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 2.668528 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALPK2	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		H719Q	single base exchange	rs12103986		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (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)

chr18:56205262A>CN/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.2157T>G
cDNA.2371T>G
g.90928T>G

AA changes

H719Q Score: 24 explain score(s)

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

719

frameshift

known variant

Reference ID: rs12103986

database	homozygous (C/C)	heterozygous	allele carriers
1000G	458	1109	1567
ExAC	14137	4493	18630

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
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
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.955	0
	-1.457	0
(flanking)	-0.173	0.002

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 marginally increased	90928	wt: 0.6163 / mu: 0.6734 (marginal change - not scored)	wt: CAGCATGAAGAAAAA mu: CAGCAGGAAGAAAAA	GCAT\|gaag
Donor gained	90927	0.81	mu: ACAGCAGGAAGAAAA	AGCA\|ggaa
Donor gained	90924	0.54	mu: TCCACAGCAGGAAGA	CACA\|gcag

distance from splice site

195

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

719

mutated

not conserved

719

Ptroglodytes

not conserved

ENSPTRG00000010052

719

Mmulatta

not conserved

ENSMMUG00000006635

233

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000032845

701

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
829	829	CONFLICT	K -> S (in Ref. 1; CAD89922).	might get lost (downstream of altered splice site)
912	912	CONFLICT	A -> T (in Ref. 1; BX647796).	might get lost (downstream of altered splice site)
959	959	CONFLICT	G -> E (in Ref. 4; BAC03812).	might get lost (downstream of altered splice site)
1067	1067	CONFLICT	K -> E (in Ref. 1; CAD89922).	might get lost (downstream of altered splice site)
1165	1165	CONFLICT	E -> G (in Ref. 1; CAD89922).	might get lost (downstream of altered splice site)
1217	1217	CONFLICT	I -> T (in Ref. 4; BAC03812).	might get lost (downstream of altered splice site)
1402	1402	CONFLICT	S -> P (in Ref. 1; BX647796).	might get lost (downstream of altered splice site)
1428	1428	CONFLICT	Q -> R (in Ref. 4; BAC03812).	might get lost (downstream of altered splice site)
1443	1443	CONFLICT	H -> R (in Ref. 1; BX647796).	might get lost (downstream of altered splice site)
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

2157

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

2371

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

90928

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

56205262

original gDNA sequence snippet

TGTACCTGTGGTCCACAGCATGAAGAAAAACAAGACAGAGA

altered gDNA sequence snippet

TGTACCTGTGGTCCACAGCAGGAAGAAAAACAAGACAGAGA

original cDNA sequence snippet

TGTACCTGTGGTCCACAGCATGAAGAAAAACAAGACAGAGA

altered cDNA sequence snippet

TGTACCTGTGGTCCACAGCAGGAAGAAAAACAAGACAGAGA

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 KPCTCGPQQE
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 *

speed

0.61 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems