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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000261336
Querying Taster for transcript #2: ENST00000381997
MT speed 1.6 s - this script 6.159229 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PZP	polymorphism_automatic	0.000177472583221983	simple_aae		affected		I1229N	single base exchange	rs10842971		show file
PZP	polymorphism_automatic	0.000177472583221983	simple_aae		affected		I1443N	single base exchange	rs10842971		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999822527416778 (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)

chr12:9303296A>TN/A show variant in all transcripts IGV

HGNC symbol

PZP

Ensembl transcript ID

ENST00000381997

Genbank transcript ID

N/A

UniProt peptide

P20742

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3686T>A
cDNA.3686T>A
g.57671T>A

AA changes

I1229N Score: 194 explain score(s)

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

1229

frameshift

known variant

Reference ID: rs10842971

database	homozygous (T/T)	heterozygous	allele carriers
1000G	121	712	833
ExAC	4897	22728	27625

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.312	0.397
	3.847	0.411
(flanking)	-0.795	0.011

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
Acc marginally increased	57666	wt: 0.8075 / mu: 0.8144 (marginal change - not scored)	wt: TTTTCCTTCATGGTTCTGCAAGACATCCCAGTAGGAGACTT mu: TTTTCCTTCATGGTTCTGCAAGACAACCCAGTAGGAGACTT	gcaa\|GACA
Acc marginally increased	57664	wt: 0.7811 / mu: 0.8038 (marginal change - not scored)	wt: GTTTTTCCTTCATGGTTCTGCAAGACATCCCAGTAGGAGAC mu: GTTTTTCCTTCATGGTTCTGCAAGACAACCCAGTAGGAGAC	ctgc\|AAGA
Acc marginally increased	57662	wt: 0.3394 / mu: 0.3466 (marginal change - not scored)	wt: AAGTTTTTCCTTCATGGTTCTGCAAGACATCCCAGTAGGAG mu: AAGTTTTTCCTTCATGGTTCTGCAAGACAACCCAGTAGGAG	ttct\|GCAA
Donor increased	57666	wt: 0.81 / mu: 0.99	wt: CTGCAAGACATCCCA mu: CTGCAAGACAACCCA	GCAA\|gaca
Donor increased	57670	wt: 0.72 / mu: 0.81	wt: AAGACATCCCAGTAG mu: AAGACAACCCAGTAG	GACA\|tccc
Donor increased	57675	wt: 0.34 / mu: 0.56	wt: ATCCCAGTAGGAGAC mu: AACCCAGTAGGAGAC	CCCA\|gtag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1229

mutated

not conserved

1229

Ptroglodytes

all identical

ENSPTRG00000004652

1443

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000005067

1187

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

not conserved

ZK337.1

1434

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1430	1430	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3807 / 3807

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

1269 / 1269

position of stopcodon in wt / mu cDNA

3807 / 3807

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

-1

last intron/exon boundary

3785

theoretical NMD boundary in CDS

3734

length of CDS

3807

coding sequence (CDS) position

3686

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

3686

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

57671

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

9303296

original gDNA sequence snippet

CTTCATGGTTCTGCAAGACATCCCAGTAGGAGACTTGAAGC

altered gDNA sequence snippet

CTTCATGGTTCTGCAAGACAACCCAGTAGGAGACTTGAAGC

original cDNA sequence snippet

CTTCATGGTTCTGCAAGACATCCCAGTAGGAGACTTGAAGC

altered cDNA sequence snippet

CTTCATGGTTCTGCAAGACAACCCAGTAGGAGACTTGAAGC

wildtype AA sequence

MSESYRRTTF PVRFRVVSVD ENFRPRNELI PLIYLENPRR NRIAQWQSLK LEAGINQLSF
PLSSEPIQGS YRVVVQTESG GRIQHPFTVE EFVLPKFEVK VQVPKIISIM DEKVNITVCG
EYTYGKPVPG LATVSLCRKL SRVLNCDKQE VCEEFSQQLN SNGCITQQVH TKMLQITNTG
FEMKLRVEAR IREEGTDLEV TANRISEITN IVSKLKFVKV DSHFRQGIPF FAQVLLVDGK
GVPIPNKLFF ISVNDANYYS NATTNEQGLA QFSINTTSIS VNKLFVRVFT VHPNLCFHYS
WVAEDHQGAQ HTANRVFSLS GSYIHLEPVA GTLPCGHTET ITAHYTLNRQ AMGELSELSF
HYLIMAKGVI VRSGTHTLPV ESGDMKGSFA LSFPVESDVA PIARMFIFAI LPDGEVVGDS
EKFEIENCLA NKVDLSFSPA QSPPASHAHL QVAAAPQSLC ALRAVDQSVL LMKPEAELSV
SSVYNLLTVK DLTNFPDNVD QQEEEQGHCP RPFFIHNGAI YVPLSSNEAD IYSFLKGMGL
KVFTNSKIRK PKSCSVIPSV SAGAVGQGYY GAGLGVVERP YVPQLGTYNV IPLNNEQSSG
PVPETVRSYF PETWIWELVA VNSSGVAEVG VTVPDTITEW KAGAFCLSED AGLGISSTAS
LRAFQPFFVE LTMPYSVIRG EVFTLKATVL NYLPKCIRAE GIEQEKTFSS MTCASGANVS
EQLSLKLPSN VVKESARASF SVLGDILGSA MQNIQNLLQM PYGCGEQNMV LFAPNIYVLN
YLNETQQLTQ EIKAKAVGYL ITGYQRQLNY KHQDGSYSTF GERYGRNQGN TWLTAFVLKT
FAQARSYIFI DEAHITQSLT WLSQMQKDNG CFRSSGSLLN NAIKGGVEDE ATLSAYVTIA
LLEIPLPVTN PIVRNALFCL ESAWNVAKEG THGSHVYTKA LLAYAFSLLG KQNQNREILN
SLDKEAVKED NLVHWERPQR PKAPVGHLYQ TQAPSAEVEM TSYVLLAYLT AQPAPTSGDL
TSATNIVKWI MKQQNAQGGF SSTQDTVVAL HALSRYGAAT FTRTEKTAQV TVQDSQTFST
NFQVDNNNLL LLQQISLPEL PGEYVITVTG ERCVYLQTSM KYNILPEKED SPFALKVQTV
PQTCDGHKAH TSFQISLTIS YTGNRPASNM VIVDVKMVSG FIPLKPTVKM LERSSSVSRT
EVSNNHVLIY VEQVTNQTLS FSFMVLQDIP VGDLKPAIVK VYDYYETDES VVAEYIAPCS
TDTEHGNV*

mutated AA sequence

speed

0.79 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: 0.999822527416778 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:9303296A>TN/A show variant in all transcripts IGV

HGNC symbol

PZP

Ensembl transcript ID

ENST00000261336

Genbank transcript ID

NM_002864

UniProt peptide

P20742

alteration type

single base exchange

alteration region

CDS

DNA changes

c.4328T>A
cDNA.4357T>A
g.57671T>A

AA changes

I1443N Score: 194 explain score(s)

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

1443

frameshift

known variant

Reference ID: rs10842971

database	homozygous (T/T)	heterozygous	allele carriers
1000G	121	712	833
ExAC	4897	22728	27625

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.312	0.397
	3.847	0.411
(flanking)	-0.795	0.011

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
Acc marginally increased	57666	wt: 0.8075 / mu: 0.8144 (marginal change - not scored)	wt: TTTTCCTTCATGGTTCTGCAAGACATCCCAGTAGGAGACTT mu: TTTTCCTTCATGGTTCTGCAAGACAACCCAGTAGGAGACTT	gcaa\|GACA
Acc marginally increased	57664	wt: 0.7811 / mu: 0.8038 (marginal change - not scored)	wt: GTTTTTCCTTCATGGTTCTGCAAGACATCCCAGTAGGAGAC mu: GTTTTTCCTTCATGGTTCTGCAAGACAACCCAGTAGGAGAC	ctgc\|AAGA
Acc marginally increased	57662	wt: 0.3394 / mu: 0.3466 (marginal change - not scored)	wt: AAGTTTTTCCTTCATGGTTCTGCAAGACATCCCAGTAGGAG mu: AAGTTTTTCCTTCATGGTTCTGCAAGACAACCCAGTAGGAG	ttct\|GCAA
Donor increased	57666	wt: 0.81 / mu: 0.99	wt: CTGCAAGACATCCCA mu: CTGCAAGACAACCCA	GCAA\|gaca
Donor increased	57670	wt: 0.72 / mu: 0.81	wt: AAGACATCCCAGTAG mu: AAGACAACCCAGTAG	GACA\|tccc
Donor increased	57675	wt: 0.34 / mu: 0.56	wt: ATCCCAGTAGGAGAC mu: AACCCAGTAGGAGAC	CCCA\|gtag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1443

mutated

not conserved

1443

Ptroglodytes

all identical

ENSPTRG00000004652

1443

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000005067

1187

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

not conserved

ZK337.1

1434

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4449 / 4449

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

1483 / 1483

position of stopcodon in wt / mu cDNA

4478 / 4478

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

30 / 30

chromosome

strand

-1

last intron/exon boundary

4456

theoretical NMD boundary in CDS

4376

length of CDS

4449

coding sequence (CDS) position

4328

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

4357

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

57671

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

9303296

original gDNA sequence snippet

CTTCATGGTTCTGCAAGACATCCCAGTAGGAGACTTGAAGC

altered gDNA sequence snippet

CTTCATGGTTCTGCAAGACAACCCAGTAGGAGACTTGAAGC

original cDNA sequence snippet

CTTCATGGTTCTGCAAGACATCCCAGTAGGAGACTTGAAGC

altered cDNA sequence snippet

CTTCATGGTTCTGCAAGACAACCCAGTAGGAGACTTGAAGC

wildtype AA sequence

MRKDRLLHLC LVLLLILLSA SDSNSTEPQY MVLVPSLLHT EAPKKGCVLL SHLNETVTVS
ASLESGRENR SLFTDLVAEK DLFHCVSFTL PRISASSEVA FLSIQIKGPT QDFRKRNTVL
VLNTQSLVFV QTDKPMYKPG QTVRFRVVSV DENFRPRNEL IPLIYLENPR RNRIAQWQSL
KLEAGINQLS FPLSSEPIQG SYRVVVQTES GGRIQHPFTV EEFVLPKFEV KVQVPKIISI
MDEKVNITVC GEYTYGKPVP GLATVSLCRK LSRVLNCDKQ EVCEEFSQQL NSNGCITQQV
HTKMLQITNT GFEMKLRVEA RIREEGTDLE VTANRISEIT NIVSKLKFVK VDSHFRQGIP
FFAQVLLVDG KGVPIPNKLF FISVNDANYY SNATTNEQGL AQFSINTTSI SVNKLFVRVF
TVHPNLCFHY SWVAEDHQGA QHTANRVFSL SGSYIHLEPV AGTLPCGHTE TITAHYTLNR
QAMGELSELS FHYLIMAKGV IVRSGTHTLP VESGDMKGSF ALSFPVESDV APIARMFIFA
ILPDGEVVGD SEKFEIENCL ANKVDLSFSP AQSPPASHAH LQVAAAPQSL CALRAVDQSV
LLMKPEAELS VSSVYNLLTV KDLTNFPDNV DQQEEEQGHC PRPFFIHNGA IYVPLSSNEA
DIYSFLKGMG LKVFTNSKIR KPKSCSVIPS VSAGAVGQGY YGAGLGVVER PYVPQLGTYN
VIPLNNEQSS GPVPETVRSY FPETWIWELV AVNSSGVAEV GVTVPDTITE WKAGAFCLSE
DAGLGISSTA SLRAFQPFFV ELTMPYSVIR GEVFTLKATV LNYLPKCIRV SVQLKASPAF
LASQNTKGEE SYCICGNERQ TLSWTVTPKT LGNVNFSVSA EAMQSLELCG NEVVEVPEIK
RKDTVIKTLL VEAEGIEQEK TFSSMTCASG ANVSEQLSLK LPSNVVKESA RASFSVLGDI
LGSAMQNIQN LLQMPYGCGE QNMVLFAPNI YVLNYLNETQ QLTQEIKAKA VGYLITGYQR
QLNYKHQDGS YSTFGERYGR NQGNTWLTAF VLKTFAQARS YIFIDEAHIT QSLTWLSQMQ
KDNGCFRSSG SLLNNAIKGG VEDEATLSAY VTIALLEIPL PVTNPIVRNA LFCLESAWNV
AKEGTHGSHV YTKALLAYAF SLLGKQNQNR EILNSLDKEA VKEDNLVHWE RPQRPKAPVG
HLYQTQAPSA EVEMTSYVLL AYLTAQPAPT SGDLTSATNI VKWIMKQQNA QGGFSSTQDT
VVALHALSRY GAATFTRTEK TAQVTVQDSQ TFSTNFQVDN NNLLLLQQIS LPELPGEYVI
TVTGERCVYL QTSMKYNILP EKEDSPFALK VQTVPQTCDG HKAHTSFQIS LTISYTGNRP
ASNMVIVDVK MVSGFIPLKP TVKMLERSSS VSRTEVSNNH VLIYVEQVTN QTLSFSFMVL
QDIPVGDLKP AIVKVYDYYE TDESVVAEYI APCSTDTEHG NV*

mutated AA sequence

speed

0.81 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems