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: ENST00000388715
Querying Taster for transcript #2: ENST00000312917
Querying Taster for transcript #3: ENST00000457797
Querying Taster for transcript #4: ENST00000394571
MT speed 0 s - this script 5.101338 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PNPLA1	polymorphism_automatic	3.95017352161631e-13	simple_aae				P337H	single base exchange	rs12199580		show file
PNPLA1	polymorphism_automatic	3.95017352161631e-13	simple_aae				P328H	single base exchange	rs12199580		show file
PNPLA1	polymorphism_automatic	3.95017352161631e-13	simple_aae				P424H	single base exchange	rs12199580		show file
PNPLA1	polymorphism_automatic	3.95017352161631e-13	simple_aae				P423H	single base exchange	rs12199580		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999605 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:36270130C>AN/A show variant in all transcripts IGV

HGNC symbol

PNPLA1

Ensembl transcript ID

ENST00000312917

Genbank transcript ID

NM_001145716

UniProt peptide

Q8N8W4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1010C>A
cDNA.1149C>A
g.59151C>A

AA changes

P337H Score: 77 explain score(s)

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

337

frameshift

known variant

Reference ID: rs12199580

database	homozygous (A/A)	heterozygous	allele carriers
1000G	255	904	1159
ExAC	9785	13197	22982

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.208	0
	0.39	0.003
(flanking)	1.302	0.006

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

117

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

337

mutated

not conserved

337

Ptroglodytes

all identical

ENSPTRG00000018100

423

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000043286

447

PRLLL

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000086554

n/a

Dmelanogaster

no alignment

FBgn0036449

n/a

Celegans

no alignment

C05D11.7

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
326	451	COMPBIAS	Pro-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1341 / 1341

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

447 / 447

position of stopcodon in wt / mu cDNA

1480 / 1480

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

140 / 140

chromosome

strand

last intron/exon boundary

1351

theoretical NMD boundary in CDS

1161

length of CDS

1341

coding sequence (CDS) position

1010

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

1149

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

59151

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

36270130

original gDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered gDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

original cDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered cDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

wildtype AA sequence

MVQMMRQFLY RVLPEDSYKV TTGKLHVSLT RLTDGENVVV SEFTSKEELI EALYCSCFVP
VYCGLIPPTY RGVWAFLTLP PQRYIDGGFT GMQPCAFWTD AITISTFSGQ QDICPRDCPA
IFHDFRMFNC SFQFSLENIA RMTHALFPPD LVILHDYYYR GYEDAVLYLR RLNAVYLNSS
SKRVIFPRVE VYCQIELALG NECPERSQPS LRARQASLEG ATQPHKEWVP KGDGRGSHGP
PVSQPVQTLE FTCESPVSAP VSPLEQPPAQ PLASSTPLSL SGMPPVSFPA VHKPPSSTPG
SSLPTPPPGL SPLSPQQQVQ PSGSPARSLH SQAPTSPRPS LGPSTVGAPQ TLPRSSLSAF
PAQPPVEELG QEQPQAVALL VSSKPKSAVP LVHVKETVSK PYVTESPAED SNWVNKVFKK
NKQKTSGTRK GFPRHSGSKK PSSKVQ*

mutated AA sequence

MVQMMRQFLY RVLPEDSYKV TTGKLHVSLT RLTDGENVVV SEFTSKEELI EALYCSCFVP
VYCGLIPPTY RGVWAFLTLP PQRYIDGGFT GMQPCAFWTD AITISTFSGQ QDICPRDCPA
IFHDFRMFNC SFQFSLENIA RMTHALFPPD LVILHDYYYR GYEDAVLYLR RLNAVYLNSS
SKRVIFPRVE VYCQIELALG NECPERSQPS LRARQASLEG ATQPHKEWVP KGDGRGSHGP
PVSQPVQTLE FTCESPVSAP VSPLEQPPAQ PLASSTPLSL SGMPPVSFPA VHKPPSSTPG
SSLPTPPPGL SPLSPQQQVQ PSGSPARSLH SQAPTSHRPS LGPSTVGAPQ TLPRSSLSAF
PAQPPVEELG QEQPQAVALL VSSKPKSAVP LVHVKETVSK PYVTESPAED SNWVNKVFKK
NKQKTSGTRK GFPRHSGSKK PSSKVQ*

speed

1.67 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: 0.999999999999605 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:36270130C>AN/A show variant in all transcripts IGV

HGNC symbol

PNPLA1

Ensembl transcript ID

ENST00000388715

Genbank transcript ID

NM_173676

UniProt peptide

Q8N8W4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.983C>A
cDNA.1122C>A
g.59151C>A

AA changes

P328H Score: 77 explain score(s)

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

328

frameshift

known variant

Reference ID: rs12199580

database	homozygous (A/A)	heterozygous	allele carriers
1000G	255	904	1159
ExAC	9785	13197	22982

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.208	0
	0.39	0.003
(flanking)	1.302	0.006

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

117

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

328

mutated

not conserved

328

Ptroglodytes

all identical

ENSPTRG00000018100

423

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000043286

437

PRLLL

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000086554

n/a

Dmelanogaster

no alignment

FBgn0036449

n/a

Celegans

no alignment

C05D11.7

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
326	451	COMPBIAS	Pro-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1314 / 1314

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

438 / 438

position of stopcodon in wt / mu cDNA

1453 / 1453

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

140 / 140

chromosome

strand

last intron/exon boundary

1324

theoretical NMD boundary in CDS

1134

length of CDS

1314

coding sequence (CDS) position

983

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

1122

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

59151

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

36270130

original gDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered gDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

original cDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered cDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

wildtype AA sequence

MVQMMRQFLY RVLPEDSYKV TTGKLHVSLT RLTDGENVVV SEFTSKEELI EALYCSCFVP
VYCGLIPPTY RGVRYIDGGF TGMQPCAFWT DAITISTFSG QQDICPRDCP AIFHDFRMFN
CSFQFSLENI ARMTHALFPP DLVILHDYYY RGYEDAVLYL RRLNAVYLNS SSKRVIFPRV
EVYCQIELAL GNECPERSQP SLRARQASLE GATQPHKEWV PKGDGRGSHG PPVSQPVQTL
EFTCESPVSA PVSPLEQPPA QPLASSTPLS LSGMPPVSFP AVHKPPSSTP GSSLPTPPPG
LSPLSPQQQV QPSGSPARSL HSQAPTSPRP SLGPSTVGAP QTLPRSSLSA FPAQPPVEEL
GQEQPQAVAL LVSSKPKSAV PLVHVKETVS KPYVTESPAE DSNWVNKVFK KNKQKTSGTR
KGFPRHSGSK KPSSKVQ*

mutated AA sequence

MVQMMRQFLY RVLPEDSYKV TTGKLHVSLT RLTDGENVVV SEFTSKEELI EALYCSCFVP
VYCGLIPPTY RGVRYIDGGF TGMQPCAFWT DAITISTFSG QQDICPRDCP AIFHDFRMFN
CSFQFSLENI ARMTHALFPP DLVILHDYYY RGYEDAVLYL RRLNAVYLNS SSKRVIFPRV
EVYCQIELAL GNECPERSQP SLRARQASLE GATQPHKEWV PKGDGRGSHG PPVSQPVQTL
EFTCESPVSA PVSPLEQPPA QPLASSTPLS LSGMPPVSFP AVHKPPSSTP GSSLPTPPPG
LSPLSPQQQV QPSGSPARSL HSQAPTSHRP SLGPSTVGAP QTLPRSSLSA FPAQPPVEEL
GQEQPQAVAL LVSSKPKSAV PLVHVKETVS KPYVTESPAE DSNWVNKVFK KNKQKTSGTR
KGFPRHSGSK KPSSKVQ*

speed

1.44 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999605 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:36270130C>AN/A show variant in all transcripts IGV

HGNC symbol

PNPLA1

Ensembl transcript ID

ENST00000457797

Genbank transcript ID

N/A

UniProt peptide

Q8N8W4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1271C>A
cDNA.1271C>A
g.59151C>A

AA changes

P424H Score: 77 explain score(s)

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

424

frameshift

known variant

Reference ID: rs12199580

database	homozygous (A/A)	heterozygous	allele carriers
1000G	255	904	1159
ExAC	9785	13197	22982

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.208	0
	0.39	0.003
(flanking)	1.302	0.006

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

117

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

424

mutated

not conserved

424

Ptroglodytes

all identical

ENSPTRG00000018100

423

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000043286

451

PRLLL

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000086554

n/a

Dmelanogaster

no alignment

FBgn0036449

n/a

Celegans

no alignment

C05D11.7

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
326	451	COMPBIAS	Pro-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1602 / 1602

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

534 / 534

position of stopcodon in wt / mu cDNA

1602 / 1602

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

1473

theoretical NMD boundary in CDS

1422

length of CDS

1602

coding sequence (CDS) position

1271

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

1271

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

59151

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

36270130

original gDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered gDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

original cDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered cDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

wildtype AA sequence

MEEQVFKGDP DTPHSISFSG SGFLSFYQAG AVDALRDLAP RMLETAHRFA GTSAGAVIAA
LAICGIEMDE YLRVLNVGVA EVKKSFLGPL SPSCKMVQMM RQFLYRVLPE DSYKVTTGKL
HVSLTRLTDG ENVVVSEFTS KEELIEAALY CSCFVPVYCG LIPPTYRGVR YIDGGFTGMQ
PCAFWTDAIT ISTFSGQQDI CPRDCPAIFH DFRMFNCSFQ FSLENIARMT HALFPPDLVI
LHDYYYRGYE DAVLYLRRLN AVYLNSSSKR VIFPRVEVYC QIELALGNEC PERSQPSLRA
RQASLEGATQ PHKEWVPKGD GRGSHGPPVS QPVQTLEFTC ESPVSAPVSP LEQPPAQPLA
SSTPLSLSGM PPVSFPAVHK PPSSTPGSSL PTPPPGLSPL SPQQQVQPSG SPARSLHSQA
PTSPRPSLGP STVGAPQTLP RSSLSAFPAQ PPVEELGQEQ PQAVALLVSS KPKSAVPLVH
VKETVSKPYV TESPAEDSNW VNKVFKKNKQ KTSGTRKGFP RHSGSKKPSS KVQ*

mutated AA sequence

MEEQVFKGDP DTPHSISFSG SGFLSFYQAG AVDALRDLAP RMLETAHRFA GTSAGAVIAA
LAICGIEMDE YLRVLNVGVA EVKKSFLGPL SPSCKMVQMM RQFLYRVLPE DSYKVTTGKL
HVSLTRLTDG ENVVVSEFTS KEELIEAALY CSCFVPVYCG LIPPTYRGVR YIDGGFTGMQ
PCAFWTDAIT ISTFSGQQDI CPRDCPAIFH DFRMFNCSFQ FSLENIARMT HALFPPDLVI
LHDYYYRGYE DAVLYLRRLN AVYLNSSSKR VIFPRVEVYC QIELALGNEC PERSQPSLRA
RQASLEGATQ PHKEWVPKGD GRGSHGPPVS QPVQTLEFTC ESPVSAPVSP LEQPPAQPLA
SSTPLSLSGM PPVSFPAVHK PPSSTPGSSL PTPPPGLSPL SPQQQVQPSG SPARSLHSQA
PTSHRPSLGP STVGAPQTLP RSSLSAFPAQ PPVEELGQEQ PQAVALLVSS KPKSAVPLVH
VKETVSKPYV TESPAEDSNW VNKVFKKNKQ KTSGTRKGFP RHSGSKKPSS KVQ*

speed

0.54 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999605 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:36270130C>AN/A show variant in all transcripts IGV

