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: ENST00000369567
Querying Taster for transcript #2: ENST00000369569
Querying Taster for transcript #3: ENST00000256658
MT speed 0 s - this script 2.512241 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AP4B1	polymorphism_automatic	0.994798759842463	simple_aae		affected		L312S	single base exchange	rs1217401		show file
AP4B1	polymorphism_automatic	0.994798759842463	simple_aae		affected		L480S	single base exchange	rs1217401		show file
AP4B1	polymorphism_automatic	0.994798759842463	simple_aae		affected		L480S	single base exchange	rs1217401		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00520124015753655 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1314879)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:114438951A>GN/A show variant in all transcripts IGV

HGNC symbol

AP4B1

Ensembl transcript ID

ENST00000369567

Genbank transcript ID

N/A

UniProt peptide

Q9Y6B7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.935T>C
cDNA.1046T>C
g.8873T>C

AA changes

L312S Score: 145 explain score(s)

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

312

frameshift

known variant

Reference ID: rs1217401

database	homozygous (G/G)	heterozygous	allele carriers
1000G	534	820	1354
ExAC	7516	17735	25251

known disease mutation at this position, please check HGMD for details (HGMD ID CM1314879)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.456	0.991
	3.767	0.99
(flanking)	0.106	0.028

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	8873	0.39	mu: TGCTTCGCTGCGCCT	CTTC\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

312

mutated

not conserved

312

Ptroglodytes

all identical

ENSPTRG00000001127

480

Mmulatta

all identical

ENSMMUG00000019528

480

Fcatus

all identical

ENSFCAG00000009240

480

Mmusculus

all identical

ENSMUSG00000032952

480

Ggallus

all identical

ENSGALG00000021654

480

Trubripes

not conserved

ENSTRUG00000005006

480

Drerio

not conserved

ENSDARG00000013726

480

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000013187

381

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1716 / 1716

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

572 / 572

position of stopcodon in wt / mu cDNA

1827 / 1827

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

112 / 112

chromosome

strand

-1

last intron/exon boundary

1400

theoretical NMD boundary in CDS

1238

length of CDS

1716

coding sequence (CDS) position

935

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

1046

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

8873

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

114438951

original gDNA sequence snippet

GATGGAGCTGCTCACTGCTTTGCTGCGCCTTTTCCTCTCCC

altered gDNA sequence snippet

GATGGAGCTGCTCACTGCTTCGCTGCGCCTTTTCCTCTCCC

original cDNA sequence snippet

GATGGAGCTGCTCACTGCTTTGCTGCGCCTTTTCCTCTCCC

altered cDNA sequence snippet

GATGGAGCTGCTCACTGCTTCGCTGCGCCTTTTCCTCTCCC

wildtype AA sequence

MPYLGSEDVV KELKKALCNP HIQADRLRYR NVIQRVIRMS KLDQWGQAEV LNFLLRYQPR
SEEELFDILN LLDSFLKSSS PGVVMGATKL FLILAKMFPH VQTDVLVRVK GPLLAACSSE
SRELCFVALC HVRQILHSLP GHFSSHYKKF FCSYSEPHYI KLQKVEVLCE LVNDENVQQV
LEELRGYCTD VSADFAQAAI FAIGGIARTY TDQCVQILTE LLGLRQEHIT TVVVQTFRDL
VWLCPQCTEA VCQALPGCEE NIQDSEGKQA LIWLLGVHGE RIPNAPYVLE DFVENVKSET
FPAVKMELLT ALLRLFLSRP AECQDMLGRL LYYCIEEEKD MAVRDRGLFY YRLLLVGIDE
VKRILCSPKS DPTLGLLEDP AERPVNSWAS DFNTLVPVYG KAHWATISKC QGAERCDPEL
PKTSSFAASG PLIPEENKER VQELPDSGAL MLVPNRQLTA DYFEKTWLSL KVAHQQVLPW
RGEFHPDTLQ MALQVVNIQT IAMSRAGSRP WKAYLSAQDD TGCLFLTELL LEPGNSEMQI
SVKQNEARTE TLNSFISVLE TVIGTIEEIK S*

mutated AA sequence

MPYLGSEDVV KELKKALCNP HIQADRLRYR NVIQRVIRMS KLDQWGQAEV LNFLLRYQPR
SEEELFDILN LLDSFLKSSS PGVVMGATKL FLILAKMFPH VQTDVLVRVK GPLLAACSSE
SRELCFVALC HVRQILHSLP GHFSSHYKKF FCSYSEPHYI KLQKVEVLCE LVNDENVQQV
LEELRGYCTD VSADFAQAAI FAIGGIARTY TDQCVQILTE LLGLRQEHIT TVVVQTFRDL
VWLCPQCTEA VCQALPGCEE NIQDSEGKQA LIWLLGVHGE RIPNAPYVLE DFVENVKSET
FPAVKMELLT ASLRLFLSRP AECQDMLGRL LYYCIEEEKD MAVRDRGLFY YRLLLVGIDE
VKRILCSPKS DPTLGLLEDP AERPVNSWAS DFNTLVPVYG KAHWATISKC QGAERCDPEL
PKTSSFAASG PLIPEENKER VQELPDSGAL MLVPNRQLTA DYFEKTWLSL KVAHQQVLPW
RGEFHPDTLQ MALQVVNIQT IAMSRAGSRP WKAYLSAQDD TGCLFLTELL LEPGNSEMQI
SVKQNEARTE TLNSFISVLE TVIGTIEEIK S*

speed

0.24 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: 0.00520124015753654 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1314879)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:114438951A>GN/A show variant in all transcripts IGV

HGNC symbol

AP4B1

Ensembl transcript ID

ENST00000369569

Genbank transcript ID

NM_001253852

UniProt peptide

Q9Y6B7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1439T>C
cDNA.1720T>C
g.8873T>C

AA changes

L480S Score: 145 explain score(s)

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

480

frameshift

known variant

Reference ID: rs1217401

database	homozygous (G/G)	heterozygous	allele carriers
1000G	534	820	1354
ExAC	7516	17735	25251

known disease mutation at this position, please check HGMD for details (HGMD ID CM1314879)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.456	0.991
	3.767	0.99
(flanking)	0.106	0.028

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	8873	0.39	mu: TGCTTCGCTGCGCCT	CTTC\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

480

mutated

not conserved

480

Ptroglodytes

all identical

ENSPTRG00000001127

480

Mmulatta

all identical

ENSMMUG00000019528

480

Fcatus

all identical

ENSFCAG00000009240

480

Mmusculus

all identical

ENSMUSG00000032952

480

Ggallus

all identical

ENSGALG00000021654

480

Trubripes

not conserved

ENSTRUG00000005006

480

Drerio

not conserved

ENSDARG00000013726

480

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000013187

381

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2220 / 2220

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

740 / 740

position of stopcodon in wt / mu cDNA

2501 / 2501

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

282 / 282

chromosome

strand

-1

last intron/exon boundary

2074

theoretical NMD boundary in CDS

1742

length of CDS

2220

coding sequence (CDS) position

1439

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

1720

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

8873

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

114438951

original gDNA sequence snippet

GATGGAGCTGCTCACTGCTTTGCTGCGCCTTTTCCTCTCCC

altered gDNA sequence snippet

GATGGAGCTGCTCACTGCTTCGCTGCGCCTTTTCCTCTCCC

original cDNA sequence snippet

GATGGAGCTGCTCACTGCTTTGCTGCGCCTTTTCCTCTCCC

altered cDNA sequence snippet

GATGGAGCTGCTCACTGCTTCGCTGCGCCTTTTCCTCTCCC

wildtype AA sequence

MPYLGSEDVV KELKKALCNP HIQADRLRYR NVIQRVIRYM TQGLDMSGVF MEMVKASATV
DIVQKKLVYL YMCTYAPLKP DLALLAINTL CKDCSDPNPM VRGLALRSMC SLRMPGVQEY
IQQPILNGLR DKASYVRRVA VLGCAKMHNL HGDSEVDGAL VNELYSLLRD QDPIVVVNCL
RSLEEILKQE GGVVINKPIA HHLLNRMSKL DQWGQAEVLN FLLRYQPRSE EELFDILNLL
DSFLKSSSPG VVMGATKLFL ILAKMFPHVQ TDVLVRVKGP LLAACSSESR ELCFVALCHV
RQILHSLPGH FSSHYKKFFC SYSEPHYIKL QKVEVLCELV NDENVQQVLE ELRGYCTDVS
ADFAQAAIFA IGGIARTYTD QCVQILTELL GLRQEHITTV VVQTFRDLVW LCPQCTEAVC
QALPGCEENI QDSEGKQALI WLLGVHGERI PNAPYVLEDF VENVKSETFP AVKMELLTAL
LRLFLSRPAE CQDMLGRLLY YCIEEEKDMA VRDRGLFYYR LLLVGIDEVK RILCSPKSDP
TLGLLEDPAE RPVNSWASDF NTLVPVYGKA HWATISKCQG AERCDPELPK TSSFAASGPL
IPEENKERVQ ELPDSGALML VPNRQLTADY FEKTWLSLKV AHQQVLPWRG EFHPDTLQMA
LQVVNIQTIA MSRAGSRPWK AYLSAQDDTG CLFLTELLLE PGNSEMQISV KQNEARTETL
NSFISVLETV IGTIEEIKS*

mutated AA sequence

MPYLGSEDVV KELKKALCNP HIQADRLRYR NVIQRVIRYM TQGLDMSGVF MEMVKASATV
DIVQKKLVYL YMCTYAPLKP DLALLAINTL CKDCSDPNPM VRGLALRSMC SLRMPGVQEY
IQQPILNGLR DKASYVRRVA VLGCAKMHNL HGDSEVDGAL VNELYSLLRD QDPIVVVNCL
RSLEEILKQE GGVVINKPIA HHLLNRMSKL DQWGQAEVLN FLLRYQPRSE EELFDILNLL
DSFLKSSSPG VVMGATKLFL ILAKMFPHVQ TDVLVRVKGP LLAACSSESR ELCFVALCHV
RQILHSLPGH FSSHYKKFFC SYSEPHYIKL QKVEVLCELV NDENVQQVLE ELRGYCTDVS
ADFAQAAIFA IGGIARTYTD QCVQILTELL GLRQEHITTV VVQTFRDLVW LCPQCTEAVC
QALPGCEENI QDSEGKQALI WLLGVHGERI PNAPYVLEDF VENVKSETFP AVKMELLTAS
LRLFLSRPAE CQDMLGRLLY YCIEEEKDMA VRDRGLFYYR LLLVGIDEVK RILCSPKSDP
TLGLLEDPAE RPVNSWASDF NTLVPVYGKA HWATISKCQG AERCDPELPK TSSFAASGPL
IPEENKERVQ ELPDSGALML VPNRQLTADY FEKTWLSLKV AHQQVLPWRG EFHPDTLQMA
LQVVNIQTIA MSRAGSRPWK AYLSAQDDTG CLFLTELLLE PGNSEMQISV KQNEARTETL
NSFISVLETV IGTIEEIKS*

speed

0.13 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00520124015753655 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1314879)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:114438951A>GN/A show variant in all transcripts IGV

HGNC symbol

AP4B1

Ensembl transcript ID

ENST00000256658

Genbank transcript ID

NM_006594

UniProt peptide

Q9Y6B7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1439T>C
cDNA.1644T>C
g.8873T>C

AA changes

L480S Score: 145 explain score(s)

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

480

frameshift

known variant

Reference ID: rs1217401

database	homozygous (G/G)	heterozygous	allele carriers
1000G	534	820	1354
ExAC	7516	17735	25251

known disease mutation at this position, please check HGMD for details (HGMD ID CM1314879)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.456	0.991
	3.767	0.99
(flanking)	0.106	0.028

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	8873	0.39	mu: TGCTTCGCTGCGCCT	CTTC\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

480

mutated

not conserved

480

Ptroglodytes

all identical

ENSPTRG00000001127

480

Mmulatta

all identical

ENSMMUG00000019528

480

Fcatus

all identical

ENSFCAG00000009240

480

Mmusculus

all identical

ENSMUSG00000032952

480

Ggallus

all identical

ENSGALG00000021654

480

Trubripes

not conserved

ENSTRUG00000005006

480

Drerio

not conserved

ENSDARG00000013726

480

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000013187

381

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2220 / 2220

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

740 / 740

position of stopcodon in wt / mu cDNA

2425 / 2425

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

206 / 206

chromosome

strand

-1

last intron/exon boundary

1998

theoretical NMD boundary in CDS

1742

length of CDS

2220

coding sequence (CDS) position

1439

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

1644

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

8873

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

114438951

original gDNA sequence snippet

GATGGAGCTGCTCACTGCTTTGCTGCGCCTTTTCCTCTCCC

altered gDNA sequence snippet

GATGGAGCTGCTCACTGCTTCGCTGCGCCTTTTCCTCTCCC

original cDNA sequence snippet

GATGGAGCTGCTCACTGCTTTGCTGCGCCTTTTCCTCTCCC

altered cDNA sequence snippet

GATGGAGCTGCTCACTGCTTCGCTGCGCCTTTTCCTCTCCC

wildtype AA sequence

mutated AA sequence

MPYLGSEDVV KELKKALCNP HIQADRLRYR NVIQRVIRYM TQGLDMSGVF MEMVKASATV
DIVQKKLVYL YMCTYAPLKP DLALLAINTL CKDCSDPNPM VRGLALRSMC SLRMPGVQEY
IQQPILNGLR DKASYVRRVA VLGCAKMHNL HGDSEVDGAL VNELYSLLRD QDPIVVVNCL
RSLEEILKQE GGVVINKPIA HHLLNRMSKL DQWGQAEVLN FLLRYQPRSE EELFDILNLL
DSFLKSSSPG VVMGATKLFL ILAKMFPHVQ TDVLVRVKGP LLAACSSESR ELCFVALCHV
RQILHSLPGH FSSHYKKFFC SYSEPHYIKL QKVEVLCELV NDENVQQVLE ELRGYCTDVS
ADFAQAAIFA IGGIARTYTD QCVQILTELL GLRQEHITTV VVQTFRDLVW LCPQCTEAVC
QALPGCEENI QDSEGKQALI WLLGVHGERI PNAPYVLEDF VENVKSETFP AVKMELLTAS
LRLFLSRPAE CQDMLGRLLY YCIEEEKDMA VRDRGLFYYR LLLVGIDEVK RILCSPKSDP
TLGLLEDPAE RPVNSWASDF NTLVPVYGKA HWATISKCQG AERCDPELPK TSSFAASGPL
IPEENKERVQ ELPDSGALML VPNRQLTADY FEKTWLSLKV AHQQVLPWRG EFHPDTLQMA
LQVVNIQTIA MSRAGSRPWK AYLSAQDDTG CLFLTELLLE PGNSEMQISV KQNEARTETL
NSFISVLETV IGTIEEIKS*

speed

0.17 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