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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000301732(MANE Select) | ABCA3 | Deleterious | 94|6 | simple_ | Yes | Single base exchange | Normal |
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ABCA3 | Deleterious | 97|3 | simple_ | Yes | Single base exchange | Normal |
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Analysed issue | Analysis result | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Variant | Chr16:2317763T>A (GRCh38) | |||||||||||||||||||||
Gene symbol | ABCA3 | |||||||||||||||||||||
Gene constraints | LOEUF: 0.61, LOF (oe): 0.51, misssense (oe): 0.93, synonymous (oe): 1.07 (gnomAD) | |||||||||||||||||||||
Ensembl transcript ID | ENST00000301732.10 | |||||||||||||||||||||
Genbank transcript ID | NM_001089 (exact from MANE) | |||||||||||||||||||||
UniProt / AlphaMissense peptide | ABCA3_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
Variant type | Single base exchange | |||||||||||||||||||||
Gene region | CDS | |||||||||||||||||||||
DNA changes | c.875A>T g.22984A>T | |||||||||||||||||||||
AA changes |
| |||||||||||||||||||||
Frameshift | No | |||||||||||||||||||||
Length of protein | Normal | |||||||||||||||||||||
Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
Variant DBs |
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Protein conservation | ||||||||||||||||||||||
Protein features |
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Phylogenetic conservation |
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Splice sites | MaxEntScan:
| |||||||||||||||||||||
Distance from splice site | 2 | |||||||||||||||||||||
Kozak consensus sequence altered? | No | |||||||||||||||||||||
poly(A) signal | N/A | |||||||||||||||||||||
AA sequence altered | Yes | |||||||||||||||||||||
Chromosome | 16 | |||||||||||||||||||||
Strand | -1 | |||||||||||||||||||||
Original gDNA sequence snippet | TGATGGCTTCTCTCCCCAGGAGTACATGCGCATGATGGGGC | |||||||||||||||||||||
Altered gDNA sequence snippet | TGATGGCTTCTCTCCCCAGGTGTACATGCGCATGATGGGGC | |||||||||||||||||||||
Original cDNA sequence snippet | GAAGGAAAGGAGGCTGAAGGAGTACATGCGCATGATGGGGC | |||||||||||||||||||||
Altered cDNA sequence snippet | GAAGGAAAGGAGGCTGAAGGTGTACATGCGCATGATGGGGC | |||||||||||||||||||||
Wildtype AA sequence | MAVLRQLALL LWKNYTLQKR KVLVTVLELF LPLLFSGILI WLRLKIQSEN VPNATIYPGQ SIQELPLFFT FPPPGDTWEL AYIPSHSDAA KTVTETVRRA LVINMRVRGF PSEKDFEDYI RYDNCSSSVL AAVVFEHPFN HSKEPLPLAV KYHLRFSYTR RNYMWTQTGS FFLKETEGWH TTSLFPLFPN PGPREPTSPD GGEPGYIREG FLAVQHAVDR AIMEYHADAA TRQLFQRLTV TIKRFPYPPF IADPFLVAIQ YQLPLLLLLS FTYTALTIAR AVVQEKERRL KEYMRMMGLS SWLHWSAWFL LFFLFLLIAA SFMTLLFCVK VKPNVAVLSR SDPSLVLAFL LCFAISTISF SFMVSTFFSK ANMAAAFGGF LYFFTYIPYF FVAPRYNWMT LSQKLCSCLL SNVAMAMGAQ LIGKFEAKGM GIQWRDLLSP VNVDDDFCFG QVLGMLLLDS VLYGLVTWYM EAVFPGQFGV PQPWYFFIMP SYWCGKPRAV AGKEEEDSDP EKALRNEYFE AEPEDLVAGI KIKHLSKVFR VGNKDRAAVR DLNLNLYEGQ ITVLLGHNGA GKTTTLSMLT GLFPPTSGRA YISGYEISQD MVQIRKSLGL CPQHDILFDN LTVAEHLYFY AQLKGLSRQK CPEEVKQMLH IIGLEDKWNS RSRFLSGGMR RKLSIGIALI AGSKVLILDE PTSGMDAISR RAIWDLLQRQ KSDRTIVLTT HFMDEADLLG DRIAIMAKGE LQCCGSSLFL KQKYGAGYHM TLVKEPHCNP EDISQLVHHH VPNATLESSA GAELSFILPR ESTHRFEGLF AKLEKKQKEL GIASFGASIT TMEEVFLRVG KLVDSSMDIQ AIQLPALQYQ HERRASDWAV DSNLCGAMDP SDGIGALIEE ERTAVKLNTG LALHCQQFWA MFLKKAAYSW REWKMVAAQV LVPLTCVTLA LLAINYSSEL FDDPMLRLTL GEYGRTVVPF SVPGTSQLGQ QLSEHLKDAL QAEGQEPREV LGDLEEFLIF RASVEGGGFN ERCLVAASFR DVGERTVVNA LFNNQAYHSP ATALAVVDNL LFKLLCGPHA SIVVSNFPQP RSALQAAKDQ FNEGRKGFDI ALNLLFAMAF LASTFSILAV SERAVQAKHV QFVSGVHVAS FWLSALLWDL ISFLIPSLLL LVVFKAFDVR AFTRDGHMAD TLLLLLLYGW AIIPLMYLMN FFFLGAATAY TRLTIFNILS GIATFLMVTI MRIPAVKLEE LSKTLDHVFL VLPNHCLGMA VSSFYENYET RRYCTSSEVA AHYCKKYNIQ YQENFYAWSA PGVGRFVASM AASGCAYLIL LFLIETNLLQ RLRGILCALR RRRTLTELYT RMPVLPEDQD VADERTRILA PSPDSLLHTP LIIKELSKVY EQRVPLLAVD RLSLAVQKGE CFGLLGFNGA GKTTTFKMLT GEESLTSGDA FVGGHRISSD VGKVRQRIGY CPQFDALLDH MTGREMLVMY ARLRGIPERH IGACVENTLR GLLLEPHANK LVRTYSGGNK RKLSTGIALI GEPAVIFLDE PSTGMDPVAR RLLWDTVARA RESGKAIIIT SHSMEECEAL CTRLAIMVQG QFKCLGSPQH LKSKFGSGYS LRAKVQSEGQ QEALEEFKAF VDLTFPGSVL EDEHQGMVHY HLPGRDLSWA KVFGILEKAK EKYGVDDYSV SQISLEQVFL SFAHLQPPTA EEGR* | |||||||||||||||||||||
Mutated AA sequence | MAVLRQLALL LWKNYTLQKR KVLVTVLELF LPLLFSGILI WLRLKIQSEN VPNATIYPGQ SIQELPLFFT FPPPGDTWEL AYIPSHSDAA KTVTETVRRA LVINMRVRGF PSEKDFEDYI RYDNCSSSVL AAVVFEHPFN HSKEPLPLAV KYHLRFSYTR RNYMWTQTGS FFLKETEGWH TTSLFPLFPN PGPREPTSPD GGEPGYIREG FLAVQHAVDR AIMEYHADAA TRQLFQRLTV TIKRFPYPPF IADPFLVAIQ YQLPLLLLLS FTYTALTIAR AVVQEKERRL KVYMRMMGLS SWLHWSAWFL LFFLFLLIAA SFMTLLFCVK VKPNVAVLSR SDPSLVLAFL LCFAISTISF SFMVSTFFSK ANMAAAFGGF LYFFTYIPYF FVAPRYNWMT LSQKLCSCLL SNVAMAMGAQ LIGKFEAKGM GIQWRDLLSP VNVDDDFCFG QVLGMLLLDS VLYGLVTWYM EAVFPGQFGV PQPWYFFIMP SYWCGKPRAV AGKEEEDSDP EKALRNEYFE AEPEDLVAGI KIKHLSKVFR VGNKDRAAVR DLNLNLYEGQ ITVLLGHNGA GKTTTLSMLT GLFPPTSGRA YISGYEISQD MVQIRKSLGL CPQHDILFDN LTVAEHLYFY AQLKGLSRQK CPEEVKQMLH IIGLEDKWNS RSRFLSGGMR RKLSIGIALI AGSKVLILDE PTSGMDAISR RAIWDLLQRQ KSDRTIVLTT HFMDEADLLG DRIAIMAKGE LQCCGSSLFL KQKYGAGYHM TLVKEPHCNP