

2364

coding sequence (CDS) position

1385

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

1516

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

60782

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

129043204

original gDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered gDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

original cDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered cDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

wildtype AA sequence

mutated AA sequence

MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRANKHKWVP LHLDVVRSES QERPGSRNSS RCQPEANKPT HNNRRNDTRS
WKRDREKRDD QDDVSSVRSE GGNIRGSFRG RGRGRGRGRG RGRGNPRLNF DYSYGYQEHG
ERTDQPFQTE LNTSMMYYYD DGTGVQVYPV EEALLKEYIK RQIEYYFSVE NLERDFFLRG
KMDEQGFLPI SLIAGFQRVQ ALTTNLNLIL EALKDSTEVE IVDEKMRKKI EPEKWPIPGP
PPRSVPPTDF SQLIDCPEFV PGQAFCSHTE SAPNSPRIGS PLSPKKNSET SILQAMSRGL
STSLPDLDSE PWIEVKKRHQ PAPVKLRESV SVPEGSLNQL CSSEEPEQEE LDFLFDEEIE
QIGRKNTFTD WSDNDSDYEI DDQDLNKILI VTQTPPYVKK HRGGDRTGTH MSRAKITSEL
AKVINDGLYY YEQDLWMEED ENKHTAIKQE VENFKKLNLI SKEQFENLTP ELPFEPNQEV
PVAPSQSRQG GVQGVLHIPK KDLTDELAQK LFDVSEITSA AMVHSLPTAV PESPRIHPTR
TPKTPRTPRL QDPNKTPRFY PVVKEPKAID VKSPRKRKTR HSTNPPLECH VGWVMDSRDR
GPGTSSVSTS NASPSEGAPL AGSYGCTPHS FPKFQHPSHE LLKENGFTQQ VYHKYRRRCL
SERKRLGIGQ SQEMNTLFRF WSFFLRDHFN KKMYEEFRQL AWEDAKENYR SAVWTRKVLG
LFEIFSI*

speed

0.85 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00694424079836709 (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)

chr4:129043204C>GN/A show variant in all transcripts IGV

HGNC symbol

LARP1B

Ensembl transcript ID

ENST00000427266

Genbank transcript ID

NM_178043

UniProt peptide

Q659C4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1385C>G
cDNA.1516C>G
g.60782C>G

AA changes

P462R Score: 103 explain score(s)

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

462

frameshift

known variant

Reference ID: rs12508837

database	homozygous (G/G)	heterozygous	allele carriers
1000G	938	1080	2018
ExAC	26429	-20091	6338

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.389	1
	2.543	1
(flanking)	0.036	0.993

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	60773	wt: 0.5189 / mu: 0.5599 (marginal change - not scored)	wt: TGTGAAAAAACATCC mu: TGTGAAAAAACATCG	TGAA\|aaaa
Donor increased	60781	wt: 0.82 / mu: 0.99	wt: AACATCCTGGAGGAG mu: AACATCGTGGAGGAG	CATC\|ctgg
Donor gained	60776	0.49	mu: GAAAAAACATCGTGG	AAAA\|acat

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

462

mutated

not conserved

462

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000021347

462

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000037814

n/a

Ggallus

all identical

ENSGALG00000010207

426

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0261618

1150

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022512

556

protein features

start (aa)	end (aa)	feature	details
473	473	CONFLICT	R -> Q (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
639	639	CONFLICT	T -> A (in Ref. 2; CAD97908).	might get lost (downstream of altered splice site)
671	671	CONFLICT	N -> S (in Ref. 4; AAH62606).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1569 / 1569

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

523 / 523

position of stopcodon in wt / mu cDNA

1700 / 1700

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

132 / 132

chromosome

strand

last intron/exon boundary

1293

theoretical NMD boundary in CDS

1111

length of CDS

1569

coding sequence (CDS) position

1385

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

1516

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

60782

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

129043204

original gDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered gDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

original cDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered cDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

wildtype AA sequence

mutated AA sequence

speed

0.86 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00694424079836709 (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)

chr4:129043204C>GN/A show variant in all transcripts IGV

HGNC symbol

LARP1B

Ensembl transcript ID

ENST00000264584

Genbank transcript ID

N/A

UniProt peptide

Q659C4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1244C>G
cDNA.1375C>G
g.60782C>G

AA changes

P415R Score: 103 explain score(s)

