Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000301732
Querying Taster for transcript #2: ENST00000382381
Querying Taster for transcript #3: ENST00000567910
MT speed 0 s - this script 3.102967 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCA3disease_causing_automatic5.31557638325639e-05simple_aae0L101Psingle base exchangers121909182show file
ABCA3disease_causing_automatic5.31557638325639e-05simple_aae0L101Psingle base exchangers121909182show file
ABCA3disease_causing_automatic0.00102831711027559simple_aae0L101Psingle base exchangers121909182show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 5.31557638325639e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040354)
  • known disease mutation: rs8012 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:2376028A>GN/A show variant in all transcripts   IGV
HGNC symbol ABCA3
Ensembl transcript ID ENST00000301732
Genbank transcript ID NM_001089
UniProt peptide Q99758
alteration type single base exchange
alteration region CDS
DNA changes c.302T>C
cDNA.1003T>C
g.14720T>C
AA changes L101P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 101
frameshift no
known variant Reference ID: rs121909182
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8012 (pathogenic for Surfactant metabolism dysfunction, pulmonary, 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8370
2.9870.009
(flanking)-0.10
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      101AKTVTETVRRALVINMRVRGFPSE
mutated  not conserved    101AKTVTETVRRAPVINMRVRGFPS
Ptroglodytes  all identical  ENSPTRG00000007647  101AKTVTETVRRALVINMRVRGFPS
Mmulatta  all identical  ENSMMUG00000019242  163AKTVTETVRRALVINMRVRGFPS
Fcatus  all identical  ENSFCAG00000007691  160VKTITETARRTLVINMRARGFRS
Mmusculus  not conserved  ENSMUSG00000024130  101ARTITETVKREFMIKMRVHGFSS
Ggallus  all conserved  ENSGALG00000001967  93PERCTAACQQPWKSPLKMLINTRAQ
Trubripes  no alignment  ENSTRUG00000007310  n/a
Drerio  no alignment  ENSDARG00000091729  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
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 5816 / 5816
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 702 / 702
chromosome 16
strand -1
last intron/exon boundary 5685
theoretical NMD boundary in CDS 4933
length of CDS 5115
coding sequence (CDS) position 302
cDNA position
(for ins/del: last normal base / first normal base)		 1003
gDNA position
(for ins/del: last normal base / first normal base)		 14720
chromosomal position
(for ins/del: last normal base / first normal base)		 2376028
original gDNA sequence snippet TGAGACAGTGCGCAGGGCACTTGTGATCAACATGCGAGGTG
altered gDNA sequence snippet TGAGACAGTGCGCAGGGCACCTGTGATCAACATGCGAGGTG
original cDNA sequence snippet TGAGACAGTGCGCAGGGCACTTGTGATCAACATGCGAGTGC
altered cDNA sequence snippet TGAGACAGTGCGCAGGGCACCTGTGATCAACATGCGAGTGC
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 PVINMRVRGF 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*
speed 0.89 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 5.31557638325639e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040354)
  • known disease mutation: rs8012 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:2376028A>GN/A show variant in all transcripts   IGV
HGNC symbol ABCA3
Ensembl transcript ID ENST00000382381
Genbank transcript ID N/A
UniProt peptide Q99758
alteration type single base exchange
alteration region CDS
DNA changes c.302T>C
cDNA.1014T>C
g.14720T>C
AA changes L101P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 101
frameshift no
known variant Reference ID: rs121909182
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8012 (pathogenic for Surfactant metabolism dysfunction, pulmonary, 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8370
2.9870.009
(flanking)-0.10
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      101AKTVTETVRRALVINMRVRGFPSE
mutated  not conserved    101AKTVTETVRRAPVINMRVRGFPS
Ptroglodytes  all identical  ENSPTRG00000007647  101AKTVTETVRRALVINMRVRGFPS
Mmulatta  all identical  ENSMMUG00000019242  163AKTVTETVRRALVINMRVRGFPS
Fcatus  all identical  ENSFCAG00000007691  160VKTITETARRTLVINMRARGFRS
Mmusculus  not conserved  ENSMUSG00000024130  101ARTITETVKREFMIKMRVHGFSS
Ggallus  all conserved  ENSGALG00000001967  93PERCTAACQQPWKSPLKMLINTRAQ
Trubripes  no alignment  ENSTRUG00000007310  n/a
Drerio  no alignment  ENSDARG00000091729  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
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
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 713 / 713
chromosome 16
strand -1
last intron/exon boundary 5522
theoretical NMD boundary in CDS 4759
length of CDS 4941
coding sequence (CDS) position 302
cDNA position
(for ins/del: last normal base / first normal base)		 1014
gDNA position
(for ins/del: last normal base / first normal base)		 14720
chromosomal position
(for ins/del: last normal base / first normal base)		 2376028
original gDNA sequence snippet TGAGACAGTGCGCAGGGCACTTGTGATCAACATGCGAGGTG
altered gDNA sequence snippet TGAGACAGTGCGCAGGGCACCTGTGATCAACATGCGAGGTG
original cDNA sequence snippet TGAGACAGTGCGCAGGGCACTTGTGATCAACATGCGAGTGC
altered cDNA sequence snippet TGAGACAGTGCGCAGGGCACCTGTGATCAACATGCGAGTGC
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 PVINMRVRGF 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*
speed 0.88 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.00102831711027559 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040354)
  • known disease mutation: rs8012 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:2376028A>GN/A show variant in all transcripts   IGV
HGNC symbol ABCA3
Ensembl transcript ID ENST00000567910
Genbank transcript ID N/A
UniProt peptide Q99758
alteration type single base exchange
alteration region CDS
DNA changes c.302T>C
cDNA.710T>C
g.14720T>C
AA changes L101P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 101
frameshift no
known variant Reference ID: rs121909182
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8012 (pathogenic for Surfactant metabolism dysfunction, pulmonary, 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040354)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8370
2.9870.009
(flanking)-0.10
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      101AKTVTETVRRALVINMRVRGFPSE
mutated  not conserved    101AKTVTETVRRAPVINMRVRGFPS
Ptroglodytes  all identical  ENSPTRG00000007647  101AKTVTETVRRALVINMRVRGFPS
Mmulatta  all identical  ENSMMUG00000019242  163AKTVTETVRRALVINMRVRGFPS
Fcatus  all identical  ENSFCAG00000007691  160VKTITETARRTLVINMRARGFRS
Mmusculus  not conserved  ENSMUSG00000024130  101ARTITETVKREFMIKMRVHGFSS
Ggallus  all conserved  ENSGALG00000001967  93PERCTAACQQPWKSPLKMLINTRAQ
Trubripes  all identical  ENSTRUG00000007310  1271TGRETLSMYARLRGIP-
Drerio  no alignment  ENSDARG00000091729  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 630 / 630
position (AA) of stopcodon in wt / mu AA sequence 210 / 210
position of stopcodon in wt / mu cDNA 1038 / 1038
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 409 / 409
chromosome 16
strand -1
last intron/exon boundary 856
theoretical NMD boundary in CDS 397
length of CDS 630
coding sequence (CDS) position 302
cDNA position
(for ins/del: last normal base / first normal base)		 710
gDNA position
(for ins/del: last normal base / first normal base)		 14720
chromosomal position
(for ins/del: last normal base / first normal base)		 2376028
original gDNA sequence snippet TGAGACAGTGCGCAGGGCACTTGTGATCAACATGCGAGGTG
altered gDNA sequence snippet TGAGACAGTGCGCAGGGCACCTGTGATCAACATGCGAGGTG
original cDNA sequence snippet TGAGACAGTGCGCAGGGCACTTGTGATCAACATGCGAGTGC
altered cDNA sequence snippet TGAGACAGTGCGCAGGGCACCTGTGATCAACATGCGAGTGC
wildtype AA sequence MAVLRQLALL LWKNYTLQKR KVLVTVLELF LPLLFSGILI WLRLKIQSEN VPNATIYPGQ
SIQELPLFFT FPPPGDTWEL AYIPSHSDAA KTVTETVRRA LVINMRVRGF PSEKDFEDYI
RYDNCSSSVL AAVVFEHPFN HSKEPLPLAV KYHLRFSYTR RNYMWTQTGS FFLKETEGWH
TTSLFPLFPN PGPREPTSPD GGEPGEKLG*
mutated AA sequence MAVLRQLALL LWKNYTLQKR KVLVTVLELF LPLLFSGILI WLRLKIQSEN VPNATIYPGQ
SIQELPLFFT FPPPGDTWEL AYIPSHSDAA KTVTETVRRA PVINMRVRGF PSEKDFEDYI
RYDNCSSSVL AAVVFEHPFN HSKEPLPLAV KYHLRFSYTR RNYMWTQTGS FFLKETEGWH
TTSLFPLFPN PGPREPTSPD GGEPGEKLG*
speed 0.13 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
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Problems