| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AGBL5 | Deleterious | 161|39 | without_ | No | Single base exchange | Normal | |||||||
ENST00000360131(MANE Select) | AGBL5 | Deleterious | 164|36 | without_ | No | Single base exchange | Normal |
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:27053006A>G (GRCh38) | |||||||||||||
| Gene symbol | AGBL5 | |||||||||||||
| Gene constraints | LOEUF: 0.71, LOF (oe): 0.54, misssense (oe): 0.82, synonymous (oe): 0.95 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000323064.12 | |||||||||||||
| Genbank transcript ID | NM_001035507 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.48A>G g.10643A>G | |||||||||||||
| AA changes | no AA changes | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| 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? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | No | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TTCAGTTCTCGCTTTGATTCAGGGAATCTAGCCCACGTGGA | |||||||||||||
| Altered gDNA sequence snippet | TTCAGTTCTCGCTTTGATTCGGGGAATCTAGCCCACGTGGA | |||||||||||||
| Original cDNA sequence snippet | TTCAGTTCTCGCTTTGATTCAGGGAATCTAGCCCACGTGGA | |||||||||||||
| Altered cDNA sequence snippet | TTCAGTTCTCGCTTTGATTCGGGGAATCTAGCCCACGTGGA | |||||||||||||
| Wildtype AA sequence | MELRCGGLLF SSRFDSGNLA HVEKVESLSS DGEGVGGGAS ALTSGIASSP DYEFNVWTRP DCAETEFENG NRSWFYFSVR GGMPGKLIKI NIMNMNKQSK LYSQGMAPFV RTLPTRPRWE RIRDRPTFEM TETQFVLSFV HRFVEGRGAT TFFAFCYPFS YSDCQELLNQ LDQRFPENHP THSSPLDTIY YHRELLCYSL DGLRVDLLTI TSCHGLREDR EPRLEQLFPD TSTPRPFRFA GKRIFFLSSR VHPGETPSSF VFNGFLDFIL RPDDPRAQTL RRLFVFKLIP MLNPDGVVRG HYRTDSRGVN LNRQYLKPDA VLHPAIYGAK AVLLYHHVHS RLNSQSSSEH QPSSCLPPDA PVSDLEKANN LQNEAQCGHS ADRHNAEAWK QTEPAEQKLN SVWIMPQQSA GLEESAPDTI PPKESGVAYY VDLHGHASKR GCFMYGNSFS DESTQVENML YPKLISLNSA HFDFQGCNFS EKNMYARDRR DGQSKEGSGR VAIYKASGII HSYTLECNYN TGRSVNSIPA ACHDNGRASP PPPPAFPSRY TVELFEQVGR AMAIAALDMA ECNPWPRIVL SEHSSLTNLR AWMLKHVRNS RGLSSTLNVG VNKKRGLRTP PKSHNGLPVS CSENTLSRAR SFSTGTSAGG SSSSQQNSPQ MKNSPSFPFH GSRPAGLPGL GSSTQKVTHR VLGPVRGKPV WEPLQHVFGC LGHCWGK* | |||||||||||||
| Mutated AA sequence | MELRCGGLLF SSRFDSGNLA HVEKVESLSS DGEGVGGGAS ALTSGIASSP DYEFNVWTRP DCAETEFENG NRSWFYFSVR GGMPGKLIKI NIMNMNKQSK LYSQGMAPFV RTLPTRPRWE RIRDRPTFEM TETQFVLSFV HRFVEGRGAT TFFAFCYPFS YSDCQELLNQ LDQRFPENHP THSSPLDTIY YHRELLCYSL DGLRVDLLTI TSCHGLREDR EPRLEQLFPD TSTPRPFRFA GKRIFFLSSR VHPGETPSSF VFNGFLDFIL RPDDPRAQTL RRLFVFKLIP MLNPDGVVRG HYRTDSRGVN LNRQYLKPDA VLHPAIYGAK AVLLYHHVHS RLNSQSSSEH QPSSCLPPDA PVSDLEKANN LQNEAQCGHS ADRHNAEAWK QTEPAEQKLN SVWIMPQQSA GLEESAPDTI PPKESGVAYY VDLHGHASKR GCFMYGNSFS DESTQVENML YPKLISLNSA HFDFQGCNFS EKNMYARDRR DGQSKEGSGR VAIYKASGII HSYTLECNYN TGRSVNSIPA ACHDNGRASP PPPPAFPSRY TVELFEQVGR AMAIAALDMA ECNPWPRIVL SEHSSLTNLR AWMLKHVRNS RGLSSTLNVG VNKKRGLRTP PKSHNGLPVS CSENTLSRAR SFSTGTSAGG SSSSQQNSPQ MKNSPSFPFH GSRPAGLPGL GSSTQKVTHR VLGPVRGKPV WEPLQHVFGC LGHCWGK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2154 / 2154 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 718 / 718 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2316 / 2316 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 163 / 163 | |||||||||||||
| Last intron/exon boundary | 2036 | |||||||||||||
| Theoretical NMD boundary in CDS | 1823 | |||||||||||||
| Length of CDS | 2154 | |||||||||||||
| Coding sequence (CDS) position | 48 | |||||||||||||
| cDNA position | 210 | |||||||||||||
| gDNA position | 10643 | |||||||||||||
| Chromosomal position | 27053006 | |||||||||||||
| 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 | Chr2:27053006A>G (GRCh38) | |||||||||||||
| Gene symbol | AGBL5 | |||||||||||||
| Gene constraints | LOEUF: 0.71, LOF (oe): 0.56, misssense (oe): 0.85, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000360131.5 | |||||||||||||
| Genbank transcript ID | NM_021831 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.48A>G g.10643A>G | |||||||||||||
| AA changes | no AA changes | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| 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? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | No | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TTCAGTTCTCGCTTTGATTCAGGGAATCTAGCCCACGTGGA | |||||||||||||
| Altered gDNA sequence snippet | TTCAGTTCTCGCTTTGATTCGGGGAATCTAGCCCACGTGGA | |||||||||||||
| Original cDNA sequence snippet | TTCAGTTCTCGCTTTGATTCAGGGAATCTAGCCCACGTGGA | |||||||||||||
| Altered cDNA sequence snippet | TTCAGTTCTCGCTTTGATTCGGGGAATCTAGCCCACGTGGA | |||||||||||||
| Wildtype AA sequence | MELRCGGLLF SSRFDSGNLA HVEKVESLSS DGEGVGGGAS ALTSGIASSP DYEFNVWTRP DCAETEFENG NRSWFYFSVR GGMPGKLIKI NIMNMNKQSK LYSQGMAPFV RTLPTRPRWE RIRDRPTFEM TETQFVLSFV HRFVEGRGAT TFFAFCYPFS YSDCQELLNQ LDQRFPENHP THSSPLDTIY YHRELLCYSL DGLRVDLLTI TSCHGLREDR EPRLEQLFPD TSTPRPFRFA GKRIFFLSSR VHPGETPSSF VFNGFLDFIL RPDDPRAQTL RRLFVFKLIP MLNPDGVVRG HYRTDSRGVN LNRQYLKPDA VLHPAIYGAK AVLLYHHVHS RLNSQSSSEH QPSSCLPPDA PVSDLEKANN LQNEAQCGHS ADRHNAEAWK QTEPAEQKLN SVWIMPQQSA GLEESAPDTI PPKESGVAYY VDLHGHASKR GCFMYGNSFS DESTQVENML YPKLISLNSA HFDFQGCNFS EKNMYARDRR DGQSKEGSGR VAIYKASGII HSYTLECNYN TGRSVNSIPA ACHDNGRASP PPPPAFPSRY TVELFEQVGR AMAIAALDMA ECNPWPRIVL SEHSSLTNLR AWMLKHVRNS RGLSSTLNVG VNKKRGLRTP PKSHNGLPVS CSENTLSRAR SFSTGTSAGG SSSSQQNSPQ MKNSPSFPFH GSRPAGLPGL GSSTQKVTHR VLGPVREPRS QDRRRQQQPL NHRPAGSLAP SPAPTSSGPA SSHKLGSCLL PDSFNIPGSS CSLLSSGDKP EAVMVIGKGL LGTGARMPCI KTRLQARPRL GRGSPPTRRG MKGSSGPTSP TPRTRESSEL ELGSCSATPG LPQARPPRPR SAPAFSPISC SLSDSPSWNC YSRGPLGQPE VCFVPKSPPL TVSPRV* | |||||||||||||
| Mutated AA sequence | MELRCGGLLF SSRFDSGNLA HVEKVESLSS DGEGVGGGAS ALTSGIASSP DYEFNVWTRP DCAETEFENG NRSWFYFSVR GGMPGKLIKI NIMNMNKQSK LYSQGMAPFV RTLPTRPRWE RIRDRPTFEM TETQFVLSFV HRFVEGRGAT TFFAFCYPFS YSDCQELLNQ LDQRFPENHP THSSPLDTIY YHRELLCYSL DGLRVDLLTI TSCHGLREDR EPRLEQLFPD TSTPRPFRFA GKRIFFLSSR VHPGETPSSF VFNGFLDFIL RPDDPRAQTL RRLFVFKLIP MLNPDGVVRG HYRTDSRGVN LNRQYLKPDA VLHPAIYGAK AVLLYHHVHS RLNSQSSSEH QPSSCLPPDA PVSDLEKANN LQNEAQCGHS ADRHNAEAWK QTEPAEQKLN SVWIMPQQSA GLEESAPDTI PPKESGVAYY VDLHGHASKR GCFMYGNSFS DESTQVENML YPKLISLNSA HFDFQGCNFS EKNMYARDRR DGQSKEGSGR VAIYKASGII HSYTLECNYN TGRSVNSIPA ACHDNGRASP PPPPAFPSRY TVELFEQVGR AMAIAALDMA ECNPWPRIVL SEHSSLTNLR AWMLKHVRNS RGLSSTLNVG VNKKRGLRTP PKSHNGLPVS CSENTLSRAR SFSTGTSAGG SSSSQQNSPQ MKNSPSFPFH GSRPAGLPGL GSSTQKVTHR VLGPVREPRS QDRRRQQQPL NHRPAGSLAP SPAPTSSGPA SSHKLGSCLL PDSFNIPGSS CSLLSSGDKP EAVMVIGKGL LGTGARMPCI KTRLQARPRL GRGSPPTRRG MKGSSGPTSP TPRTRESSEL ELGSCSATPG LPQARPPRPR SAPAFSPISC SLSDSPSWNC YSRGPLGQPE VCFVPKSPPL TVSPRV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2661 / 2661 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 887 / 887 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2833 / 2833 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 173 / 173 | |||||||||||||
| Last intron/exon boundary | 2661 | |||||||||||||
| Theoretical NMD boundary in CDS | 2438 | |||||||||||||
| Length of CDS | 2661 | |||||||||||||
| Coding sequence (CDS) position | 48 | |||||||||||||
| cDNA position | 220 | |||||||||||||
| gDNA position | 10643 | |||||||||||||
| Chromosomal position | 27053006 | |||||||||||||
| Speed | 0.01 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