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

415

frameshift

known variant

Reference ID: rs12508837

database	homozygous (G/G)	heterozygous	allele carriers
1000G	938	1080	2018
ExAC	26429	-20091	6338

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.389	1
	2.543	1
(flanking)	0.036	0.993

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	60773	wt: 0.5189 / mu: 0.5599 (marginal change - not scored)	wt: TGTGAAAAAACATCC mu: TGTGAAAAAACATCG	TGAA\|aaaa
Donor increased	60781	wt: 0.82 / mu: 0.99	wt: AACATCCTGGAGGAG mu: AACATCGTGGAGGAG	CATC\|ctgg
Donor gained	60776	0.49	mu: GAAAAAACATCGTGG	AAAA\|acat

distance from splice site

140

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

415

mutated

not conserved

415

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000021347

462

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000037814

n/a

Ggallus

all identical

ENSGALG00000010207

426

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0261618

1150

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022512

556

protein features

start (aa)	end (aa)	feature	details
432	432	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
454	454	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
473	473	CONFLICT	R -> Q (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
639	639	CONFLICT	T -> A (in Ref. 2; CAD97908).	might get lost (downstream of altered splice site)
671	671	CONFLICT	N -> S (in Ref. 4; AAH62606).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2568 / 2568

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

856 / 856

position of stopcodon in wt / mu cDNA

2699 / 2699

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

132 / 132

chromosome

strand

last intron/exon boundary

2502

theoretical NMD boundary in CDS

2320

length of CDS

2568

coding sequence (CDS) position

1244

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

1375

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

60782

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

129043204

original gDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered gDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

original cDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered cDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

wildtype AA sequence

MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRGWKRDREK RDDQDDVSSV RSEGGNIRGS FRGRGRGRGR GRGRGRGNPR
LNFDYSYGYQ EHGERTDQPF QTELNTSMMY YYDDGTGVQV YPVEEALLKE YIKRQIEYYF
SVENLERDFF LRGKMDEQGF LPISLIAGFQ RVQALTTNLN LILEALKDST EVEIVDEKMR
KKIEPEKWPI PGPPPRSVPP TDFSQLIDCP EFVPGQAFCS HTESAPNSPR IGSPLSPKKN
SETSILQAMS RGLSTSLPDL DSEPWIEVKK RHQPAPVKLR ESVSVPEGSL NQLCSSEEPE
QEELDFLFDE EIEQIGRKNT FTDWSDNDSD YEIDDQDLNK ILIVTQTPPY VKKHPGGDRT
GTHMSRAKIT SELAKVINDG LYYYEQDLWM EEDENKHTAI KQEVENFKKL NLISKEQFEN
LTPELPFEPN QEVPVAPSQS RQDLTDELAQ KLFDVSEITS AAMVHSLPTA VPESPRIHPT
RTPKTPRTPR LQDPNKTPRF YPVVKEPKAI DVKSPRKRKT RHSTNPPLEC HVGWVMDSRD
RGPGTSSVST SNASPSEGAP LAGSYGCTPH SFPKFQHPSH ELLKENGFTQ QVYHKYRRRC
LSERKRLGIG QSQEMNTLFR FWSFFLRDHF NKKMYEEFRQ LAWEDAKENY RYGLECLFRF
YSYGLEKKFR REIFQDFQEE TKKDYESGQL YGLEKFWAYL KYSQSKTQSI DPKLQEYLCS
FKRLEDFRVD PPISDEFGRK RHSSTSGEES NRHRLPPNSS TKPPNAAKPT STSELQVPIN
SPRRNISPES SDNSH*

