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: ENST00000379370
MT speed 0 s - this script 2.70695 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AGRN	disease_causing_automatic	0.999999957759057	simple_aae		affected	0	G1709R	single base exchange	rs199476396		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999957759057 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM094737)
known disease mutation: rs18241 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:985955G>CN/A show variant in all transcripts IGV

HGNC symbol

AGRN

Ensembl transcript ID

ENST00000379370

Genbank transcript ID

NM_198576

UniProt peptide

O00468

alteration type

single base exchange

alteration region

CDS

DNA changes

c.5125G>C
cDNA.5175G>C
g.30453G>C

AA changes

G1709R Score: 125 explain score(s)

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

1709

frameshift

known variant

Reference ID: rs199476396
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs18241 (pathogenic for Myasthenic syndrome, congenital, 8|Congenital myasthenic syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM094737)

known disease mutation at this position, please check HGMD for details (HGMD ID CM094737)
known disease mutation at this position, please check HGMD for details (HGMD ID CM094737)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.649	1
	5.582	1
(flanking)	3.947	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 marginally increased	30446	wt: 0.9930 / mu: 0.9943 (marginal change - not scored)	wt: GACCTGGGCAAGGGG mu: GACCTGGGCAAGCGG	CCTG\|ggca
Donor gained	30455	0.48	mu: AAGCGGGCAGCGGTC	GCGG\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1709

mutated

not conserved

1709

Ptroglodytes

all identical

ENSPTRG00000022742

1709

Mmulatta

not conserved

ENSMMUG00000000838

1690

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000041936

1591

Ggallus

all identical

ENSGALG00000002041

1655

Trubripes

all identical

ENSTRUG00000006249

1016

Drerio

all identical

ENSDARG00000079388

1454

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001763

1539

protein features

start (aa)	end (aa)	feature	details
1635	1818	DOMAIN	Laminin G-like 2.	lost
1814	1853	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
1818	1818	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1826	1826	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1832	1832	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1841	1841	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1843	1843	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1852	1852	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1864	2042	DOMAIN	Laminin G-like 3.	might get lost (downstream of altered splice site)
2016	2016	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2042	2042	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6138 / 6138

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

2046 / 2046

position of stopcodon in wt / mu cDNA

6188 / 6188

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

51 / 51

chromosome

strand

last intron/exon boundary

6031

theoretical NMD boundary in CDS

5930

length of CDS

6138

coding sequence (CDS) position

5125

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

5175

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

30453

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

985955

original gDNA sequence snippet

TCCGCTACGACCTGGGCAAGGGGGCAGCGGTCATCAGGTGG

altered gDNA sequence snippet

TCCGCTACGACCTGGGCAAGCGGGCAGCGGTCATCAGGTGG

original cDNA sequence snippet

TCCGCTACGACCTGGGCAAGGGGGCAGCGGTCATCAGGAGC

altered cDNA sequence snippet

TCCGCTACGACCTGGGCAAGCGGGCAGCGGTCATCAGGAGC

wildtype AA sequence

MAGRSHPGPL RPLLPLLVVA ACVLPGAGGT CPERALERRE EEANVVLTGT VEEILNVDPV
QHTYSCKVRV WRYLKGKDLV ARESLLDGGN KVVISGFGDP LICDNQVSTG DTRIFFVNPA
PPYLWPAHKN ELMLNSSLMR ITLRNLEEVE FCVEDKPGTH FTPVPPTPPD ACRGMLCGFG
AVCEPNAEGP GRASCVCKKS PCPSVVAPVC GSDASTYSNE CELQRAQCSQ QRRIRLLSRG
PCGSRDPCSN VTCSFGSTCA RSADGLTASC LCPATCRGAP EGTVCGSDGA DYPGECQLLR
RACARQENVF KKFDGPCDPC QGALPDPSRS CRVNPRTRRP EMLLRPESCP ARQAPVCGDD
GVTYENDCVM GRSGAARGLL LQKVRSGQCQ GRDQCPEPCR FNAVCLSRRG RPRCSCDRVT
CDGAYRPVCA QDGRTYDSDC WRQQAECRQQ RAIPSKHQGP CDQAPSPCLG VQCAFGATCA
VKNGQAACEC LQACSSLYDP VCGSDGVTYG SACELEATAC TLGREIQVAR KGPCDRCGQC
RFGALCEAET GRCVCPSECV ALAQPVCGSD GHTYPSECML HVHACTHQIS LHVASAGPCE
TCGDAVCAFG AVCSAGQCVC PRCEHPPPGP VCGSDGVTYG SACELREAAC LQQTQIEEAR
AGPCEQAECG SGGSGSGEDG DCEQELCRQR GGIWDEDSED GPCVCDFSCQ SVPGSPVCGS
DGVTYSTECE LKKARCESQR GLYVAAQGAC RGPTFAPLPP VAPLHCAQTP YGCCQDNITA
ARGVGLAGCP SACQCNPHGS YGGTCDPATG QCSCRPGVGG LRCDRCEPGF WNFRGIVTDG
RSGCTPCSCD PQGAVRDDCE QMTGLCSCKP GVAGPKCGQC PDGRALGPAG CEADASAPAT
CAEMRCEFGA RCVEESGSAH CVCPMLTCPE ANATKVCGSD GVTYGNECQL KTIACRQGLQ
ISIQSLGPCQ EAVAPSTHPT SASVTVTTPG LLLSQALPAP PGALPLAPSS TAHSQTTPPP
SSRPRTTASV PRTTVWPVLT VPPTAPSPAP SLVASAFGES GSTDGSSDEE LSGDQEASGG
GSGGLEPLEG SSVATPGPPV ERASCYNSAL GCCSDGKTPS LDAEGSNCPA TKVFQGVLEL
EGVEGQELFY TPEMADPKSE LFGETARSIE STLDDLFRNS DVKKDFRSVR LRDLGPGKSV
RAIVDVHFDP TTAFRAPDVA RALLRQIQVS RRRSLGVRRP LQEHVRFMDF DWFPAFITGA
TSGAIAAGAT ARATTASRLP SSAVTPRAPH PSHTSQPVAK TTAAPTTRRP PTTAPSRVPG
RRPPAPQQPP KPCDSQPCFH GGTCQDWALG GGFTCSCPAG RGGAVCEKVL GAPVPAFEGR
SFLAFPTLRA YHTLRLALEF RALEPQGLLL YNGNARGKDF LALALLDGRV QLRFDTGSGP
AVLTSAVPVE PGQWHRLELS RHWRRGTLSV DGETPVLGES PSGTDGLNLD TDLFVGGVPE
DQAAVALERT FVGAGLRGCI RLLDVNNQRL ELGIGPGAAT RGSGVGECGD HPCLPNPCHG
GAPCQNLEAG RFHCQCPPGR VGPTCADEKS PCQPNPCHGA APCRVLPEGG AQCECPLGRE
GTFCQTASGQ DGSGPFLADF NGFSHLELRG LHTFARDLGE KMALEVVFLA RGPSGLLLYN
GQKTDGKGDF VSLALRDRRL EFRYDLGKGA AVIRSREPVT LGAWTRVSLE RNGRKGALRV
GDGPRVLGES PVPHTVLNLK EPLYVGGAPD FSKLARAAAV SSGFDGAIQL VSLGGRQLLT
PEHVLRQVDV TSFAGHPCTR ASGHPCLNGA SCVPREAAYV CLCPGGFSGP HCEKGLVEKS
AGDVDTLAFD GRTFVEYLNA VTESEKALQS NHFELSLRTE ATQGLVLWSG KATERADYVA
LAIVDGHLQL SYNLGSQPVV LRSTVPVNTN RWLRVVAHRE QREGSLQVGN EAPVTGSSPL
GATQLDTDGA LWLGGLPELP VGPALPKAYG TGFVGCLRDV VVGRHPLHLL EDAVTKPELR
PCPTP*

mutated AA sequence

MAGRSHPGPL RPLLPLLVVA ACVLPGAGGT CPERALERRE EEANVVLTGT VEEILNVDPV
QHTYSCKVRV WRYLKGKDLV ARESLLDGGN KVVISGFGDP LICDNQVSTG DTRIFFVNPA
PPYLWPAHKN ELMLNSSLMR ITLRNLEEVE FCVEDKPGTH FTPVPPTPPD ACRGMLCGFG
AVCEPNAEGP GRASCVCKKS PCPSVVAPVC GSDASTYSNE CELQRAQCSQ QRRIRLLSRG
PCGSRDPCSN VTCSFGSTCA RSADGLTASC LCPATCRGAP EGTVCGSDGA DYPGECQLLR
RACARQENVF KKFDGPCDPC QGALPDPSRS CRVNPRTRRP EMLLRPESCP ARQAPVCGDD
GVTYENDCVM GRSGAARGLL LQKVRSGQCQ GRDQCPEPCR FNAVCLSRRG RPRCSCDRVT
CDGAYRPVCA QDGRTYDSDC WRQQAECRQQ RAIPSKHQGP CDQAPSPCLG VQCAFGATCA
VKNGQAACEC LQACSSLYDP VCGSDGVTYG SACELEATAC TLGREIQVAR KGPCDRCGQC
RFGALCEAET GRCVCPSECV ALAQPVCGSD GHTYPSECML HVHACTHQIS LHVASAGPCE
TCGDAVCAFG AVCSAGQCVC PRCEHPPPGP VCGSDGVTYG SACELREAAC LQQTQIEEAR
AGPCEQAECG SGGSGSGEDG DCEQELCRQR GGIWDEDSED GPCVCDFSCQ SVPGSPVCGS
DGVTYSTECE LKKARCESQR GLYVAAQGAC RGPTFAPLPP VAPLHCAQTP YGCCQDNITA
ARGVGLAGCP SACQCNPHGS YGGTCDPATG QCSCRPGVGG LRCDRCEPGF WNFRGIVTDG
RSGCTPCSCD PQGAVRDDCE QMTGLCSCKP GVAGPKCGQC PDGRALGPAG CEADASAPAT
CAEMRCEFGA RCVEESGSAH CVCPMLTCPE ANATKVCGSD GVTYGNECQL KTIACRQGLQ
ISIQSLGPCQ EAVAPSTHPT SASVTVTTPG LLLSQALPAP PGALPLAPSS TAHSQTTPPP
SSRPRTTASV PRTTVWPVLT VPPTAPSPAP SLVASAFGES GSTDGSSDEE LSGDQEASGG
GSGGLEPLEG SSVATPGPPV ERASCYNSAL GCCSDGKTPS LDAEGSNCPA TKVFQGVLEL
EGVEGQELFY TPEMADPKSE LFGETARSIE STLDDLFRNS DVKKDFRSVR LRDLGPGKSV
RAIVDVHFDP TTAFRAPDVA RALLRQIQVS RRRSLGVRRP LQEHVRFMDF DWFPAFITGA
TSGAIAAGAT ARATTASRLP SSAVTPRAPH PSHTSQPVAK TTAAPTTRRP PTTAPSRVPG
RRPPAPQQPP KPCDSQPCFH GGTCQDWALG GGFTCSCPAG RGGAVCEKVL GAPVPAFEGR
SFLAFPTLRA YHTLRLALEF RALEPQGLLL YNGNARGKDF LALALLDGRV QLRFDTGSGP
AVLTSAVPVE PGQWHRLELS RHWRRGTLSV DGETPVLGES PSGTDGLNLD TDLFVGGVPE
DQAAVALERT FVGAGLRGCI RLLDVNNQRL ELGIGPGAAT RGSGVGECGD HPCLPNPCHG
GAPCQNLEAG RFHCQCPPGR VGPTCADEKS PCQPNPCHGA APCRVLPEGG AQCECPLGRE
GTFCQTASGQ DGSGPFLADF NGFSHLELRG LHTFARDLGE KMALEVVFLA RGPSGLLLYN
GQKTDGKGDF VSLALRDRRL EFRYDLGKRA AVIRSREPVT LGAWTRVSLE RNGRKGALRV
GDGPRVLGES PVPHTVLNLK EPLYVGGAPD FSKLARAAAV SSGFDGAIQL VSLGGRQLLT
PEHVLRQVDV TSFAGHPCTR ASGHPCLNGA SCVPREAAYV CLCPGGFSGP HCEKGLVEKS
AGDVDTLAFD GRTFVEYLNA VTESEKALQS NHFELSLRTE ATQGLVLWSG KATERADYVA
LAIVDGHLQL SYNLGSQPVV LRSTVPVNTN RWLRVVAHRE QREGSLQVGN EAPVTGSSPL
GATQLDTDGA LWLGGLPELP VGPALPKAYG TGFVGCLRDV VVGRHPLHLL EDAVTKPELR
PCPTP*

speed

0.66 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

disease causing

Problems