MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000361673
MT speed 0 s - this script 2.864888 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALPK2	polymorphism_automatic	2.46203057940875e-12	simple_aae		affected		A1551S	single base exchange	rs3809983		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997538 (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)

chr18:56202768C>AN/A show variant in all transcripts IGV

HGNC symbol

ALPK2

Ensembl transcript ID

ENST00000361673

Genbank transcript ID

NM_052947

UniProt peptide

Q86TB3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.4651G>T
cDNA.4865G>T
g.93422G>T

AA changes

A1551S Score: 99 explain score(s)

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

1551

frameshift

known variant

Reference ID: rs3809983

database	homozygous (A/A)	heterozygous	allele carriers
1000G	320	1020	1340
ExAC	11791	9185	20976

regulatory features

p300, Transcription Factor, p300 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
BATF, Transcription Factor, BATF Transcription Factor Binding
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
BCL11A, Transcription Factor, BCL11A Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
Jund, Transcription Factor, Jund TF binding
Cjun, Transcription Factor, Cjun TF binding
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
MEF2A, Transcription Factor, MEF2A Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
IRF4, Transcription Factor, IRF4 Transcription Factor Binding
EBF, Transcription Factor, EBF Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
PU1, Transcription Factor, PU1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.522	0
	0.035	0
(flanking)	-3.47	0

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 increased	93432	wt: 0.86 / mu: 0.96	wt: AATGACTCACGCTTCTCTTGGGGTTGACACGCACAACTCCA mu: AATGACTCACTCTTCTCTTGGGGTTGACACGCACAACTCCA	ttgg\|GGTT
Acc increased	93430	wt: 0.71 / mu: 0.94	wt: ATAATGACTCACGCTTCTCTTGGGGTTGACACGCACAACTC mu: ATAATGACTCACTCTTCTCTTGGGGTTGACACGCACAACTC	tctt\|GGGG
Acc marginally increased	93413	wt: 0.3423 / mu: 0.3485 (marginal change - not scored)	wt: TTTCTAGTTGTCTTCCAATAATGACTCACGCTTCTCTTGGG mu: TTTCTAGTTGTCTTCCAATAATGACTCACTCTTCTCTTGGG	ataa\|TGAC
Acc increased	93431	wt: 0.78 / mu: 0.95	wt: TAATGACTCACGCTTCTCTTGGGGTTGACACGCACAACTCC mu: TAATGACTCACTCTTCTCTTGGGGTTGACACGCACAACTCC	cttg\|GGGT
Acc gained	93429	0.32	mu: AATAATGACTCACTCTTCTCTTGGGGTTGACACGCACAACT	ctct\|TGGG
Acc gained	93433	0.36	mu: ATGACTCACTCTTCTCTTGGGGTTGACACGCACAACTCCAC	tggg\|GTTG
Acc gained	93428	0.32	mu: CAATAATGACTCACTCTTCTCTTGGGGTTGACACGCACAAC	tctc\|TTGG

distance from splice site

703

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1551

mutated

all conserved

1551

Ptroglodytes

all identical

ENSPTRG00000010052

1446

Mmulatta

all identical

ENSMMUG00000006635

1056

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000032845

1526

Ggallus

no alignment

ENSGALG00000002898

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000079637

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1602	1602	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1644	1649	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)
1784	1784	CONFLICT	R -> S (in Ref. 1; BX647639).	might get lost (downstream of altered splice site)
1786	1874	DOMAIN	Ig-like 2.	might get lost (downstream of altered splice site)
1808	1808	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1814	1814	CONFLICT	H -> R (in Ref. 1; BX647796).	might get lost (downstream of altered splice site)
1858	1858	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1901	2133	DOMAIN	Alpha-type protein kinase.	might get lost (downstream of altered splice site)
1939	1939	CONFLICT	M -> V (in Ref. 1; CAD89922).	might get lost (downstream of altered splice site)
2042	2042	CONFLICT	I -> V (in Ref. 1; CAD89922).	might get lost (downstream of altered splice site)
2092	2092	CONFLICT	G -> D (in Ref. 1; BX647796).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6513 / 6513