HGNC symbol

PNPLA1

Ensembl transcript ID

ENST00000394571

Genbank transcript ID

NM_001145717

UniProt peptide

Q8N8W4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1268C>A
cDNA.1268C>A
g.59151C>A

AA changes

P423H Score: 77 explain score(s)

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

423

frameshift

known variant

Reference ID: rs12199580

database	homozygous (A/A)	heterozygous	allele carriers
1000G	255	904	1159
ExAC	9785	13197	22982

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.208	0
	0.39	0.003
(flanking)	1.302	0.006

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

117

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

423

mutated

not conserved

423

Ptroglodytes

all identical

ENSPTRG00000018100

423

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000043286

451

PRLLL

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000086554

n/a

Dmelanogaster

no alignment

FBgn0036449

n/a

Celegans

no alignment

C05D11.7

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
326	451	COMPBIAS	Pro-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1599 / 1599

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

533 / 533

position of stopcodon in wt / mu cDNA

1599 / 1599

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

1470

theoretical NMD boundary in CDS

1419

length of CDS

1599

coding sequence (CDS) position

1268

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

1268

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

59151

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

36270130

original gDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered gDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

original cDNA sequence snippet

CTCTCAGGCACCCACTTCACCCAGGCCATCCCTGGGGCCTT

altered cDNA sequence snippet

CTCTCAGGCACCCACTTCACACAGGCCATCCCTGGGGCCTT

wildtype AA sequence

MEEQVFKGDP DTPHSISFSG SGFLSFYQAG AVDALRDLAP RMLETAHRFA GTSAGAVIAA
LAICGIEMDE YLRVLNVGVA EVKKSFLGPL SPSCKMVQMM RQFLYRVLPE DSYKVTTGKL
HVSLTRLTDG ENVVVSEFTS KEELIEALYC SCFVPVYCGL IPPTYRGVRY IDGGFTGMQP
CAFWTDAITI STFSGQQDIC PRDCPAIFHD FRMFNCSFQF SLENIARMTH ALFPPDLVIL
HDYYYRGYED AVLYLRRLNA VYLNSSSKRV IFPRVEVYCQ IELALGNECP ERSQPSLRAR
QASLEGATQP HKEWVPKGDG RGSHGPPVSQ PVQTLEFTCE SPVSAPVSPL EQPPAQPLAS
STPLSLSGMP PVSFPAVHKP PSSTPGSSLP TPPPGLSPLS PQQQVQPSGS PARSLHSQAP
TSPRPSLGPS TVGAPQTLPR SSLSAFPAQP PVEELGQEQP QAVALLVSSK PKSAVPLVHV
KETVSKPYVT ESPAEDSNWV NKVFKKNKQK TSGTRKGFPR HSGSKKPSSK VQ*

mutated AA sequence

MEEQVFKGDP DTPHSISFSG SGFLSFYQAG AVDALRDLAP RMLETAHRFA GTSAGAVIAA
LAICGIEMDE YLRVLNVGVA EVKKSFLGPL SPSCKMVQMM RQFLYRVLPE DSYKVTTGKL
HVSLTRLTDG ENVVVSEFTS KEELIEALYC SCFVPVYCGL IPPTYRGVRY IDGGFTGMQP
CAFWTDAITI STFSGQQDIC PRDCPAIFHD FRMFNCSFQF SLENIARMTH ALFPPDLVIL
HDYYYRGYED AVLYLRRLNA VYLNSSSKRV IFPRVEVYCQ IELALGNECP ERSQPSLRAR
QASLEGATQP HKEWVPKGDG RGSHGPPVSQ PVQTLEFTCE SPVSAPVSPL EQPPAQPLAS
STPLSLSGMP PVSFPAVHKP PSSTPGSSLP TPPPGLSPLS PQQQVQPSGS PARSLHSQAP
TSHRPSLGPS TVGAPQTLPR SSLSAFPAQP PVEELGQEQP QAVALLVSSK PKSAVPLVHV
KETVSKPYVT ESPAEDSNWV NKVFKKNKQK TSGTRKGFPR HSGSKKPSSK VQ*

speed

0.87 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