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 0.86 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