MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000255194
Querying Taster for transcript #2: ENST00000519295
MT speed 0 s - this script 3.057165 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AP3B1	disease_causing_automatic	0.999999967367666	simple_aae		affected	0	L580R	single base exchange	rs121908904		show file
AP3B1	disease_causing_automatic	0.999999967367666	simple_aae		affected	0	L531R	single base exchange	rs121908904		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999967367666 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM991256)
known disease mutation: rs6372 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:77425043A>CN/A show variant in all transcripts IGV

HGNC symbol

AP3B1

Ensembl transcript ID

ENST00000255194

Genbank transcript ID

NM_003664

UniProt peptide

O00203

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1739T>G
cDNA.1915T>G
g.165537T>G

AA changes

L580R Score: 102 explain score(s)

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

580

frameshift

known variant

Reference ID: rs121908904
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6372 (pathogenic for Hermansky-Pudlak syndrome 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM991256)

known disease mutation at this position, please check HGMD for details (HGMD ID CM991256)
known disease mutation at this position, please check HGMD for details (HGMD ID CM991256)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.37	1
	5.076	1
(flanking)	4.46	1

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 increased	165534	wt: 0.23 / mu: 0.28	wt: TAGGCAGCTTATTGT mu: TAGGCAGCGTATTGT	GGCA\|gctt
Donor increased	165531	wt: 0.46 / mu: 0.99	wt: TATTAGGCAGCTTAT mu: TATTAGGCAGCGTAT	TTAG\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

580

mutated

not conserved

580

Ptroglodytes

all identical

ENSPTRG00000017015

580

Mmulatta

all identical

ENSMMUG00000001360

541

Fcatus

no alignment

ENSFCAG00000007759

n/a

Mmusculus

all identical

ENSMUSG00000021686

581

Ggallus

all identical

ENSGALG00000004390

583

Trubripes

all identical

ENSTRUG00000018286

583

Drerio

no alignment

ENSDARG00000089282

n/a

Dmelanogaster

all conserved

FBgn0003210

616

Celegans

all identical

R11A5.1

541

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
592	592	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
609	609	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
661	661	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
677	802	COMPBIAS	Glu/Ser-rich.	might get lost (downstream of altered splice site)
804	804	CONFLICT	Missing (in Ref. 1; AAD03778).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3285 / 3285

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

1095 / 1095

position of stopcodon in wt / mu cDNA

3461 / 3461

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

177 / 177

chromosome

strand

-1

last intron/exon boundary

3308

theoretical NMD boundary in CDS

3081

length of CDS

3285

coding sequence (CDS) position

1739

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

1915

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

165537

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

77425043

original gDNA sequence snippet

TACAAGATTTATTAGGCAGCTTATTGTTCCGAATGTAAAGA

altered gDNA sequence snippet

TACAAGATTTATTAGGCAGCGTATTGTTCCGAATGTAAAGA

original cDNA sequence snippet

TACAAGATTTATTAGGCAGCTTATTGTTCCGAATGTAAAGA

altered cDNA sequence snippet

TACAAGATTTATTAGGCAGCGTATTGTTCCGAATGTAAAGA

wildtype AA sequence

MSSNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL
DAMKRIVGMI AKGKNASELF PAVVKNVASK NIEIKKLVYV YLVRYAEEQQ DLALLSISTF
QRALKDPNQL IRASALRVLS SIRVPIIVPI MMLAIKEASA DLSPYVRKNA AHAIQKLYSL
DPEQKEMLIE VIEKLLKDKS TLVAGSVVMA FEEVCPDRID LIHKNYRKLC NLLVDVEEWG
QVVIIHMLTR YARTQFVSPW KEGDELEDNG KNFYESDDDQ KEKTDKKKKP YTMDPDHRLL
IRNTKPLLQS RNAAVVMAVA QLYWHISPKS EAGIISKSLV RLLRSNREVQ YIVLQNIATM
SIQRKGMFEP YLKSFYVRST DPTMIKTLKL EILTNLANEA NISTLLREFQ TYVKSQDKQF
AAATIQTIGR CATNILEVTD TCLNGLVCLL SNRDEIVVAE SVVVIKKLLQ MQPAQHGEII
KHMAKLLDSI TVPVARASIL WLIGENCERV PKIAPDVLRK MAKSFTSEDD LVKLQILNLG
AKLYLTNSKQ TKLLTQYILN LGKYDQNYDI RDRTRFIRQL IVPNVKSGAL SKYAKKIFLA
QKPAPLLESP FKDRDHFQLG TLSHTLNIKA TGYLELSNWP EVAPDPSVRN VEVIELAKEW
TPAGKAKQEN SAKKFYSESE EEEDSSDSSS DSESESGSES GEQGESGEEG DSNEDSSEDS
SSEQDSESGR ESGLENKRTA KRNSKAKGKS DSEDGEKENE KSKTSDSSND ESSSIEDSSS
DSESESEPES ESESRRVTKE KEKKTKQDRT PLTKDVSLLD LDDFNPVSTP VALPTPALSP
SLMADLEGLH LSTSSSVISV STPAFVPTKT HVLLHRMSGK GLAAHYFFPR QPCIFGDKMV
SIQITLNNTT DRKIENIHIG EKKLPIGMKM HVFNPIDSLE PEGSITVSMG IDFCDSTQTA
SFQLCTKDDC FNVNIQPPVG ELLLPVAMSE KDFKKEQGVL TGMNETSAVI IAAPQNFTPS
VIFQKVVNVA NVGAVPSGQD NIHRFAAKTV HSGSLMLVTV ELKEGSTAQL IINTEKTVIG
SVLLRELKPV LSQG*

mutated AA sequence

MSSNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL
DAMKRIVGMI AKGKNASELF PAVVKNVASK NIEIKKLVYV YLVRYAEEQQ DLALLSISTF
QRALKDPNQL IRASALRVLS SIRVPIIVPI MMLAIKEASA DLSPYVRKNA AHAIQKLYSL
DPEQKEMLIE VIEKLLKDKS TLVAGSVVMA FEEVCPDRID LIHKNYRKLC NLLVDVEEWG
QVVIIHMLTR YARTQFVSPW KEGDELEDNG KNFYESDDDQ KEKTDKKKKP YTMDPDHRLL
IRNTKPLLQS RNAAVVMAVA QLYWHISPKS EAGIISKSLV RLLRSNREVQ YIVLQNIATM
SIQRKGMFEP YLKSFYVRST DPTMIKTLKL EILTNLANEA NISTLLREFQ TYVKSQDKQF
AAATIQTIGR CATNILEVTD TCLNGLVCLL SNRDEIVVAE SVVVIKKLLQ MQPAQHGEII
KHMAKLLDSI TVPVARASIL WLIGENCERV PKIAPDVLRK MAKSFTSEDD LVKLQILNLG
AKLYLTNSKQ TKLLTQYILN LGKYDQNYDI RDRTRFIRQR IVPNVKSGAL SKYAKKIFLA
QKPAPLLESP FKDRDHFQLG TLSHTLNIKA TGYLELSNWP EVAPDPSVRN VEVIELAKEW
TPAGKAKQEN SAKKFYSESE EEEDSSDSSS DSESESGSES GEQGESGEEG DSNEDSSEDS
SSEQDSESGR ESGLENKRTA KRNSKAKGKS DSEDGEKENE KSKTSDSSND ESSSIEDSSS
DSESESEPES ESESRRVTKE KEKKTKQDRT PLTKDVSLLD LDDFNPVSTP VALPTPALSP
SLMADLEGLH LSTSSSVISV STPAFVPTKT HVLLHRMSGK GLAAHYFFPR QPCIFGDKMV
SIQITLNNTT DRKIENIHIG EKKLPIGMKM HVFNPIDSLE PEGSITVSMG IDFCDSTQTA
SFQLCTKDDC FNVNIQPPVG ELLLPVAMSE KDFKKEQGVL TGMNETSAVI IAAPQNFTPS
VIFQKVVNVA NVGAVPSGQD NIHRFAAKTV HSGSLMLVTV ELKEGSTAQL IINTEKTVIG
SVLLRELKPV LSQG*

speed

0.32 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

disease causing

Model: simple_aae, prob: 0.999999967367666 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM991256)
known disease mutation: rs6372 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:77425043A>CN/A show variant in all transcripts IGV

HGNC symbol

AP3B1

Ensembl transcript ID

ENST00000519295

Genbank transcript ID

N/A

UniProt peptide

O00203

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1592T>G
cDNA.1864T>G
g.165537T>G

AA changes

L531R Score: 102 explain score(s)

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

531

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.37	1
	5.076	1
(flanking)	4.46	1

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 increased	165534	wt: 0.23 / mu: 0.28	wt: TAGGCAGCTTATTGT mu: TAGGCAGCGTATTGT	GGCA\|gctt
Donor increased	165531	wt: 0.46 / mu: 0.99	wt: TATTAGGCAGCTTAT mu: TATTAGGCAGCGTAT	TTAG\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

531

mutated

not conserved

531

Ptroglodytes

all identical

ENSPTRG00000017015

580

Mmulatta

all identical

ENSMMUG00000001360

540

Fcatus

no alignment

ENSFCAG00000007759

n/a

Mmusculus

all identical

ENSMUSG00000021686

581

Ggallus

all identical

ENSGALG00000004390

583

Trubripes

all identical

ENSTRUG00000018286

583

Drerio

no alignment

ENSDARG00000089282

n/a

Dmelanogaster

all conserved

FBgn0003210

616

Celegans

all identical

R11A5.1

541

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
592	592	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
609	609	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
661	661	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
677	802	COMPBIAS	Glu/Ser-rich.	might get lost (downstream of altered splice site)
804	804	CONFLICT	Missing (in Ref. 1; AAD03778).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3138 / 3138

