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: ENST00000280979
Querying Taster for transcript #2: ENST00000557272
MT speed 0 s - this script 3.61799 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AKAP6	polymorphism_automatic	1.67364799796843e-09	simple_aae		affected		A1492V	single base exchange	rs11845640		show file
AKAP6	polymorphism_automatic	6.51814573420229e-05	without_aae		affected			single base exchange	rs11845640		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999998326352 (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)

chr14:33291494C>TN/A show variant in all transcripts IGV

HGNC symbol

AKAP6

Ensembl transcript ID

ENST00000280979

Genbank transcript ID

NM_004274

UniProt peptide

Q13023

alteration type

single base exchange

alteration region

CDS

DNA changes

c.4475C>T
cDNA.4645C>T
g.493016C>T

AA changes

A1492V Score: 64 explain score(s)

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

1492

frameshift

known variant

Reference ID: rs11845640

database	homozygous (T/T)	heterozygous	allele carriers
1000G	236	857	1093
ExAC	2121	14261	16382

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.647	0.051
	0.464	0.202
(flanking)	0.44	0.522

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	493009	wt: 0.9898 / mu: 0.9943 (marginal change - not scored)	wt: AAAGCGAAAAAGCGC mu: AAAGCGAAAAAGTGC	AGCG\|aaaa
Donor increased	493020	wt: 0.87 / mu: 0.97	wt: GCGCATGTGGAGGAT mu: GTGCATGTGGAGGAT	GCAT\|gtgg

distance from splice site

887

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1492

mutated

not conserved

1492

Ptroglodytes

not conserved

ENSPTRG00000006247

1492

Mmulatta

not conserved

ENSMMUG00000015128

1492

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000061603

1488

Ggallus

not conserved

ENSGALG00000009995

1488

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000077295

1332

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1560	1701	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
2063	2076	REGION	PKA-RII subunit binding domain.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6960 / 6960

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

2320 / 2320

position of stopcodon in wt / mu cDNA

7130 / 7130

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

171 / 171

chromosome

strand

last intron/exon boundary

7173

theoretical NMD boundary in CDS

6952

length of CDS

6960

coding sequence (CDS) position

4475

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

4645

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

493016

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

33291494

original gDNA sequence snippet

ACAGTCACAAAGCGAAAAAGCGCATGTGGAGGATCCCCTGC

altered gDNA sequence snippet

ACAGTCACAAAGCGAAAAAGTGCATGTGGAGGATCCCCTGC

original cDNA sequence snippet

ACAGTCACAAAGCGAAAAAGCGCATGTGGAGGATCCCCTGC

altered cDNA sequence snippet

ACAGTCACAAAGCGAAAAAGTGCATGTGGAGGATCCCCTGC

wildtype AA sequence

MLTMSVTLSP LRSQDLDPMA TDASPMAINM TPTVEQGEGE EAMKDMDSDQ QYEKPPPLHT
GADWKIVLHL PEIETWLRMT SERVRDLTYS VQQDSDSKHV DVHLVQLKDI CEDISDHVEQ
IHALLETEFS LKLLSYSVNV IVDIHAVQLL WHQLRVSVLV LRERILQGLQ DANGNYTRQT
DILQAFSEET KEGRLDSLTE VDDSGQLTIK CSQNYLSLDC GITAFELSDY SPSEDLLSGL
GDMTSSQVKT KPFDSWSYSE MEKEFPELIR SVGLLTVAAD SISTNGSEAV TEEVSQVSLS
VDDKGGCEED NASAVEEQPG LTLGVSSSSG EALTNAAQPS SETVQQESSS SSHHDAKNQQ
PVPCENATPK RTIRDCFNYN EDSPTQPTLP KRGLFLKEET FKNDLKGNGG KRQMVDLKPE
MSRSTPSLVD PPDRSKLCLV LQSSYPNSPS AASQSYECLH KVGNGNLENT VKFHIKEISS
SLGRLNDCYK EKSRLKKPHK TSEEVPPCRT PKRGTGSGKQ AKNTKSSAVP NGELSYTSKA
IEGPQTNSAS TSSLEPCNQR SWNAKLQLQS ETSSSPAFTQ SSESSVGSDN IMSPVPLLSK
HKSKKGQASS PSHVTRNGEV VEAWYGSDEY LALPSHLKQT EVLALKLENL TKLLPQKPRG
ETIQNIDDWE LSEMNSDSEI YPTYHVKKKH TRLGRVSPSS SSDIASSLGE SIESGPLSDI
LSDEESSMPL AGMKKYADEK SERASSSEKN ESHSATKSAL IQKLMQDIQH QDNYEAIWEK
IEGFVNKLDE FIQWLNEAME TTENWTPPKA EMDDLKLYLE THLSFKLNVD SHCALKEAVE
EEGHQLLELI ASHKAGLKDM LRMIASQWKE LQRQIKRQHS WILRALDTIK AEILATDVSV
EDEEGTGSPK AEVQLCYLEA QRDAVEQMSL KLYSEQYTSS SKRKEEFADM SKVHSVGSNG
LLDFDSEYQE LWDWLIDMES LVMDSHDLMM SEEQQQHLYK RYSVEMSIRH LKKTELLSKV
EALKKGGVLL PNDLLEKVDS INEKWELLGK TLGEKIQDTM AGHSGSSPRD LLSPESGSLV
RQLEVRIKEL KGWLRDTELF IFNSCLRQEK EGTMNTEKQL QYFKSLCREI KQRRRGVASI
LRLCQHLLDD RETCNLNADH QPMQLIIVNL ERRWEAIVMQ AVQWQTRLQK KMGKESETLN
VIDPGLMDLN GMSEDALEWD EMDISNKLIS LNEESNDLDQ ELQPVIPSLK LGETSNEDPG
YDEEADNHGG SQYASNITAP SSPHIYQVYS LHNVELYEDN HMPFLKNNPK VTGMTQPNVL
TKSLSKDSSF SSTKSLPDLL GGSNLVKPCA CHGGDMSQNS GSESGIVSEG DTETTTNSEM
CLLNAVDGSP SNLETEHLDP QMGDAVNVLK QKFTDEGESI KLPNSSQSSI SPVGCVNGKV
GDLNSITKHT PDCLGEELQG KHDVFTFYDY SYLQGSKLKL PMIMKQSQSE KAHVEDPLLR
GFYFDKKSCK SKHQTTELQP DVPPHERILA SASHEMDRIS YKSGNIEKTF TGMQNAKQLS
LLSHSSSIES LSPGGDLFGL GIFKNGSDSL QRSTSLESWL TSYKSNEDLF SCHSSGDISV
SSGSVGELSK RTLDLLNRLE NIQSPSEQKI KRSVSDITLQ SSSQKMSFTG QMSLDIASSI
NEDSAASLTE LSSSDELSLC SEDIVLHKNK IPESNASFRK RLTRSVADES DVNVSMIVNV
SCTSACTDDE DDSDLLSSST LTLTEEELCI KDEDDDSSIA TDDEIYEDCT LMSGLDYIKN
ELQTWIRPKL SLTRDKKRCN VSDEMKGSKD ISSSEMTNPS DTLNIETLLN GSVKRVSENN
GNGKNSSHTH ELGTKRENKK TIFKVNKDPY VADMENGNIE GIPERQKGKP NVTSKVSENL
GSHGKEISES EHCKCKALMD SLDDSNTAGK EFVSQDVRHL PKKCPNHHHF ENQSTASTPT
EKSFSELALE TRFNNRQDSD ALKSSDDAPS MAGKSAGCCL ALEQNGTEEN ASISNISCCN
CEPDVFHQKD AEDCSVHNFV KEIIDMASTA LKSKSQPENE VAAPTSLTQI KEKVLEHSHR
PIQLRKGDFY SYLSLSSHDS DCGEVTNYIE EKSSTPLPLD TTDSGLDDKE DIECFFEACV
EGDSDGEEPC FSSAPPNESA VPSEAAMPLQ ATACSSEFSD SSLSADDADT VALSSPSSQE
RAEVGKEVNG LPQTSSGCAE NLEFTPSKLD SEKESSGKPG ESGMPEEHNA ASAKSKVQDL
SLKANQPTDK AALHPSPKTL TCEENLLNLH EKRHRNMHR*

mutated AA sequence

MLTMSVTLSP LRSQDLDPMA TDASPMAINM TPTVEQGEGE EAMKDMDSDQ QYEKPPPLHT
GADWKIVLHL PEIETWLRMT SERVRDLTYS VQQDSDSKHV DVHLVQLKDI CEDISDHVEQ
IHALLETEFS LKLLSYSVNV IVDIHAVQLL WHQLRVSVLV LRERILQGLQ DANGNYTRQT
DILQAFSEET KEGRLDSLTE VDDSGQLTIK CSQNYLSLDC GITAFELSDY SPSEDLLSGL
GDMTSSQVKT KPFDSWSYSE MEKEFPELIR SVGLLTVAAD SISTNGSEAV TEEVSQVSLS
VDDKGGCEED NASAVEEQPG LTLGVSSSSG EALTNAAQPS SETVQQESSS SSHHDAKNQQ
PVPCENATPK RTIRDCFNYN EDSPTQPTLP KRGLFLKEET FKNDLKGNGG KRQMVDLKPE
MSRSTPSLVD PPDRSKLCLV LQSSYPNSPS AASQSYECLH KVGNGNLENT VKFHIKEISS
SLGRLNDCYK EKSRLKKPHK TSEEVPPCRT PKRGTGSGKQ AKNTKSSAVP NGELSYTSKA
IEGPQTNSAS TSSLEPCNQR SWNAKLQLQS ETSSSPAFTQ SSESSVGSDN IMSPVPLLSK
HKSKKGQASS PSHVTRNGEV VEAWYGSDEY LALPSHLKQT EVLALKLENL TKLLPQKPRG
ETIQNIDDWE LSEMNSDSEI YPTYHVKKKH TRLGRVSPSS SSDIASSLGE SIESGPLSDI
LSDEESSMPL AGMKKYADEK SERASSSEKN ESHSATKSAL IQKLMQDIQH QDNYEAIWEK
IEGFVNKLDE FIQWLNEAME TTENWTPPKA EMDDLKLYLE THLSFKLNVD SHCALKEAVE
EEGHQLLELI ASHKAGLKDM LRMIASQWKE LQRQIKRQHS WILRALDTIK AEILATDVSV
EDEEGTGSPK AEVQLCYLEA QRDAVEQMSL KLYSEQYTSS SKRKEEFADM SKVHSVGSNG
LLDFDSEYQE LWDWLIDMES LVMDSHDLMM SEEQQQHLYK RYSVEMSIRH LKKTELLSKV
EALKKGGVLL PNDLLEKVDS INEKWELLGK TLGEKIQDTM AGHSGSSPRD LLSPESGSLV
RQLEVRIKEL KGWLRDTELF IFNSCLRQEK EGTMNTEKQL QYFKSLCREI KQRRRGVASI
LRLCQHLLDD RETCNLNADH QPMQLIIVNL ERRWEAIVMQ AVQWQTRLQK KMGKESETLN
VIDPGLMDLN GMSEDALEWD EMDISNKLIS LNEESNDLDQ ELQPVIPSLK LGETSNEDPG
YDEEADNHGG SQYASNITAP SSPHIYQVYS LHNVELYEDN HMPFLKNNPK VTGMTQPNVL
TKSLSKDSSF SSTKSLPDLL GGSNLVKPCA CHGGDMSQNS GSESGIVSEG DTETTTNSEM
CLLNAVDGSP SNLETEHLDP QMGDAVNVLK QKFTDEGESI KLPNSSQSSI SPVGCVNGKV
GDLNSITKHT PDCLGEELQG KHDVFTFYDY SYLQGSKLKL PMIMKQSQSE KVHVEDPLLR
GFYFDKKSCK SKHQTTELQP DVPPHERILA SASHEMDRIS YKSGNIEKTF TGMQNAKQLS
LLSHSSSIES LSPGGDLFGL GIFKNGSDSL QRSTSLESWL TSYKSNEDLF SCHSSGDISV
SSGSVGELSK RTLDLLNRLE NIQSPSEQKI KRSVSDITLQ SSSQKMSFTG QMSLDIASSI
NEDSAASLTE LSSSDELSLC SEDIVLHKNK IPESNASFRK RLTRSVADES DVNVSMIVNV
SCTSACTDDE DDSDLLSSST LTLTEEELCI KDEDDDSSIA TDDEIYEDCT LMSGLDYIKN
ELQTWIRPKL SLTRDKKRCN VSDEMKGSKD ISSSEMTNPS DTLNIETLLN GSVKRVSENN
GNGKNSSHTH ELGTKRENKK TIFKVNKDPY VADMENGNIE GIPERQKGKP NVTSKVSENL
GSHGKEISES EHCKCKALMD SLDDSNTAGK EFVSQDVRHL PKKCPNHHHF ENQSTASTPT
EKSFSELALE TRFNNRQDSD ALKSSDDAPS MAGKSAGCCL ALEQNGTEEN ASISNISCCN
CEPDVFHQKD AEDCSVHNFV KEIIDMASTA LKSKSQPENE VAAPTSLTQI KEKVLEHSHR
PIQLRKGDFY SYLSLSSHDS DCGEVTNYIE EKSSTPLPLD TTDSGLDDKE DIECFFEACV
EGDSDGEEPC FSSAPPNESA VPSEAAMPLQ ATACSSEFSD SSLSADDADT VALSSPSSQE
RAEVGKEVNG LPQTSSGCAE NLEFTPSKLD SEKESSGKPG ESGMPEEHNA ASAKSKVQDL
SLKANQPTDK AALHPSPKTL TCEENLLNLH EKRHRNMHR*

speed

0.93 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: without_aae, prob: 0.999934818542658 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr14:33291494C>TN/A show variant in all transcripts IGV

HGNC symbol

AKAP6

Ensembl transcript ID

ENST00000557272

Genbank transcript ID

N/A

UniProt peptide

Q13023

alteration type

single base exchange

alteration region

intron

DNA changes

g.493016C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11845640

database	homozygous (T/T)	heterozygous	allele carriers
1000G	236	857	1093
ExAC	2121	14261	16382

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.647	0.051
	0.464	0.202
(flanking)	0.44	0.522

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	493009	wt: 0.9898 / mu: 0.9943 (marginal change - not scored)	wt: AAAGCGAAAAAGCGC mu: AAAGCGAAAAAGTGC	AGCG\|aaaa
Donor increased	493020	wt: 0.87 / mu: 0.97	wt: GCGCATGTGGAGGAT mu: GTGCATGTGGAGGAT	GCAT\|gtgg

distance from splice site

7560

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1560	1701	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
2063	2076	REGION	PKA-RII subunit binding domain.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

44 / 44

chromosome

strand

last intron/exon boundary

3632

theoretical NMD boundary in CDS

3538

length of CDS

3738

coding sequence (CDS) position

N/A

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

N/A

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

493016

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

33291494

original gDNA sequence snippet

ACAGTCACAAAGCGAAAAAGCGCATGTGGAGGATCCCCTGC

altered gDNA sequence snippet

ACAGTCACAAAGCGAAAAAGTGCATGTGGAGGATCCCCTGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.69 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems