Yum, tasty mutations...

MutationT@ster 2025

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...
Querying Taster for transcript #1: ENST00000301732
Querying Taster for transcript #2: ENST00000382381
MT speed 0.45 s - this script 2.930901 s

Transcript summary:

Permalink

Yum, tasty mutations...

MutationT@ster 2025

Variant:

16:2317763T>A_1_ENST00000301732

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 94|6 (del | benign) ?
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
AAE:E292V?
Score:121
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs149989682
gnomADhomozygous (A/A)heterozygousallele carriers
2072767296
Protein conservation
SpeciesMatchGeneAAAlignment
Human      292AVVQEKERRLKEYMRMMGLSSWLH
mutated  not conserved    292AVVQEKERRLKVYMRMMGLS
Ptroglodytes  all identical    292AVVQEKERRLKEYMRMMGLS
Mmulatta  all identical    292AVVQEKERRLKEYMRMMGLS
Fcatus  all identical    292AVVQEKERRLKEYMRMMGLS
Mmusculus  all identical    292AVVQEKEKKLKEYMRMMGLN
Ggallus  all identical    318AVVHEKEKKLKEYMHMMGLS
Trubripes  all identical    284SVVQEKERKLKEYMKMMGL
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical    308ALVLEKERKLKEYMRV
Protein features
Start (aa)End (aa)FeatureDetails 
11704CHAINlost
1751704CHAINlost
290295HELIXlost
Phylogenetic conservation
PhyloPPhastCons
(flanking)1.8721
7.4121
(flanking)7.3091
?
Splice sites MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor weakened22982wt: 9.88 / mu: 11.27- wt: ctctccccag|GAGTACATGC
 mu: ctctccccag|GTGTACATGC
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

Back to summary table

Yum, tasty mutations...

MutationT@ster 2025

Variant:

16:2317763T>A_2_ENST00000382381

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

  • Model: simple_aae
  • Tree vote: 97|3 (del | benign) ?
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
AAE:E292V?
Score:121
Frameshift No
Length of protein Normal
Pathogenic variant (ClinVar) Variant not listed in ClinVar as (likely) pathogenic.
Variant DBs
dbSNP IDrs149989682
gnomADhomozygous (A/A)heterozygousallele carriers
2072767296
Protein conservation
SpeciesMatchGeneAAAlignment
Human      292AVVQEKERRLKEYMRMMGLSSWLH
mutated  not conserved    292AVVQEKERRLKVYMRMMGLS
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
Protein features N/A
Phylogenetic conservation
PhyloPPhastCons
(flanking)1.8721
7.4121
(flanking)7.3091
?
Splice sites MaxEntScan:
effectgDNA positionscoresequence exon-intron border
Acceptor weakened22982wt: 9.88 / mu: 11.27- wt: ctctccccag|GAGTACATGC
 mu: ctctccccag|GTGTACATGC
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

Back to summary table