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

1046 / 1046

position of stopcodon in wt / mu cDNA

3410 / 3410

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

273 / 273

chromosome

strand

-1

last intron/exon boundary

3257

theoretical NMD boundary in CDS

2934

length of CDS

3138

coding sequence (CDS) position

1592

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

1864

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

165537

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

77425043

original gDNA sequence snippet

TACAAGATTTATTAGGCAGCTTATTGTTCCGAATGTAAAGA

altered gDNA sequence snippet

TACAAGATTTATTAGGCAGCGTATTGTTCCGAATGTAAAGA

original cDNA sequence snippet

TACAAGATTTATTAGGCAGCTTATTGTTCCGAATGTAAAGA

altered cDNA sequence snippet

TACAAGATTTATTAGGCAGCGTATTGTTCCGAATGTAAAGA

wildtype AA sequence

MLESNKDSAK LDAMKRIVGM IAKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ
QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS ADLSPYVRKN
AAHAIQKLYS LDPEQKEMLI EVIEKLLKDK STLVAGSVVM AFEEVCPDRI DLIHKNYRKL
CNLLVDVEEW GQVVIIHMLT RYARTQFVSP WKEGDELEDN GKNFYESDDD QKEKTDKKKK
PYTMDPDHRL LIRNTKPLLQ SRNAAVVMAV AQLYWHISPK SEAGIISKSL VRLLRSNREV
QYIVLQNIAT MSIQRKGMFE PYLKSFYVRS TDPTMIKTLK LEILTNLANE ANISTLLREF
QTYVKSQDKQ FAAATIQTIG RCATNILEVT DTCLNGLVCL LSNRDEIVVA ESVVVIKKLL
QMQPAQHGEI IKHMAKLLDS ITVPVARASI LWLIGENCER VPKIAPDVLR KMAKSFTSED
DLVKLQILNL GAKLYLTNSK QTKLLTQYIL NLGKYDQNYD IRDRTRFIRQ LIVPNVKSGA
LSKYAKKIFL AQKPAPLLES PFKDRDHFQL GTLSHTLNIK ATGYLELSNW PEVAPDPSVR
NVEVIELAKE WTPAGKAKQE NSAKKFYSES EEEEDSSDSS SDSESESGSE SGEQGESGEE
GDSNEDSSED SSSEQDSESG RESGLENKRT AKRNSKAKGK SDSEDGEKEN EKSKTSDSSN
DESSSIEDSS SDSESESEPE SESESRRVTK EKEKKTKQDR TPLTKDVSLL DLDDFNPVST
PVALPTPALS PSLMADLEGL HLSTSSSVIS VSTPAFVPTK THVLLHRMSG KGLAAHYFFP
RQPCIFGDKM VSIQITLNNT TDRKIENIHI GEKKLPIGMK MHVFNPIDSL EPEGSITVSM
GIDFCDSTQT ASFQLCTKDD CFNVNIQPPV GELLLPVAMS EKDFKKEQGV LTGMNETSAV
IIAAPQNFTP SVIFQKVVNV ANVGAVPSGQ DNIHRFAAKT VHSGSLMLVT VELKEGSTAQ
LIINTEKTVI GSVLLRELKP VLSQG*

mutated AA sequence

MLESNKDSAK LDAMKRIVGM IAKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ
QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS ADLSPYVRKN
AAHAIQKLYS LDPEQKEMLI EVIEKLLKDK STLVAGSVVM AFEEVCPDRI DLIHKNYRKL
CNLLVDVEEW GQVVIIHMLT RYARTQFVSP WKEGDELEDN GKNFYESDDD QKEKTDKKKK
PYTMDPDHRL LIRNTKPLLQ SRNAAVVMAV AQLYWHISPK SEAGIISKSL VRLLRSNREV
QYIVLQNIAT MSIQRKGMFE PYLKSFYVRS TDPTMIKTLK LEILTNLANE ANISTLLREF
QTYVKSQDKQ FAAATIQTIG RCATNILEVT DTCLNGLVCL LSNRDEIVVA ESVVVIKKLL
QMQPAQHGEI IKHMAKLLDS ITVPVARASI LWLIGENCER VPKIAPDVLR KMAKSFTSED
DLVKLQILNL GAKLYLTNSK QTKLLTQYIL NLGKYDQNYD IRDRTRFIRQ RIVPNVKSGA
LSKYAKKIFL AQKPAPLLES PFKDRDHFQL GTLSHTLNIK ATGYLELSNW PEVAPDPSVR
NVEVIELAKE WTPAGKAKQE NSAKKFYSES EEEEDSSDSS SDSESESGSE SGEQGESGEE
GDSNEDSSED SSSEQDSESG RESGLENKRT AKRNSKAKGK SDSEDGEKEN EKSKTSDSSN
DESSSIEDSS SDSESESEPE SESESRRVTK EKEKKTKQDR TPLTKDVSLL DLDDFNPVST
PVALPTPALS PSLMADLEGL HLSTSSSVIS VSTPAFVPTK THVLLHRMSG KGLAAHYFFP
RQPCIFGDKM VSIQITLNNT TDRKIENIHI GEKKLPIGMK MHVFNPIDSL EPEGSITVSM
GIDFCDSTQT ASFQLCTKDD CFNVNIQPPV GELLLPVAMS EKDFKKEQGV LTGMNETSAV
IIAAPQNFTP SVIFQKVVNV ANVGAVPSGQ DNIHRFAAKT VHSGSLMLVT VELKEGSTAQ
LIINTEKTVI GSVLLRELKP VLSQG*

speed

0.80 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems