Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.634208891195902 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM040800)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:22021517G>AN/A show variant in all transcripts   IGV
HGNC symbol SFTPC
Ensembl transcript ID ENST00000318561
Genbank transcript ID NM_001172410
UniProt peptide P11686
alteration type single base exchange
alteration region CDS
DNA changes c.557G>A
cDNA.731G>A
g.7092G>A
AA changes S186N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 186
frameshift no
known variant Reference ID: rs1124
databasehomozygous (A/A)heterozygousallele carriers
1000G1638561019
ExAC56382149127129

known disease mutation at this position, please check HGMD for details (HGMD ID CM040800)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.730.975
0.5810.988
(flanking)1.8251
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained70870.97mu: ATGGCCGTGAACACC GGCC|gtga
Donor gained70840.31mu: GGCATGGCCGTGAAC CATG|gccg
distance from splice site 56
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      186GGDPAFLGMAVSTLCGEVPLYYI*
mutated  all conserved    186LGMAVNTLCGEVPLYYI
Ptroglodytes  all identical  ENSPTRG00000020053  186LGMAVSTLCGEVPLYYI
Mmulatta  all identical  ENSMMUG00000013029  180LGMAVSTLCGEVPLYYI
Fcatus  all identical  ENSFCAG00000004717  184LGTTVSTLCGEVPLYYI
Mmusculus  all identical  ENSMUSG00000022097  182AFLGLAVSTLCGELPLYYI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000031314  157KVLCGSLPVYW
protein features
start (aa)end (aa)featuredetails 
59197PROPEP /FTId=PRO_0000033479.lost
94197DOMAINBRICHOS.lost
183189HELIXlost
194197STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 594 / 594
position (AA) of stopcodon in wt / mu AA sequence 198 / 198
position of stopcodon in wt / mu cDNA 768 / 768
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 175 / 175
chromosome 8
strand 1
last intron/exon boundary 787
theoretical NMD boundary in CDS 562
length of CDS 594
coding sequence (CDS) position 557
cDNA position
(for ins/del: last normal base / first normal base)		 731
gDNA position
(for ins/del: last normal base / first normal base)		 7092
chromosomal position
(for ins/del: last normal base / first normal base)		 22021517
original gDNA sequence snippet CTTCCTGGGCATGGCCGTGAGCACCCTGTGTGGCGAGGTGC
altered gDNA sequence snippet CTTCCTGGGCATGGCCGTGAACACCCTGTGTGGCGAGGTGC
original cDNA sequence snippet CTTCCTGGGCATGGCCGTGAGCACCCTGTGTGGCGAGGTGC
altered cDNA sequence snippet CTTCCTGGGCATGGCCGTGAACACCCTGTGTGGCGAGGTGC
wildtype AA sequence MDVGSKEVLM ESPPDYSAAP RGRFGIPCCP VHLKRLLIVV VVVVLIVVVI VGALLMGLHM
SQKHTEMVLE MSIGAPEAQQ RLALSEHLVT TATFSIGSTG LVVYDYQQLL IAYKPAPGTC
CYIMKIAPES IPSLEALTRK VHNFQMECSL QAKPAVPTSK LGQAEGRDAG SAPSGGDPAF
LGMAVSTLCG EVPLYYI*
mutated AA sequence MDVGSKEVLM ESPPDYSAAP RGRFGIPCCP VHLKRLLIVV VVVVLIVVVI VGALLMGLHM
SQKHTEMVLE MSIGAPEAQQ RLALSEHLVT TATFSIGSTG LVVYDYQQLL IAYKPAPGTC
CYIMKIAPES IPSLEALTRK VHNFQMECSL QAKPAVPTSK LGQAEGRDAG SAPSGGDPAF
LGMAVNTLCG EVPLYYI*
speed 0.57 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