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

2171 / 2171

position of stopcodon in wt / mu cDNA

6727 / 6727

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

215 / 215

chromosome

strand

-1

last intron/exon boundary

6511

theoretical NMD boundary in CDS

6246

length of CDS

6513

coding sequence (CDS) position

4651

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

4865

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

93422

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

56202768

original gDNA sequence snippet

GTCTTCCAATAATGACTCACGCTTCTCTTGGGGTTGACACG

altered gDNA sequence snippet

GTCTTCCAATAATGACTCACTCTTCTCTTGGGGTTGACACG

original cDNA sequence snippet

GTCTTCCAATAATGACTCACGCTTCTCTTGGGGTTGACACG

altered cDNA sequence snippet

GTCTTCCAATAATGACTCACTCTTCTCTTGGGGTTGACACG

wildtype AA sequence

MKDSEGPQRP PLCFLSTLLS QKVPEKSDAV LRCIISGQPK PEVTWYKNGQ AIDGSGIISN
YEFFENQYIH VLHLSCCTKN DAAVYQISAK NSFGMICCSA SVEVECSSEN PQLSPNLEDD
RDRGWKHETG THEEERANQI DEKEHPYKEE ESISPGTPRS ADSSPSKSNH SLSLQSLGNL
DISVSSSENP LGVKGTRHTG EAYDPSNTEE IANGLLFLNS SHIYEKQDRC CHKTVHSMAS
KFTDGDLNND GPHDEGLRSS QQNPKVQKYI SFSLPLSEAT AHIYPGDSAV ANKQPSPQLS
SEDSDSDYEL CPEITLTYTE EFSDDDLEYL ECSDVMTDYS NAVWQRNLLG TEHVFLLESD
DEEMEFGEHC LGGCEHFLSG MGCGSRVSGD AGPMVATAGF CGHHSQPQEV GVRSSRVSKH
GPSSPQTGMT LILGPHQDGT SSVTEQGRYK LPTAPEAAEN DYPGIQGETR DSHQAREEFA
SDNLLNMDES VRETEMKLLS GESENSGMSQ CWETAADKRV GGKDLWSKRG SRKSARVRQP
GMKGNPKKPN ANLRESTTEG TLHLCSAKES AEPPLTQSDK RETSHTTAAA TGRSSHADAR
ECAISTQAEQ EAKTLQTSTD SVSKEGNTNC KGEGMQVNTL FETSQVPDWS DPPQVQVQET
VRETISCSQM PAFSEPAGEE SPFTGTTTIS FSNLGGVHKE NASLAQHSEV KPCTCGPQHE
EKQDRDGNIP DNFREDLKYE QSISEANDET MSPGVFSRHL PKDARADFRE PVAVSVASPE
PTDTALTLEN VCDEPRDREA VCAMECFEAG DQGTCFDTID SLVGRPVDKY SPQEICSVDT
ELAEGQNKVS DLCSSNDKTL EVFFQTQVSE TSVSTCKSSK DGNSVMSPLF TSTFTLNISH
TASEGATGEN LAKVENSTYP LASTVHAGQE QPSPSNSGGL DETQLLSSEN NPLVQFKEGG
DKSPSPSAAD TTATPASYSS IVSFPWEKPT TLTANNECFQ ATRETEDTST VTIATEVHPA
KYLAVSIPED KHAGGTEERF PRASHEKVSQ FPSQVQLDHI LSGATIKSTK ELLCRAPSVP
GVPHHVLQLP EGEGFCSNSP LQVDNLSGDK SQTVDRADFR SYEENFQERG SETKQGVQQQ
SLSQQGSLSA PDFQQSLPTT SAAQEERNLV PTAHSPASSR EGAGQRSGWG TRVSVVAETA
GEEDSQALSN VPSLSDILLE ESKEYRPGNW EAGNKLKIIT LEASASEIWP PRQLTNSESK
ASDGGLIIPD KVWAVPDSLK ADAVVPELAP SEIAALAHSP EDAESALADS RESHKGEEPT
ISVHWRSLSS RGFSQPRLLE SSVDPVDEKE LSVTDSLSAA SETGGKENVN NVSQDQEEKQ
LKMDHTAFFK KFLTCPKILE SSVDPIDEIS VIEYTRAGKP EPSETTPQGA REGGQSNDGN
MGHEAEIQPA ILQVPCLQGT ILSENRISRS QEGSMKQEAE QIQPEEAKTA IWQVLQPSEG
GERIPSGCSI GQIQESSDGS LGEAEQSKKD KAELISPTSP LSSCLPIMTH ASLGVDTHNS
TGQIHDVPEN DIVEPRKRQY VFPVSQKRGT IENERGKPLP SSPDLTRFPC TSSPEGNVTD
FLISHKMEEP KIEVLQIGET KPPSSSSSSA KTLAFISGER ELEKAPKLLQ DPCQKGTLGC
AKKSREREKS LEARAGKSPG TLTAVTGSEE VKRKPEAPGS GHLAEGVKKK ILSRVAALRL
KLEEKENIRK NSAFLKKMPK LETSLSHTEE KQDPKKPSCK REGRAPVLLK KIQAEMFPEH
SGNVKLSCQF AEIHEDSTIC WTKDSKSIAQ VQRSAGDNST VSFAIVQASP KDQGLYYCCI
KNSYGKVTAE FNLTAEVLKQ LSSRQDTKGC EEIEFSQLIF KEDFLHDSYF GGRLRGQIAT
EELHFGEGVH RKAFRSTVMH GLMPVFKPGH ACVLKVHNAI AYGTRNNDEL IQRNYKLAAQ
ECYVQNTARY YAKIYAAEAQ PLEGFGEVPE IIPIFLIHRP ENNIPYATVE EELIGEFVKY
SIRDGKEINF LRRESEAGQK CCTFQHWVYQ KTSGCLLVTD MQGVGMKLTD VGIATLAKGY
KGFKGNCSMT FIDQFKALHQ CNKYCKMLGL KSLQNNNQKQ KQPSIGKSKV QTNSMTIKKA
GPETPGEKKT *

mutated AA sequence

MKDSEGPQRP PLCFLSTLLS QKVPEKSDAV LRCIISGQPK PEVTWYKNGQ AIDGSGIISN
YEFFENQYIH VLHLSCCTKN DAAVYQISAK NSFGMICCSA SVEVECSSEN PQLSPNLEDD
RDRGWKHETG THEEERANQI DEKEHPYKEE ESISPGTPRS ADSSPSKSNH SLSLQSLGNL
DISVSSSENP LGVKGTRHTG EAYDPSNTEE IANGLLFLNS SHIYEKQDRC CHKTVHSMAS
KFTDGDLNND GPHDEGLRSS QQNPKVQKYI SFSLPLSEAT AHIYPGDSAV ANKQPSPQLS
SEDSDSDYEL CPEITLTYTE EFSDDDLEYL ECSDVMTDYS NAVWQRNLLG TEHVFLLESD
DEEMEFGEHC LGGCEHFLSG MGCGSRVSGD AGPMVATAGF CGHHSQPQEV GVRSSRVSKH
GPSSPQTGMT LILGPHQDGT SSVTEQGRYK LPTAPEAAEN DYPGIQGETR DSHQAREEFA
SDNLLNMDES VRETEMKLLS GESENSGMSQ CWETAADKRV GGKDLWSKRG SRKSARVRQP
GMKGNPKKPN ANLRESTTEG TLHLCSAKES AEPPLTQSDK RETSHTTAAA TGRSSHADAR
ECAISTQAEQ EAKTLQTSTD SVSKEGNTNC KGEGMQVNTL FETSQVPDWS DPPQVQVQET
VRETISCSQM PAFSEPAGEE SPFTGTTTIS FSNLGGVHKE NASLAQHSEV KPCTCGPQHE
EKQDRDGNIP DNFREDLKYE QSISEANDET MSPGVFSRHL PKDARADFRE PVAVSVASPE
PTDTALTLEN VCDEPRDREA VCAMECFEAG DQGTCFDTID SLVGRPVDKY SPQEICSVDT
ELAEGQNKVS DLCSSNDKTL EVFFQTQVSE TSVSTCKSSK DGNSVMSPLF TSTFTLNISH
TASEGATGEN LAKVENSTYP LASTVHAGQE QPSPSNSGGL DETQLLSSEN NPLVQFKEGG
DKSPSPSAAD TTATPASYSS IVSFPWEKPT TLTANNECFQ ATRETEDTST VTIATEVHPA
KYLAVSIPED KHAGGTEERF PRASHEKVSQ FPSQVQLDHI LSGATIKSTK ELLCRAPSVP
GVPHHVLQLP EGEGFCSNSP LQVDNLSGDK SQTVDRADFR SYEENFQERG SETKQGVQQQ
SLSQQGSLSA PDFQQSLPTT SAAQEERNLV PTAHSPASSR EGAGQRSGWG TRVSVVAETA
GEEDSQALSN VPSLSDILLE ESKEYRPGNW EAGNKLKIIT LEASASEIWP PRQLTNSESK
ASDGGLIIPD KVWAVPDSLK ADAVVPELAP SEIAALAHSP EDAESALADS RESHKGEEPT
ISVHWRSLSS RGFSQPRLLE SSVDPVDEKE LSVTDSLSAA SETGGKENVN NVSQDQEEKQ
LKMDHTAFFK KFLTCPKILE SSVDPIDEIS VIEYTRAGKP EPSETTPQGA REGGQSNDGN
MGHEAEIQPA ILQVPCLQGT ILSENRISRS QEGSMKQEAE QIQPEEAKTA IWQVLQPSEG
GERIPSGCSI GQIQESSDGS LGEAEQSKKD KAELISPTSP LSSCLPIMTH SSLGVDTHNS
TGQIHDVPEN DIVEPRKRQY VFPVSQKRGT IENERGKPLP SSPDLTRFPC TSSPEGNVTD
FLISHKMEEP KIEVLQIGET KPPSSSSSSA KTLAFISGER ELEKAPKLLQ DPCQKGTLGC
AKKSREREKS LEARAGKSPG TLTAVTGSEE VKRKPEAPGS GHLAEGVKKK ILSRVAALRL
KLEEKENIRK NSAFLKKMPK LETSLSHTEE KQDPKKPSCK REGRAPVLLK KIQAEMFPEH
SGNVKLSCQF AEIHEDSTIC WTKDSKSIAQ VQRSAGDNST VSFAIVQASP KDQGLYYCCI
KNSYGKVTAE FNLTAEVLKQ LSSRQDTKGC EEIEFSQLIF KEDFLHDSYF GGRLRGQIAT
EELHFGEGVH RKAFRSTVMH GLMPVFKPGH ACVLKVHNAI AYGTRNNDEL IQRNYKLAAQ
ECYVQNTARY YAKIYAAEAQ PLEGFGEVPE IIPIFLIHRP ENNIPYATVE EELIGEFVKY
SIRDGKEINF LRRESEAGQK CCTFQHWVYQ KTSGCLLVTD MQGVGMKLTD VGIATLAKGY
KGFKGNCSMT FIDQFKALHQ CNKYCKMLGL KSLQNNNQKQ KQPSIGKSKV QTNSMTIKKA
GPETPGEKKT *

speed

0.81 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems