| Transcript | Gene symbol | Prediction | Tree vote | Model | Prediction problem | Splice site change | Known ClinVar disease mutation | Potential ClinVar disease mutation | Amino acid changes | Variant type | dbSNP ID | Protein length | Features at a glance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000379370(MANE Select) | AGRN | Benign | 0|200 | without_ | No | Single base exchange | N/A |
| |||||
| AGRN | Benign | 0|200 | without_ | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr1:1022518G>T (GRCh38) | |||||||||||||
| Gene symbol | AGRN | |||||||||||||
| Gene constraints | LOEUF: 0.73, LOF (oe): 0.62, misssense (oe): 1.14, synonymous (oe): 1.29 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000379370.7 | |||||||||||||
| Genbank transcript ID | NM_198576 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.463+56G>T g.2399G>T | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 1 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | GGTCAGGGCAGTGGCCAAGGGGGACAGGTTGCAGGGGTCGC | |||||||||||||
| Altered gDNA sequence snippet | GGTCAGGGCAGTGGCCAAGGTGGACAGGTTGCAGGGGTCGC | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| 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 | ||||||||||||||
| 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 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 54 / 54 | |||||||||||||
| Last intron/exon boundary | 6033 | |||||||||||||
| Theoretical NMD boundary in CDS | 5929 | |||||||||||||
| Length of CDS | 6138 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 2399 | |||||||||||||
| Chromosomal position | 1022518 | |||||||||||||
| Speed | 0.02 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr1:1022518G>T (GRCh38) | |||||||||||||
| Gene symbol | AGRN | |||||||||||||
| Gene constraints | LOEUF: 0.73, LOF (oe): 0.62, misssense (oe): 1.14, synonymous (oe): 1.29 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000620552.4 | |||||||||||||
| Genbank transcript ID | NM_001305275 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.49+56G>T g.2399G>T | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 1 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | GGTCAGGGCAGTGGCCAAGGGGGACAGGTTGCAGGGGTCGC | |||||||||||||
| Altered gDNA sequence snippet | GGTCAGGGCAGTGGCCAAGGTGGACAGGTTGCAGGGGTCGC | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MRITLRNLEE VEFCVEDKPG THFTPVPPTP PDACRGMLCG FGAVCEPNAE GPGRASCVCK KSPCPSVVAP VCGSDASTYS NECELQRAQC SQQRRIRLLS RGPCGSRDPC SNVTCSFGST CARSADGLTA SCLCPATCRG APEGTVCGSD GADYPGECQL LRRACARQEN VFKKFDGPCD PCQGALPDPS RSCRVNPRTR RPEMLLRPES CPARQAPVCG DDGVTYENDC VMGRSGAARG LLLQKVRSGQ CQGRDQCPEP CRFNAVCLSR RGRPRCSCDR VTCDGAYRPV CAQDGRTYDS DCWRQQAECR QQRAIPSKHQ GPCDQAPSPC LGVQCAFGAT CAVKNGQAAC ECLQACSSLY DPVCGSDGVT YGSACELEAT ACTLGREIQV ARKGPCDRCG QCRFGALCEA ETGRCVCPSE CVALAQPVCG SDGHTYPSEC MLHVHACTHQ ISLHVASAGP CETCGDAVCA FGAVCSAGQC VCPRCEHPPP GPVCGSDGVT YGSACELREA ACLQQTQIEE ARAGPCEQAE CGSGGSGSGE DGDCEQELCR QRGGIWDEDS EDGPCVCDFS CQSVPGSPVC GSDGVTYSTE CELKKARCES QRGLYVAAQG ACRGPTFAPL PPVAPLHCAQ TPYGCCQDNI TAARGVGLAG CPSACQCNPH GSYGGTCDPA TGQCSCRPGV GGLRCDRCEP GFWNFRGIVT DGRSGCTPCS CDPQGAVRDD CEQMTGLCSC KPGVAGPKCG QCPDGRALGP AGCEADASAP ATCAEMRCEF GARCVEESGS AHCVCPMLTC PEANATKVCG SDGVTYGNEC QLKTIACRQG LQISIQSLGP CQEAVAPSTH PTSASVTVTT PGLLLSQALP APPGALPLAP SSTAHSQTTP PPSSRPRTTA SVPRTTVWPV LTVPPTAPSP APSLVASAFG ESGSTDGSSD EELSGDQEAS GGGSGGLEPL EGSSVATPGP PVERASCYNS ALGCCSDGKT PSLDAEGSNC PATKVFQGVL ELEGVEGQEL FYTPEMADPK SELFGETARS IESTLDDLFR NSDVKKDFRS VRLRDLGPGK SVRAIVDVHF DPTTAFRAPD VARALLRQIQ VSRRRSLGVR RPLQEHVRFM DFDWFPAFIT GATSGAIAAG ATARATTASR LPSSAVTPRA PHPSHTSQPV AKTTAAPTTR RPPTTAPSRV PGRRPPAPQQ PPKPCDSQPC FHGGTCQDWA LGGGFTCSCP AGRGGAVCEK VLGAPVPAFE GRSFLAFPTL RAYHTLRLAL EFRALEPQGL LLYNGNARGK DFLALALLDG RVQLRFDTGS GPAVLTSAVP VEPGQWHRLE LSRHWRRGTL SVDGETPVLG ESPSGTDGLN LDTDLFVGGV PEDQAAVALE RTFVGAGLRG CIRLLDVNNQ RLELGIGPGA ATRGSGVGEC GDHPCLPNPC HGGAPCQNLE AGRFHCQCPP GRVGPTCADE KSPCQPNPCH GAAPCRVLPE GGAQCECPLG REGTFCQTAS GQDGSGPFLA DFNGFSHLEL RGLHTFARDL GEKMALEVVF LARGPSGLLL YNGQKTDGKG DFVSLALRDR RLEFRYDLGK GAAVIRSREP VTLGAWTRVS LERNGRKGAL RVGDGPRVLG ESPKSRKVPH TVLNLKEPLY VGGAPDFSKL ARAAAVSSGF DGAIQLVSLG GRQLLTPEHV LRQVDVTSFA GHPCTRASGH PCLNGASCVP REAAYVCLCP GGFSGPHCEK GLVEKSAGDV DTLAFDGRTF VEYLNAVTES ELANEIPVPE TLDSGALHSE KALQSNHFEL SLRTEATQGL VLWSGKATER ADYVALAIVD GHLQLSYNLG SQPVVLRSTV PVNTNRWLRV VAHREQREGS LQVGNEAPVT GSSPLGATQL DTDGALWLGG LPELPVGPAL PKAYGTGFVG CLRDVVVGRH PLHLLEDAVT KPELRPCPTP * | |||||||||||||
| Mutated AA sequence | ||||||||||||||
| 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 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 465 / 465 | |||||||||||||
| Last intron/exon boundary | 6099 | |||||||||||||
| Theoretical NMD boundary in CDS | 5584 | |||||||||||||
| Length of CDS | 5793 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 2399 | |||||||||||||
| Chromosomal position | 1022518 | |||||||||||||
| Speed | 0.02 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project