| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LDLR | Deleterious | 60|40 | simple_ | No | Single base exchange | Normal |
| ||||||
ENST00000558518(MANE Select) | LDLR | Deleterious | 61|39 | simple_ | No | Single base exchange | Normal |
| |||||
| LDLR | Deleterious | 64|36 | simple_ | No | Single base exchange | Normal |
| ||||||
| LDLR | Deleterious | 65|35 | simple_ | No | Single base exchange | Normal |
| ||||||
| LDLR | Deleterious | 66|34 | simple_ | No | Single base exchange | Normal |
| ||||||
| LDLR | Deleterious | 67|33 | simple_ | No | Single base exchange | Normal |
| ||||||
| LDLR | Deleterious | 67|33 | simple_ | No | Single base exchange | Normal |
| ||||||
| LDLR | Deleterious | 73|27 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr19:11107472A>G (GRCh38) | |||||||||||||||||||||||||||||||
| Gene symbol | LDLR | |||||||||||||||||||||||||||||||
| Gene constraints | LOEUF: 1.07, LOF (oe): 0.89, misssense (oe): 0.95, synonymous (oe): 0.94 (gnomAD) | |||||||||||||||||||||||||||||||
| Ensembl transcript ID | ENST00000545707.5 | |||||||||||||||||||||||||||||||
| Genbank transcript ID | NM_001195803 (by similarity) | |||||||||||||||||||||||||||||||
| UniProt / AlphaMissense peptide | LDLR_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||||||||||||
| DNA changes | c.517A>G g.18055A>G | |||||||||||||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||||||||||||
| 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 | Yes | |||||||||||||||||||||||||||||||
| Chromosome | 19 | |||||||||||||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||||||||||||
| Wildtype AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPVATCR PDEFQCSDGN CIHGSRQCDR EYDCKDMSDE VGCVNVTLCE GPNKFKCHSG ECITLDKVCN MARDCRDWSD EPIKECGTNE CLDNNGGCSH VCNDLKIGYE CLCPDGFQLV AQRRCEDIDE CQDPDTCSQL CVNLEGGYKC QCEEGFQLDP HTKACKAVGS IAYLFFTNRH EVRKMTLDRS EYTSLIPNLR NVVALDTEVA SNRIYWSDLS QRMICSTQLD RAHGVSSYDT VISRDIQAPD GLAVDWIHSN IYWTDSVLGT VSVADTKGVK RKTLFRENGS KPRAIVVDPV HGFMYWTDWG TPAKIKKGGL NGVDIYSLVT ENIQWPNGIT LDLLSGRLYW VDSKLHSISS IDVNGGNRKT ILEDEKRLAH PFSLAVFEDK VFWTDIINEA IFSANRLTGS DVNLLAENLL SPEDMVLFHN LTQPREAEAA VATQETSTVR LKVSSTAVRT QHTTTRPVPD TSRLPGATPG LTTVEIVTMS HQALGDVAGR GNEKKPSSVR ALSIVLPIVL LVFLCLGVFL LWKNWRLKNI NSINFDNPVY QKTTEDEVHI CHNQDGYSYP SRQMVSLEDD VA* | |||||||||||||||||||||||||||||||
| Mutated AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPVATCR PDEFQCSDGN CIHGSRQCDR EYDCKDMSDE VGCVNVTLCE GPNKFKCHSG ECITLDKVCN MAGDCRDWSD EPIKECGTNE CLDNNGGCSH VCNDLKIGYE CLCPDGFQLV AQRRCEDIDE CQDPDTCSQL CVNLEGGYKC QCEEGFQLDP HTKACKAVGS IAYLFFTNRH EVRKMTLDRS EYTSLIPNLR NVVALDTEVA SNRIYWSDLS QRMICSTQLD RAHGVSSYDT VISRDIQAPD GLAVDWIHSN IYWTDSVLGT VSVADTKGVK RKTLFRENGS KPRAIVVDPV HGFMYWTDWG TPAKIKKGGL NGVDIYSLVT ENIQWPNGIT LDLLSGRLYW VDSKLHSISS IDVNGGNRKT ILEDEKRLAH PFSLAVFEDK VFWTDIINEA IFSANRLTGS DVNLLAENLL SPEDMVLFHN LTQPREAEAA VATQETSTVR LKVSSTAVRT QHTTTRPVPD TSRLPGATPG LTTVEIVTMS HQALGDVAGR GNEKKPSSVR ALSIVLPIVL LVFLCLGVFL LWKNWRLKNI NSINFDNPVY QKTTEDEVHI CHNQDGYSYP SRQMVSLEDD VA* | |||||||||||||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2049 / 2049 | |||||||||||||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 683 / 683 | |||||||||||||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2135 / 2135 | |||||||||||||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 87 / 87 | |||||||||||||||||||||||||||||||
