MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000371500
Querying Taster for transcript #2: ENST00000312553
Querying Taster for transcript #3: ENST00000395871
MT speed 0 s - this script 4.501494 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PODN	polymorphism_automatic	4.22975199310116e-09	simple_aae		affected		V501A	single base exchange	rs1288389		show file
PODN	polymorphism_automatic	5.71327396503563e-09	simple_aae		affected		V520A	single base exchange	rs1288389		show file
PODN	polymorphism_automatic	5.71327396503563e-09	simple_aae		affected		V378A	single base exchange	rs1288389		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999995770248 (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)

chr1:53544597T>CN/A show variant in all transcripts IGV

HGNC symbol

PODN

Ensembl transcript ID

ENST00000371500

Genbank transcript ID

NM_001199080

UniProt peptide

Q7Z5L7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1502T>C
cDNA.1843T>C
g.16744T>C

AA changes

V501A Score: 64 explain score(s)

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

501

frameshift

known variant

Reference ID: rs1288389

database	homozygous (C/C)	heterozygous	allele carriers
1000G	906	997	1903
ExAC	25261	-17755	7506

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.781	0.482
	1.797	0.464
(flanking)	-1.772	0.085

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 gained	16745	0.51	mu: CTGGCGGGCATGGCT	GGCG\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

501

mutated

not conserved

501

Ptroglodytes

not conserved

ENSPTRG00000000749

520

Mmulatta

not conserved

ENSMMUG00000007604

521

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000028600

473

Ggallus

not conserved

ENSGALG00000021869

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000019025

454

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	522	REPEAT	LRR 17.	might get lost (downstream of altered splice site)
523	544	REPEAT	LRR 18.	might get lost (downstream of altered splice site)
547	568	REPEAT	LRR 19.	might get lost (downstream of altered splice site)
573	595	REPEAT	LRR 20.	might get lost (downstream of altered splice site)
598	611	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1929 / 1929

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

643 / 643

position of stopcodon in wt / mu cDNA

2270 / 2270

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

342 / 342

chromosome

strand

last intron/exon boundary

2298

theoretical NMD boundary in CDS

1906

length of CDS

1929

coding sequence (CDS) position

1502

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

1843

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

16744

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

53544597

original gDNA sequence snippet

CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG

altered gDNA sequence snippet

CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG

original cDNA sequence snippet

CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG

altered cDNA sequence snippet

CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG

wildtype AA sequence

MEGEEAEQPA WFRQPWRPGA SDSAPPAGTM AQSRVLLLLL LLPPQLHLGP VLAVRAPGFG
RSGGHSLSPE ENEFAEEEPV LVLSPEEPGP GPAAVSCPRD CACSQEGVVD CGGIDLREFP
GDLPEHTNHL SLQNNQLEKI YPEELSRLHR LETLNLQNNR LTSRGLPEKA FEHLTNLNYL
YLANNKLTLA PRFLPNALIS VDFAANYLTK IYGLTFGQKP NLRSVYLHNN KLADAGLPDN
MFNGSSNVEV LILSSNFLRH VPKHLPPALY KLHLKNNKLE KIPPGAFSEL SSLRELYLQN
NYLTDEGLDN ETFWKLSSLE YLDLSSNNLS RVPAGLPRSL VLLHLEKNAI RSVDANVLTP
IRSLEYLLLH SNQLREQGIH PLAFQGLKRL HTVHLYNNAL ERVPSGLPRR VRTLMILHNQ
ITGIGREDFA TTYFLEELNL SYNRITSPQV HRDAFRKLRL LRSLDLSGNR LHTLPPGLPR
NVHVLKVKRN ELAALARGAL VGMAQLRELY LTSNRLRSRA LGPRAWVDLA HLQLLDIAGN
QLTEIPEGLP ESLEYLYLQN NKISAVPANA FDSTPNLKGI FLRFNKLAVG SVVDSAFRRL
KHLQVLDIEG NLEFGDISKD RGRLGKEKEE EEEEEEEEEE TR*