EDISQLVHHH VPNATLESSA GAELSFILPR ESTHRFEGLF AKLEKKQKEL GIASFGASIT TMEEVFLRVG KLVDSSMDIQ AIQLPALQYQ HERRASDWAV DSNLCGAMDP SDGIGALIEE ERTAVKLNTG LALHCQQFWA MFLKKAAYSW REWKMVAAQV LVPLTCVTLA LLAINYSSEL FDDPMLRLTL GEYGRTVVPF SVPGTSQLGQ QLSEHLKDAL QAEGQEPREV LGDLEEFLIF RASVEGGGFN ERCLVAASFR DVGERTVVNA LFNNQAYHSP ATALAVVDNL LFKLLCGPHA SIVVSNFPQP RSALQAAKDQ FNEGRKGFDI ALNLLFAMAF LASTFSILAV SERAVQAKHV QFVSGVHVAS FWLSALLWDL ISFLIPSLLL LVVFKAFDVR AFTRDGHMAD TLLLLLLYGW AIIPLMYLMN FFFLGAATAY TRLTIFNILS GIATFLMVTI MRIPAVKLEE LSKTLDHVFL VLPNHCLGMA VSSFYENYET RRYCTSSEVA AHYCKKYNIQ YQENFYAWSA PGVGRFVASM AASGCAYLIL LFLIETNLLQ RLRGILCALR RRRTLTELYT RMPVLPEDQD VADERTRILA PSPDSLLHTP LIIKELSKVY EQRVPLLAVD RLSLAVQKGE CFGLLGFNGA GKTTTFKMLT GEESLTSGDA FVGGHRISSD VGKVRQRIGY CPQFDALLDH MTGREMLVMY ARLRGIPERH IGACVENTLR GLLLEPHANK LVRTYSGGNK RKLSTGIALI GEPAVIFLDE PSTGMDPVAR RLLWDTVARA RESGKAIIIT SHSMEECEAL CTRLAIMVQG QFKCLGSPQH LKSKFGSGYS LRAKVQSEGQ QEALEEFKAF VDLTFPGSVL EDEHQGMVHY HLPGRDLSWA KVFGILEKAK EKYGVDDYSV SQISLEQVFL SFAHLQPPTA EEGR* | |||||||||||||||||||||
Position of stopcodon in wt / mu CDS | 5115 / 5115 | |||||||||||||||||||||
Position (AA) of stopcodon in wt / mu AA sequence | 1705 / 1705 | |||||||||||||||||||||
Position of stopcodon in wt / mu cDNA | 5809 / 5809 | |||||||||||||||||||||
Position of start ATG in wt / mu cDNA | 695 / 695 | |||||||||||||||||||||
Last intron/exon boundary | 5677 | |||||||||||||||||||||
Theoretical NMD boundary in CDS | 4932 | |||||||||||||||||||||
Length of CDS | 5115 | |||||||||||||||||||||
Coding sequence (CDS) position | 875 | |||||||||||||||||||||
cDNA position | 1569 | |||||||||||||||||||||
gDNA position | 22984 | |||||||||||||||||||||
Chromosomal position | 2317763 | |||||||||||||||||||||
Speed | 0.23 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 | Chr16:2317763T>A (GRCh38) | |||||||||||||
Gene symbol | ABCA3 | |||||||||||||
Gene constraints | LOEUF: 0.61, LOF (oe): 0.51, misssense (oe): 0.92, synonymous (oe): 1.06 (gnomAD) | |||||||||||||
Ensembl transcript ID | ENST00000382381.7 | |||||||||||||
Genbank transcript ID | ||||||||||||||
UniProt / AlphaMissense peptide | N/A | |||||||||||||
Variant type | Single base exchange | |||||||||||||
Gene region | CDS | |||||||||||||
DNA changes | c.875A>T g.22984A>T | |||||||||||||
AA changes |
| |||||||||||||
Frameshift | No | |||||||||||||
Length of protein | Normal | |||||||||||||
Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
Variant DBs |
| |||||||||||||
Protein conservation | ||||||||||||||
Protein features | N/A | |||||||||||||
Phylogenetic conservation |
| |||||||||||||
Splice sites | MaxEntScan:
| |||||||||||||
Distance from splice site | 2 | |||||||||||||
Kozak consensus sequence altered? | No | |||||||||||||
poly(A) signal | N/A | |||||||||||||
AA sequence altered | Yes | |||||||||||||
Chromosome | 16 | |||||||||||||
Strand | -1 | |||||||||||||
Original gDNA sequence snippet | TGATGGCTTCTCTCCCCAGGAGTACATGCGCATGATGGGGC | |||||||||||||
Altered gDNA sequence snippet | TGATGGCTTCTCTCCCCAGGTGTACATGCGCATGATGGGGC | |||||||||||||
Original cDNA sequence snippet | GAAGGAAAGGAGGCTGAAGGAGTACATGCGCATGATGGGGC | |||||||||||||
Altered cDNA sequence snippet | GAAGGAAAGGAGGCTGAAGGTGTACATGCGCATGATGGGGC | |||||||||||||
Wildtype AA sequence | MAVLRQLALL LWKNYTLQKR KVLVTVLELF LPLLFSGILI WLRLKIQSEN VPNATIYPGQ SIQELPLFFT FPPPGDTWEL AYIPSHSDAA KTVTETVRRA LVINMRVRGF PSEKDFEDYI RYDNCSSSVL AAVVFEHPFN HSKEPLPLAV KYHLRFSYTR RNYMWTQTGS FFLKETEGWH TTSLFPLFPN PGPREPTSPD GGEPGYIREG FLAVQHAVDR AIMEYHADAA TRQLFQRLTV TIKRFPYPPF IADPFLVAIQ YQLPLLLLLS FTYTALTIAR AVVQEKERRL KEYMRMMGLS SWLHWSAWFL LFFLFLLIAA SFMTLLFCVK VKPNVAVLSR SDPSLVLAFL LCFAISTISF SFMVSTFFSK GMGIQWRDLL SPVNVDDDFC FGQVLGMLLL DSVLYGLVTW YMEAVFPGQF GVPQPWYFFI MPSYWCGKPR AVAGKEEEDS DPEKALRNEY FEAEPEDLVA GIKIKHLSKV FRVGNKDRAA VRDLNLNLYE GQITVLLGHN GAGKTTTLSM LTGLFPPTSG RAYISGYEIS QDMVQIRKSL GLCPQHDILF DNLTVAEHLY FYAQLKGLSR QKCPEEVKQM LHIIGLEDKW NSRSRFLSGG MRRKLSIGIA LIAGSKVLIL DEPTSGMDAI SRRAIWDLLQ RQKSDRTIVL TTHFMDEADL LGDRIAIMAK GELQCCGSSL FLKQKYGAGY HMTLVKEPHC NPEDISQLVH HHVPNATLES SAGAELSFIL PRESTHRFEG LFAKLEKKQK ELGIASFGAS ITTMEEVFLR VGKLVDSSMD IQAIQLPALQ YQHERRASDW AVDSNLCGAM DPSDGIGALI EEERTAVKLN TGLALHCQQF WAMFLKKAAY SWREWKMVAA QVLVPLTCVT LALLAINYSS ELFDDPMLRL TLGEYGRTVV PFSVPGTSQL GQQLSEHLKD ALQAEGQEPR EVLGDLEEFL IFRASVEGGG FNERCLVAAS FRDVGERTVV NALFNNQAYH SPATALAVVD NLLFKLLCGP HASIVVSNFP QPRSALQAAK DQFNEGRKGF DIALNLLFAM AFLASTFSIL AVSERAVQAK HVQFVSGVHV ASFWLSALLW DLISFLIPSL LLLVVFKAFD VRAFTRDGHM ADTLLLLLLY GWAIIPLMYL MNFFFLGAAT AYTRLTIFNI LSGIATFLMV TIMRIPAVKL EELSKTLDHV FLVLPNHCLG MAVSSFYENY ETRRYCTSSE VAAHYCKKYN IQYQENFYAW SAPGVGRFVA SMAASGCAYL ILLFLIETNL LQRLRGILCA LRRRRTLTEL YTRMPVLPED QDVADERTRI LAPSPDSLLH TPLIIKELSK VYEQRVPLLA VDRLSLAVQK GECFGLLGFN GAGKTTTFKM LTGEESLTSG DAFVGGHRIS SDVGKVRQRI GYCPQFDALL DHMTGREMLV MYARLRGIPE RHIGACVENT LRGLLLEPHA NKLVRTYSGG NKRKLSTGIA LIGEPAVIFL DEPSTGMDPV ARRLLWDTVA RARESGKAII ITSHSMEECE ALCTRLAIMV QGQFKCLGSP QHLKSKFGSG YSLRAKVQSE GQQEALEEFK AFVDLTFPGS VLEDEHQGMV HYHLPGRDLS WAKVFGILEK AKEKYGVDDY SVSQISLEQV FLSFAHLQPP TAEEGR* | |||||||||||||
Mutated AA sequence | MAVLRQLALL LWKNYTLQKR KVLVTVLELF LPLLFSGILI WLRLKIQSEN VPNATIYPGQ SIQELPLFFT FPPPGDTWEL AYIPSHSDAA KTVTETVRRA LVINMRVRGF PSEKDFEDYI RYDNCSSSVL AAVVFEHPFN HSKEPLPLAV KYHLRFSYTR RNYMWTQTGS FFLKETEGWH TTSLFPLFPN PGPREPTSPD GGEPGYIREG FLAVQHAVDR AIMEYHADAA TRQLFQRLTV TIKRFPYPPF IADPFLVAIQ YQLPLLLLLS FTYTALTIAR AVVQEKERRL KVYMRMMGLS SWLHWSAWFL LFFLFLLIAA SFMTLLFCVK VKPNVAVLSR SDPSLVLAFL LCFAISTISF SFMVSTFFSK GMGIQWRDLL SPVNVDDDFC FGQVLGMLLL DSVLYGLVTW YMEAVFPGQF GVPQPWYFFI MPSYWCGKPR AVAGKEEEDS DPEKALRNEY FEAEPEDLVA GIKIKHLSKV FRVGNKDRAA VRDLNLNLYE GQITVLLGHN GAGKTTTLSM LTGLFPPTSG RAYISGYEIS QDMVQIRKSL GLCPQHDILF DNLTVAEHLY FYAQLKGLSR QKCPEEVKQM LHIIGLEDKW NSRSRFLSGG MRRKLSIGIA LIAGSKVLIL DEPTSGMDAI SRRAIWDLLQ RQKSDRTIVL TTHFMDEADL LGDRIAIMAK GELQCCGSSL FLKQKYGAGY HMTLVKEPHC NPEDISQLVH HHVPNATLES SAGAELSFIL PRESTHRFEG LFAKLEKKQK ELGIASFGAS ITTMEEVFLR VGKLVDSSMD IQAIQLPALQ YQHERRASDW AVDSNLCGAM DPSDGIGALI EEERTAVKLN TGLALHCQQF WAMFLKKAAY SWREWKMVAA QVLVPLTCVT LALLAINYSS ELFDDPMLRL TLGEYGRTVV PFSVPGTSQL GQQLSEHLKD ALQAEGQEPR EVLGDLEEFL IFRASVEGGG FNERCLVAAS FRDVGERTVV NALFNNQAYH SPATALAVVD NLLFKLLCGP HASIVVSNFP QPRSALQAAK DQFNEGRKGF DIALNLLFAM AFLASTFSIL AVSERAVQAK HVQFVSGVHV ASFWLSALLW DLISFLIPSL LLLVVFKAFD VRAFTRDGHM ADTLLLLLLY GWAIIPLMYL MNFFFLGAAT AYTRLTIFNI LSGIATFLMV TIMRIPAVKL EELSKTLDHV FLVLPNHCLG MAVSSFYENY ETRRYCTSSE VAAHYCKKYN IQYQENFYAW SAPGVGRFVA SMAASGCAYL ILLFLIETNL LQRLRGILCA LRRRRTLTEL YTRMPVLPED QDVADERTRI LAPSPDSLLH TPLIIKELSK VYEQRVPLLA VDRLSLAVQK GECFGLLGFN GAGKTTTFKM LTGEESLTSG DAFVGGHRIS SDVGKVRQRI GYCPQFDALL DHMTGREMLV MYARLRGIPE RHIGACVENT LRGLLLEPHA NKLVRTYSGG NKRKLSTGIA LIGEPAVIFL DEPSTGMDPV ARRLLWDTVA RARESGKAII ITSHSMEECE ALCTRLAIMV QGQFKCLGSP QHLKSKFGSG YSLRAKVQSE GQQEALEEFK AFVDLTFPGS VLEDEHQGMV HYHLPGRDLS WAKVFGILEK AKEKYGVDDY SVSQISLEQV FLSFAHLQPP TAEEGR* | |||||||||||||
Position of stopcodon in wt / mu CDS | 4941 / 4941 | |||||||||||||
Position (AA) of stopcodon in wt / mu AA sequence | 1647 / 1647 | |||||||||||||
Position of stopcodon in wt / mu cDNA | 5653 / 5653 | |||||||||||||
Position of start ATG in wt / mu cDNA | 713 / 713 | |||||||||||||
Last intron/exon boundary | 5521 | |||||||||||||
Theoretical NMD boundary in CDS | 4758 | |||||||||||||
Length of CDS | 4941 | |||||||||||||
Coding sequence (CDS) position | 875 | |||||||||||||
cDNA position | 1587 | |||||||||||||
gDNA position | 22984 | |||||||||||||
Chromosomal position | 2317763 | |||||||||||||
Speed | 0.22 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