| Last intron/exon boundary | 2099 | |||||||||||||||||||||||||||||||
| Theoretical NMD boundary in CDS | 1962 | |||||||||||||||||||||||||||||||
| Length of CDS | 2049 | |||||||||||||||||||||||||||||||
| Coding sequence (CDS) position | 517 | |||||||||||||||||||||||||||||||
| cDNA position | 603 | |||||||||||||||||||||||||||||||
| gDNA position | 18055 | |||||||||||||||||||||||||||||||
| Chromosomal position | 11107472 | |||||||||||||||||||||||||||||||
| Speed | 0.03 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 | Chr19:11107472A>G (GRCh38) | |||||||||||||||||||||
| Gene symbol | LDLR | |||||||||||||||||||||
| Gene constraints | LOEUF: 1.09, LOF (oe): 0.92, misssense (oe): 0.95, synonymous (oe): 0.99 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000558518.6 | |||||||||||||||||||||
| Genbank transcript ID | NM_000527 (exact from MANE) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | LDLR_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.898A>G g.18055A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| 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 | Yes | |||||||||||||||||||||
| Chromosome | 19 | |||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Wildtype AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAR DCRDWSDEPI KECGTNECLD NNGGCSHVCN DLKIGYECLC PDGFQLVAQR RCEDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIVLLV FLCLGVFLLW KNWRLKNINS INFDNPVYQK TTEDEVHICH NQDGYSYPSR QMVSLEDDVA * | |||||||||||||||||||||
| Mutated AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAG DCRDWSDEPI KECGTNECLD NNGGCSHVCN DLKIGYECLC PDGFQLVAQR RCEDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIVLLV FLCLGVFLLW KNWRLKNINS INFDNPVYQK TTEDEVHICH NQDGYSYPSR QMVSLEDDVA * | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2583 / 2583 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 861 / 861 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2669 / 2669 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 87 / 87 | |||||||||||||||||||||
| Last intron/exon boundary | 2633 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 2496 | |||||||||||||||||||||
| Length of CDS | 2583 | |||||||||||||||||||||
| Coding sequence (CDS) position | 898 | |||||||||||||||||||||
| cDNA position | 984 | |||||||||||||||||||||
| gDNA position | 18055 | |||||||||||||||||||||
| Chromosomal position | 11107472 | |||||||||||||||||||||
| Speed | 0.04 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 | Chr19:11107472A>G (GRCh38) | |||||||||||||||||||||
| Gene symbol | LDLR | |||||||||||||||||||||
| Gene constraints | LOEUF: 1.10, LOF (oe): 0.91, misssense (oe): 0.95, synonymous (oe): 0.97 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000455727.6 | |||||||||||||||||||||
| Genbank transcript ID | NM_001195800 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | LDLR_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.394A>G g.18055A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| 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 | Yes | |||||||||||||||||||||
| Chromosome | 19 | |||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Wildtype AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCLTLCEG PNKFKCHSGE CITLDKVCNM ARDCRDWSDE PIKECGTNEC LDNNGGCSHV CNDLKIGYEC LCPDGFQLVA QRRCEDIDEC QDPDTCSQLC VNLEGGYKCQ CEEGFQLDPH TKACKAVGSI AYLFFTNRHE VRKMTLDRSE YTSLIPNLRN VVALDTEVAS NRIYWSDLSQ RMICSTQLDR AHGVSSYDTV ISRDIQAPDG LAVDWIHSNI YWTDSVLGTV SVADTKGVKR KTLFRENGSK PRAIVVDPVH GFMYWTDWGT PAKIKKGGLN GVDIYSLVTE NIQWPNGITL DLLSGRLYWV DSKLHSISSI DVNGGNRKTI LEDEKRLAHP FSLAVFEDKV FWTDIINEAI FSANRLTGSD VNLLAENLLS PEDMVLFHNL TQPRGVNWCE RTTLSNGGCQ YLCLPAPQIN PHSPKFTCAC PDGMLLARDM RSCLTEAEAA VATQETSTVR LKVSSTAVRT QHTTTRPVPD TSRLPGATPG LTTVEIVTMS HQALGDVAGR GNEKKPSSVR ALSIVLPIVL LVFLCLGVFL LWKNWRLKNI NSINFDNPVY QKTTEDEVHI CHNQDGYSYP SRQMVSLEDD VA* | |||||||||||||||||||||
| Mutated AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCLTLCEG PNKFKCHSGE CITLDKVCNM AGDCRDWSDE PIKECGTNEC LDNNGGCSHV CNDLKIGYEC LCPDGFQLVA QRRCEDIDEC QDPDTCSQLC VNLEGGYKCQ CEEGFQLDPH TKACKAVGSI AYLFFTNRHE VRKMTLDRSE YTSLIPNLRN VVALDTEVAS NRIYWSDLSQ RMICSTQLDR AHGVSSYDTV ISRDIQAPDG LAVDWIHSNI YWTDSVLGTV SVADTKGVKR KTLFRENGSK PRAIVVDPVH GFMYWTDWGT PAKIKKGGLN GVDIYSLVTE NIQWPNGITL DLLSGRLYWV DSKLHSISSI DVNGGNRKTI LEDEKRLAHP FSLAVFEDKV FWTDIINEAI FSANRLTGSD VNLLAENLLS PEDMVLFHNL TQPRGVNWCE RTTLSNGGCQ YLCLPAPQIN PHSPKFTCAC PDGMLLARDM RSCLTEAEAA VATQETSTVR LKVSSTAVRT QHTTTRPVPD TSRLPGATPG LTTVEIVTMS HQALGDVAGR GNEKKPSSVR ALSIVLPIVL LVFLCLGVFL LWKNWRLKNI NSINFDNPVY QKTTEDEVHI CHNQDGYSYP SRQMVSLEDD VA* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2079 / 2079 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 693 / 693 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2165 / 2165 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 87 / 87 | |||||||||||||||||||||
| Last intron/exon boundary | 2129 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 1992 | |||||||||||||||||||||
| Length of CDS | 2079 | |||||||||||||||||||||
| Coding sequence (CDS) position | 394 | |||||||||||||||||||||
| cDNA position | 480 | |||||||||||||||||||||
| gDNA position | 18055 | |||||||||||||||||||||
| Chromosomal position | 11107472 | |||||||||||||||||||||
| Speed | 0.04 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 | Chr19:11107472A>G (GRCh38) | |||||||||||||||||||||
| Gene symbol | LDLR | |||||||||||||||||||||
| Gene constraints | LOEUF: 1.05, LOF (oe): 0.88, misssense (oe): 0.97, synonymous (oe): 1.00 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000535915.5 | |||||||||||||||||||||
| Genbank transcript ID | NM_001195799 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | LDLR_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.775A>G g.18055A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| 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 | Yes | |||||||||||||||||||||
| Chromosome | 19 | |||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Wildtype AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCSPKTCSQ DEFRCHDGKC ISRQFVCDSD RDCLDGSDEA SCPVLTCGPA SFQCNSSTCI PQLWACDNDP DCEDGSDEWP QRCRGLYVFQ GDSSPCSAFE FHCLSGECIH SSWRCDGGPD CKDKSDEENC AVATCRPDEF QCSDGNCIHG SRQCDREYDC KDMSDEVGCV NVTLCEGPNK FKCHSGECIT LDKVCNMARD CRDWSDEPIK ECGTNECLDN NGGCSHVCND LKIGYECLCP DGFQLVAQRR CEDIDECQDP DTCSQLCVNL EGGYKCQCEE GFQLDPHTKA CKAVGSIAYL FFTNRHEVRK MTLDRSEYTS LIPNLRNVVA LDTEVASNRI YWSDLSQRMI CSTQLDRAHG VSSYDTVISR DIQAPDGLAV DWIHSNIYWT DSVLGTVSVA DTKGVKRKTL FRENGSKPRA IVVDPVHGFM YWTDWGTPAK IKKGGLNGVD IYSLVTENIQ WPNGITLDLL SGRLYWVDSK LHSISSIDVN GGNRKTILED EKRLAHPFSL AVFEDKVFWT DIINEAIFSA NRLTGSDVNL LAENLLSPED MVLFHNLTQP RGVNWCERTT LSNGGCQYLC LPAPQINPHS PKFTCACPDG MLLARDMRSC LTEAEAAVAT QETSTVRLKV SSTAVRTQHT TTRPVPDTSR LPGATPGLTT VEIVTMSHQA LGDVAGRGNE KKPSSVRALS IVLPIVLLVF LCLGVFLLWK NWRLKNINSI NFDNPVYQKT TEDEVHICHN QDGYSYPSRQ MVSLEDDVA* | |||||||||||||||||||||
| Mutated AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCSPKTCSQ DEFRCHDGKC ISRQFVCDSD RDCLDGSDEA SCPVLTCGPA SFQCNSSTCI PQLWACDNDP DCEDGSDEWP QRCRGLYVFQ GDSSPCSAFE FHCLSGECIH SSWRCDGGPD CKDKSDEENC AVATCRPDEF QCSDGNCIHG SRQCDREYDC KDMSDEVGCV NVTLCEGPNK FKCHSGECIT LDKVCNMAGD CRDWSDEPIK ECGTNECLDN NGGCSHVCND LKIGYECLCP DGFQLVAQRR CEDIDECQDP DTCSQLCVNL EGGYKCQCEE GFQLDPHTKA CKAVGSIAYL FFTNRHEVRK MTLDRSEYTS LIPNLRNVVA LDTEVASNRI YWSDLSQRMI CSTQLDRAHG VSSYDTVISR DIQAPDGLAV DWIHSNIYWT DSVLGTVSVA DTKGVKRKTL FRENGSKPRA IVVDPVHGFM YWTDWGTPAK IKKGGLNGVD IYSLVTENIQ WPNGITLDLL SGRLYWVDSK LHSISSIDVN GGNRKTILED EKRLAHPFSL AVFEDKVFWT DIINEAIFSA NRLTGSDVNL LAENLLSPED MVLFHNLTQP RGVNWCERTT LSNGGCQYLC LPAPQINPHS PKFTCACPDG MLLARDMRSC LTEAEAAVAT QETSTVRLKV SSTAVRTQHT TTRPVPDTSR LPGATPGLTT VEIVTMSHQA LGDVAGRGNE KKPSSVRALS IVLPIVLLVF LCLGVFLLWK NWRLKNINSI NFDNPVYQKT TEDEVHICHN QDGYSYPSRQ MVSLEDDVA* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2460 / 2460 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 820 / 820 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2546 / 2546 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 87 / 87 | |||||||||||||||||||||
| Last intron/exon boundary | 2510 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 2373 | |||||||||||||||||||||
| Length of CDS | 2460 | |||||||||||||||||||||
| Coding sequence (CDS) position | 775 | |||||||||||||||||||||
| cDNA position | 861 | |||||||||||||||||||||
| gDNA position | 18055 | |||||||||||||||||||||
| Chromosomal position | 11107472 | |||||||||||||||||||||
| Speed | 0.04 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 | Chr19:11107472A>G (GRCh38) | |||||||||||||||||||||
| Gene symbol | LDLR | |||||||||||||||||||||
| Gene constraints | LOEUF: 1.12, LOF (oe): 0.94, misssense (oe): 0.95, synonymous (oe): 0.99 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000558013.5 | |||||||||||||||||||||
| Genbank transcript ID | NM_001195798 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | LDLR_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.898A>G g.18055A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| 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 | Yes | |||||||||||||||||||||
| Chromosome | 19 | |||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||||||||||
| Wildtype AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAR DCRDWSDEPI KECGTNECLD NNGGCSHVCN DLKIGYECLC PDGFQLVAQR RCEDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIVLLV FLCLGVFLLW KNWRLKNINS INFDNPVYQK TTEDEVHICH NQDGYSYPSM VSLEDDVA* | |||||||||||||||||||||
| Mutated AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAG DCRDWSDEPI KECGTNECLD NNGGCSHVCN DLKIGYECLC PDGFQLVAQR RCEDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIVLLV FLCLGVFLLW KNWRLKNINS INFDNPVYQK TTEDEVHICH NQDGYSYPSM VSLEDDVA* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2577 / 2577 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 859 / 859 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2648 / 2648 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 72 / 72 | |||||||||||||||||||||
| Last intron/exon boundary | 2618 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 2496 | |||||||||||||||||||||
| Length of CDS | 2577 | |||||||||||||||||||||
| Coding sequence (CDS) position | 898 | |||||||||||||||||||||
| cDNA position | 969 | |||||||||||||||||||||
| gDNA position | 18055 | |||||||||||||||||||||
| Chromosomal position | 11107472 | |||||||||||||||||||||
| Speed | 0.04 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 | Chr19:11107472A>G (GRCh38) | |||||||||||||
| Gene symbol | LDLR | |||||||||||||
| Gene constraints | LOEUF: 1.11, LOF (oe): 0.94, misssense (oe): 0.94, synonymous (oe): 1.00 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000557933.5 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.898A>G g.18055A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| 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 | Yes | |||||||||||||
| Chromosome | 19 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||
| Wildtype AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAR DCRDWSDEPI KECGTNECLD NNGGCSHVCN DLKIGYECLC PDGFQLVAQR RCEDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIATEL GLWSRGQLCD RACLSLQCSS SSFAWGSSFY GRTGGLRTST ASTLTTPSIR RPQRMRSTFA TTRTATATPR DRWSVWRMTW REHLPGVPSL PRTLPETSPA LFYSKTEKTK ALPARALFYI FIHLGGRTGF GQCPCNGLGW DFGFFLSS* | |||||||||||||
| Mutated AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAG DCRDWSDEPI KECGTNECLD NNGGCSHVCN DLKIGYECLC PDGFQLVAQR RCEDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIATEL GLWSRGQLCD RACLSLQCSS SSFAWGSSFY GRTGGLRTST ASTLTTPSIR RPQRMRSTFA TTRTATATPR DRWSVWRMTW REHLPGVPSL PRTLPETSPA LFYSKTEKTK ALPARALFYI FIHLGGRTGF GQCPCNGLGW DFGFFLSS* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2847 / 2847 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 949 / 949 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2934 / 2934 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 88 / 88 | |||||||||||||
| Last intron/exon boundary | 2696 | |||||||||||||
| Theoretical NMD boundary in CDS | 2558 | |||||||||||||
| Length of CDS | 2847 | |||||||||||||
| Coding sequence (CDS) position | 898 | |||||||||||||
| cDNA position | 985 | |||||||||||||
| gDNA position | 18055 | |||||||||||||
| Chromosomal position | 11107472 | |||||||||||||
| Speed | 0.05 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 | Chr19:11107472A>G (GRCh38) | |||||||||||||
| Gene symbol | LDLR | |||||||||||||
| Gene constraints | LOEUF: 1.09, LOF (oe): 0.92, misssense (oe): 0.95, synonymous (oe): 1.00 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000252444.10 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1156A>G g.18055A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| 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 | Yes | |||||||||||||
| Chromosome | 19 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||
| Wildtype AA sequence | MQGRPGVPPR FLSQRRRQVP GPRSRLRDIH ESPSVILGPP GEVPGFRCAL WRHLRPHLVL GGALAPPAPI KFTEGPPATL KASVPYEVET LPQNLPAPPW SAAEIFSHVG DRCERNEFQC QDGKCISYKW VCDGSAECQD GSDESQETCL SVTCKSGDFS CGGRVNRCIP QFWRCDGQVD CDNGSDEQGC PPKTCSQDEF RCHDGKCISR QFVCDSDRDC LDGSDEASCP VLTCGPASFQ CNSSTCIPQL WACDNDPDCE DGSDEWPQRC RGLYVFQGDS SPCSAFEFHC LSGECIHSSW RCDGGPDCKD KSDEENCAVA TCRPDEFQCS DGNCIHGSRQ CDREYDCKDM SDEVGCVNVT LCEGPNKFKC HSGECITLDK VCNMARDCRD WSDEPIKECG TNECLDNNGG CSHVCNDLKI GYECLCPDGF QLVAQRRCED IDECQDPDTC SQLCVNLEGG YKCQCEEGFQ LDPHTKACKA VGSIAYLFFT NRHEVRKMTL DRSEYTSLIP NLRNVVALDT EVASNRIYWS DLSQRMICST QLDRAHGVSS YDTVISRDIQ APDGLAVDWI HSNIYWTDSV LGTVSVADTK GVKRKTLFRE NGSKPRAIVV DPVHGFMYWT DWGTPAKIKK GGLNGVDIYS LVTENIQWPN GITLDLLSGR LYWVDSKLHS ISSIDVNGGN RKTILEDEKR LAHPFSLAVF EDKVFWTDII NEAIFSANRL TGSDVNLLAE NLLSPEDMVL FHNLTQPRGV NWCERTTLSN GGCQYLCLPA PQINPHSPKF TCACPDGMLL ARDMRSCLTE AEAAVATQET STVRLKVSST AVRTQHTTTR PVPDTSRLPG ATPGLTTVEI VTMSHQALGD VAGRGNEKKP SSVRALSIVL PIVLLVFLCL GVFLLWKNWR LKNINSINFD NPVYQKTTED EVHICHNQDG YSYPSRQMVS LEDDVA* | |||||||||||||
| Mutated AA sequence | MQGRPGVPPR FLSQRRRQVP GPRSRLRDIH ESPSVILGPP GEVPGFRCAL WRHLRPHLVL GGALAPPAPI KFTEGPPATL KASVPYEVET LPQNLPAPPW SAAEIFSHVG DRCERNEFQC QDGKCISYKW VCDGSAECQD GSDESQETCL SVTCKSGDFS CGGRVNRCIP QFWRCDGQVD CDNGSDEQGC PPKTCSQDEF RCHDGKCISR QFVCDSDRDC LDGSDEASCP VLTCGPASFQ CNSSTCIPQL WACDNDPDCE DGSDEWPQRC RGLYVFQGDS SPCSAFEFHC LSGECIHSSW RCDGGPDCKD KSDEENCAVA TCRPDEFQCS DGNCIHGSRQ CDREYDCKDM SDEVGCVNVT LCEGPNKFKC HSGECITLDK VCNMAGDCRD WSDEPIKECG TNECLDNNGG CSHVCNDLKI GYECLCPDGF QLVAQRRCED IDECQDPDTC SQLCVNLEGG YKCQCEEGFQ LDPHTKACKA VGSIAYLFFT NRHEVRKMTL DRSEYTSLIP NLRNVVALDT EVASNRIYWS DLSQRMICST QLDRAHGVSS YDTVISRDIQ APDGLAVDWI HSNIYWTDSV LGTVSVADTK GVKRKTLFRE NGSKPRAIVV DPVHGFMYWT DWGTPAKIKK GGLNGVDIYS LVTENIQWPN GITLDLLSGR LYWVDSKLHS ISSIDVNGGN RKTILEDEKR LAHPFSLAVF EDKVFWTDII NEAIFSANRL TGSDVNLLAE NLLSPEDMVL FHNLTQPRGV NWCERTTLSN GGCQYLCLPA PQINPHSPKF TCACPDGMLL ARDMRSCLTE AEAAVATQET STVRLKVSST AVRTQHTTTR PVPDTSRLPG ATPGLTTVEI VTMSHQALGD VAGRGNEKKP SSVRALSIVL PIVLLVFLCL GVFLLWKNWR LKNINSINFD NPVYQKTTED EVHICHNQDG YSYPSRQMVS LEDDVA* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2841 / 2841 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 947 / 947 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2857 / 2857 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 17 / 17 | |||||||||||||
| Last intron/exon boundary | 2821 | |||||||||||||
| Theoretical NMD boundary in CDS | 2754 | |||||||||||||
| Length of CDS | 2841 | |||||||||||||
| Coding sequence (CDS) position | 1156 | |||||||||||||
| cDNA position | 1172 | |||||||||||||
| gDNA position | 18055 | |||||||||||||
| Chromosomal position | 11107472 | |||||||||||||
| Speed | 0.04 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 | Chr19:11107472A>G (GRCh38) | |||||||||||||
| Gene symbol | LDLR | |||||||||||||
| Gene constraints | LOEUF: 1.26, LOF (oe): 0.94, misssense (oe): 1.02, synonymous (oe): 1.00 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000560467.2 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.898A>G g.18055A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| 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 | Yes | |||||||||||||
| Chromosome | 19 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||
| Altered gDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||
| Original cDNA sequence snippet | ACAAAGTCTGCAACATGGCTAGAGACTGCCGGGACTGGTCA | |||||||||||||
| Altered cDNA sequence snippet | ACAAAGTCTGCAACATGGCTGGAGACTGCCGGGACTGGTCA | |||||||||||||
| Wildtype AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAR DCRDWSDEPI KECDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIVLLV FLCLGVFLLW KNWRLKNINS INFDNPVYQK TTEDEVHICH NQDGYSYPSR QMVSLEDDVA * | |||||||||||||
| Mutated AA sequence | MGPWGWKLRW TVALLLAAAG TAVGDRCERN EFQCQDGKCI SYKWVCDGSA ECQDGSDESQ ETCLSVTCKS GDFSCGGRVN RCIPQFWRCD GQVDCDNGSD EQGCPPKTCS QDEFRCHDGK CISRQFVCDS DRDCLDGSDE ASCPVLTCGP ASFQCNSSTC IPQLWACDND PDCEDGSDEW PQRCRGLYVF QGDSSPCSAF EFHCLSGECI HSSWRCDGGP DCKDKSDEEN CAVATCRPDE FQCSDGNCIH GSRQCDREYD CKDMSDEVGC VNVTLCEGPN KFKCHSGECI TLDKVCNMAG DCRDWSDEPI KECDIDECQD PDTCSQLCVN LEGGYKCQCE EGFQLDPHTK ACKAVGSIAY LFFTNRHEVR KMTLDRSEYT SLIPNLRNVV ALDTEVASNR IYWSDLSQRM ICSTQLDRAH GVSSYDTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKGGLNGV DIYSLVTENI QWPNGITLDL LSGRLYWVDS KLHSISSIDV NGGNRKTILE DEKRLAHPFS LAVFEDKVFW TDIINEAIFS ANRLTGSDVN LLAENLLSPE DMVLFHNLTQ PRGVNWCERT TLSNGGCQYL CLPAPQINPH SPKFTCACPD GMLLARDMRS CLTEAEAAVA TQETSTVRLK VSSTAVRTQH TTTRPVPDTS RLPGATPGLT TVEIVTMSHQ ALGDVAGRGN EKKPSSVRAL SIVLPIVLLV FLCLGVFLLW KNWRLKNINS INFDNPVYQK TTEDEVHICH NQDGYSYPSR QMVSLEDDVA * | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2463 / 2463 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 821 / 821 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2548 / 2548 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 86 / 86 | |||||||||||||
| Last intron/exon boundary | 2512 | |||||||||||||
| Theoretical NMD boundary in CDS | 2376 | |||||||||||||
| Length of CDS | 2463 | |||||||||||||
| Coding sequence (CDS) position | 898 | |||||||||||||
| cDNA position | 983 | |||||||||||||
| gDNA position | 18055 | |||||||||||||
| Chromosomal position | 11107472 | |||||||||||||
| Speed | 0.04 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