mutated AA sequence

MEGEEAEQPA WFRQPWRPGA SDSAPPAGTM AQSRVLLLLL LLPPQLHLGP VLAVRAPGFG
RSGGHSLSPE ENEFAEEEPV LVLSPEEPGP GPAAVSCPRD CACSQEGVVD CGGIDLREFP
GDLPEHTNHL SLQNNQLEKI YPEELSRLHR LETLNLQNNR LTSRGLPEKA FEHLTNLNYL
YLANNKLTLA PRFLPNALIS VDFAANYLTK IYGLTFGQKP NLRSVYLHNN KLADAGLPDN
MFNGSSNVEV LILSSNFLRH VPKHLPPALY KLHLKNNKLE KIPPGAFSEL SSLRELYLQN
NYLTDEGLDN ETFWKLSSLE YLDLSSNNLS RVPAGLPRSL VLLHLEKNAI RSVDANVLTP
IRSLEYLLLH SNQLREQGIH PLAFQGLKRL HTVHLYNNAL ERVPSGLPRR VRTLMILHNQ
ITGIGREDFA TTYFLEELNL SYNRITSPQV HRDAFRKLRL LRSLDLSGNR LHTLPPGLPR
NVHVLKVKRN ELAALARGAL AGMAQLRELY LTSNRLRSRA LGPRAWVDLA HLQLLDIAGN
QLTEIPEGLP ESLEYLYLQN NKISAVPANA FDSTPNLKGI FLRFNKLAVG SVVDSAFRRL
KHLQVLDIEG NLEFGDISKD RGRLGKEKEE EEEEEEEEEE TR*

speed

1.14 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: 0.999999994286726 (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)

chr1:53544597T>CN/A show variant in all transcripts IGV

HGNC symbol

PODN

Ensembl transcript ID

ENST00000312553

Genbank transcript ID

NM_153703

UniProt peptide

Q7Z5L7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1559T>C
cDNA.1566T>C
g.16744T>C

AA changes

V520A Score: 64 explain score(s)

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

520

frameshift

known variant

Reference ID: rs1288389

database	homozygous (C/C)	heterozygous	allele carriers
1000G	906	997	1903
ExAC	25261	-17755	7506

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.781	0.482
	1.797	0.464
(flanking)	-1.772	0.085

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 gained	16745	0.51	mu: CTGGCGGGCATGGCT	GGCG\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

520

mutated

not conserved

520

Ptroglodytes

not conserved

ENSPTRG00000000749

520

Mmulatta

not conserved

ENSMMUG00000007604

521

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000028600

473

Ggallus

not conserved

ENSGALG00000021869

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000019025

454

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	522	REPEAT	LRR 17.	lost
523	544	REPEAT	LRR 18.	might get lost (downstream of altered splice site)
547	568	REPEAT	LRR 19.	might get lost (downstream of altered splice site)
573	595	REPEAT	LRR 20.	might get lost (downstream of altered splice site)
598	611	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1986 / 1986

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

662 / 662

position of stopcodon in wt / mu cDNA

1993 / 1993

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

8 / 8

chromosome

strand

last intron/exon boundary

2021

theoretical NMD boundary in CDS

1963

length of CDS

1986

coding sequence (CDS) position

1559

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

1566

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

16744

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

53544597

original gDNA sequence snippet

CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG

altered gDNA sequence snippet

CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG

original cDNA sequence snippet

CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG

altered cDNA sequence snippet

CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG

wildtype AA sequence

MEGARARGAQ LRLGERVRPV GRRSAPGRSR FRQPWRPGAS DSAPPAGTMA QSRVLLLLLL
LPPQLHLGPV LAVRAPGFGR SGGHSLSPEE NEFAEEEPVL VLSPEEPGPG PAAVSCPRDC
ACSQEGVVDC GGIDLREFPG DLPEHTNHLS LQNNQLEKIY PEELSRLHRL ETLNLQNNRL
TSRGLPEKAF EHLTNLNYLY LANNKLTLAP RFLPNALISV DFAANYLTKI YGLTFGQKPN
LRSVYLHNNK LADAGLPDNM FNGSSNVEVL ILSSNFLRHV PKHLPPALYK LHLKNNKLEK
IPPGAFSELS SLRELYLQNN YLTDEGLDNE TFWKLSSLEY LDLSSNNLSR VPAGLPRSLV
LLHLEKNAIR SVDANVLTPI RSLEYLLLHS NQLREQGIHP LAFQGLKRLH TVHLYNNALE
RVPSGLPRRV RTLMILHNQI TGIGREDFAT TYFLEELNLS YNRITSPQVH RDAFRKLRLL
RSLDLSGNRL HTLPPGLPRN VHVLKVKRNE LAALARGALV GMAQLRELYL TSNRLRSRAL
GPRAWVDLAH LQLLDIAGNQ LTEIPEGLPE SLEYLYLQNN KISAVPANAF DSTPNLKGIF
LRFNKLAVGS VVDSAFRRLK HLQVLDIEGN LEFGDISKDR GRLGKEKEEE EEEEEEEEET
R*

mutated AA sequence

MEGARARGAQ LRLGERVRPV GRRSAPGRSR FRQPWRPGAS DSAPPAGTMA QSRVLLLLLL
LPPQLHLGPV LAVRAPGFGR SGGHSLSPEE NEFAEEEPVL VLSPEEPGPG PAAVSCPRDC
ACSQEGVVDC GGIDLREFPG DLPEHTNHLS LQNNQLEKIY PEELSRLHRL ETLNLQNNRL
TSRGLPEKAF EHLTNLNYLY LANNKLTLAP RFLPNALISV DFAANYLTKI YGLTFGQKPN
LRSVYLHNNK LADAGLPDNM FNGSSNVEVL ILSSNFLRHV PKHLPPALYK LHLKNNKLEK
IPPGAFSELS SLRELYLQNN YLTDEGLDNE TFWKLSSLEY LDLSSNNLSR VPAGLPRSLV
LLHLEKNAIR SVDANVLTPI RSLEYLLLHS NQLREQGIHP LAFQGLKRLH TVHLYNNALE
RVPSGLPRRV RTLMILHNQI TGIGREDFAT TYFLEELNLS YNRITSPQVH RDAFRKLRLL
RSLDLSGNRL HTLPPGLPRN VHVLKVKRNE LAALARGALA GMAQLRELYL TSNRLRSRAL
GPRAWVDLAH LQLLDIAGNQ LTEIPEGLPE SLEYLYLQNN KISAVPANAF DSTPNLKGIF
LRFNKLAVGS VVDSAFRRLK HLQVLDIEGN LEFGDISKDR GRLGKEKEEE EEEEEEEEET
R*

speed

1.25 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999994286726 (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)

chr1:53544597T>CN/A show variant in all transcripts IGV

HGNC symbol

PODN

Ensembl transcript ID

ENST00000395871

Genbank transcript ID

NM_001199082

UniProt peptide

Q7Z5L7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1133T>C
cDNA.1171T>C
g.16744T>C

AA changes

V378A Score: 64 explain score(s)

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

378

frameshift

known variant

Reference ID: rs1288389

database	homozygous (C/C)	heterozygous	allele carriers
1000G	906	997	1903
ExAC	25261	-17755	7506

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.781	0.482
	1.797	0.464
(flanking)	-1.772	0.085

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 gained	16745	0.51	mu: CTGGCGGGCATGGCT	GGCG\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