mutated AA sequence

MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRGWKRDREK RDDQDDVSSV RSEGGNIRGS FRGRGRGRGR GRGRGRGNPR
LNFDYSYGYQ EHGERTDQPF QTELNTSMMY YYDDGTGVQV YPVEEALLKE YIKRQIEYYF
SVENLERDFF LRGKMDEQGF LPISLIAGFQ RVQALTTNLN LILEALKDST EVEIVDEKMR
KKIEPEKWPI PGPPPRSVPP TDFSQLIDCP EFVPGQAFCS HTESAPNSPR IGSPLSPKKN
SETSILQAMS RGLSTSLPDL DSEPWIEVKK RHQPAPVKLR ESVSVPEGSL NQLCSSEEPE
QEELDFLFDE EIEQIGRKNT FTDWSDNDSD YEIDDQDLNK ILIVTQTPPY VKKHRGGDRT
GTHMSRAKIT SELAKVINDG LYYYEQDLWM EEDENKHTAI KQEVENFKKL NLISKEQFEN
LTPELPFEPN QEVPVAPSQS RQDLTDELAQ KLFDVSEITS AAMVHSLPTA VPESPRIHPT
RTPKTPRTPR LQDPNKTPRF YPVVKEPKAI DVKSPRKRKT RHSTNPPLEC HVGWVMDSRD
RGPGTSSVST SNASPSEGAP LAGSYGCTPH SFPKFQHPSH ELLKENGFTQ QVYHKYRRRC
LSERKRLGIG QSQEMNTLFR FWSFFLRDHF NKKMYEEFRQ LAWEDAKENY RYGLECLFRF
YSYGLEKKFR REIFQDFQEE TKKDYESGQL YGLEKFWAYL KYSQSKTQSI DPKLQEYLCS
FKRLEDFRVD PPISDEFGRK RHSSTSGEES NRHRLPPNSS TKPPNAAKPT STSELQVPIN
SPRRNISPES SDNSH*

speed

1.33 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 3.25394570988505e-26 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr4:129043204C>GN/A show variant in all transcripts IGV

HGNC symbol

LARP1B

Ensembl transcript ID

ENST00000354456

Genbank transcript ID

N/A

UniProt peptide

Q659C4

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.1516C>G
g.60782C>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs12508837

database	homozygous (G/G)	heterozygous	allele carriers
1000G	938	1080	2018
ExAC	26429	-20091	6338

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.389	1
	2.543	1
(flanking)	0.036	0.993

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

splice sites

splice site change before start ATG (at aa -121) | splice site change before start ATG (at aa -119) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	60773	wt: 0.5189 / mu: 0.5599 (marginal change - not scored)	wt: TGTGAAAAAACATCC mu: TGTGAAAAAACATCG	TGAA\|aaaa
Donor increased	60781	wt: 0.82 / mu: 0.99	wt: AACATCCTGGAGGAG mu: AACATCGTGGAGGAG	CATC\|ctgg
Donor gained	60776	0.49	mu: GAAAAAACATCGTGG	AAAA\|acat

distance from splice site

140

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
60	60	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
114	167	COMPBIAS	Arg-rich.	might get lost (downstream of altered splice site)
209	299	DOMAIN	HTH La-type RNA-binding.	might get lost (downstream of altered splice site)
272	272	CONFLICT	A -> V (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
289	289	CONFLICT	K -> E (in Ref. 1; BAA91576).	might get lost (downstream of altered splice site)
291	291	CONFLICT	E -> T (in Ref. 1; BAC05306).	might get lost (downstream of altered splice site)
340	340	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
343	343	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
363	363	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
432	432	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
454	454	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
473	473	CONFLICT	R -> Q (in Ref. 1; BAC03970).	might get lost (downstream of altered splice site)
639	639	CONFLICT	T -> A (in Ref. 2; CAD97908).	might get lost (downstream of altered splice site)
671	671	CONFLICT	N -> S (in Ref. 4; AAH62606).	might get lost (downstream of altered splice site)

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

1875 / 1875

chromosome

strand

last intron/exon boundary

2679

theoretical NMD boundary in CDS

754

length of CDS

846

coding sequence (CDS) position

N/A

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

1516

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

60782

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

129043204

original gDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered gDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

original cDNA sequence snippet

ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA

altered cDNA sequence snippet

ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA

wildtype AA sequence

MVHSLPTAVP ESPRIHPTRT PKTPRTPRLQ DPNKTPRFYP VVKEPKAIDV KSPRKRKTRH
STNPPLECHV GWVMDSRDRG PGTSSVSTSN ASPSEGAPLA GSYGCTPHSF PKFQHPSHEL
LKENGFTQQV YHKYRRRCLS ERKRLGIGQS QEMNTLFRFW SFFLRDHFNK KMYEEFRQLA
WEDAKENYRY GLECLFRFYS YGLEKKFRRE IFQDFQEETK KDYESGQLYG LEKFWAYLKY
SQSKTQSIDP KLQEYLCSFK RLEDFRVDNH HDRLLLLIIN I*

mutated AA sequence

N/A

speed

1.03 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

mutation t@sting

Prediction

polymorphism

Problems