378

mutated

not conserved

378

Ptroglodytes

not conserved

ENSPTRG00000000749

520

Mmulatta

not conserved

ENSMMUG00000007604

521

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000028600

473

Ggallus

not conserved

ENSGALG00000021869

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000019025

454

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
360	380	REPEAT	LRR 12.	lost
381	402	REPEAT	LRR 13.	might get lost (downstream of altered splice site)
405	426	REPEAT	LRR 14.	might get lost (downstream of altered splice site)
410	410	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
431	452	REPEAT	LRR 15.	might get lost (downstream of altered splice site)
476	489	REPEAT	LRR 16.	might get lost (downstream of altered splice site)
502	522	REPEAT	LRR 17.	might get lost (downstream of altered splice site)
523	544	REPEAT	LRR 18.	might get lost (downstream of altered splice site)
547	568	REPEAT	LRR 19.	might get lost (downstream of altered splice site)
573	595	REPEAT	LRR 20.	might get lost (downstream of altered splice site)
598	611	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1560 / 1560

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

520 / 520

position of stopcodon in wt / mu cDNA

1598 / 1598

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

39 / 39

chromosome

strand

last intron/exon boundary

1626

theoretical NMD boundary in CDS

1537

length of CDS

1560

coding sequence (CDS) position

1133

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

1171

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

16744

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

53544597

original gDNA sequence snippet

CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG

altered gDNA sequence snippet

CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG

original cDNA sequence snippet

CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG

altered cDNA sequence snippet

CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG

wildtype AA sequence

MEGARARGAQ LRLGERVRPV GRRSAPGRSR FRQPWRPGAS DSAPPAGTMA QSRVLLLLLL
LPPQLHLGPV LAVRAPGFGR SGGHSLSPEE NEFAEEEPVL VLSPEEPGPG PAAVSCPRDC
ACSQEGVVDC GGIDLREFPG DLPEHTNHLS LQNNKLEKIP PGAFSELSSL RELYLQNNYL
TDEGLDNETF WKLSSLEYLD LSSNNLSRVP AGLPRSLVLL HLEKNAIRSV DANVLTPIRS
LEYLLLHSNQ LREQGIHPLA FQGLKRLHTV HLYNNALERV PSGLPRRVRT LMILHNQITG
IGREDFATTY FLEELNLSYN RITSPQVHRD AFRKLRLLRS LDLSGNRLHT LPPGLPRNVH
VLKVKRNELA ALARGALVGM AQLRELYLTS NRLRSRALGP RAWVDLAHLQ LLDIAGNQLT
EIPEGLPESL EYLYLQNNKI SAVPANAFDS TPNLKGIFLR FNKLAVGSVV DSAFRRLKHL
QVLDIEGNLE FGDISKDRGR LGKEKEEEEE EEEEEEETR*

mutated AA sequence

MEGARARGAQ LRLGERVRPV GRRSAPGRSR FRQPWRPGAS DSAPPAGTMA QSRVLLLLLL
LPPQLHLGPV LAVRAPGFGR SGGHSLSPEE NEFAEEEPVL VLSPEEPGPG PAAVSCPRDC
ACSQEGVVDC GGIDLREFPG DLPEHTNHLS LQNNKLEKIP PGAFSELSSL RELYLQNNYL
TDEGLDNETF WKLSSLEYLD LSSNNLSRVP AGLPRSLVLL HLEKNAIRSV DANVLTPIRS
LEYLLLHSNQ LREQGIHPLA FQGLKRLHTV HLYNNALERV PSGLPRRVRT LMILHNQITG
IGREDFATTY FLEELNLSYN RITSPQVHRD AFRKLRLLRS LDLSGNRLHT LPPGLPRNVH
VLKVKRNELA ALARGALAGM AQLRELYLTS NRLRSRALGP RAWVDLAHLQ LLDIAGNQLT
EIPEGLPESL EYLYLQNNKI SAVPANAFDS TPNLKGIFLR FNKLAVGSVV DSAFRRLKHL
QVLDIEGNLE FGDISKDRGR LGKEKEEEEE EEEEEEETR*

speed

1.23 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems