Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999875 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:43699417A>GN/A show variant in all transcripts   IGV
HGNC symbol PSG4
Ensembl transcript ID ENST00000405312
Genbank transcript ID NM_002780
UniProt peptide Q00888
alteration type single base exchange
alteration region CDS
DNA changes c.718T>C
cDNA.956T>C
g.10510T>C
AA changes S240P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 240
frameshift no
known variant Reference ID: rs3859474
databasehomozygous (G/G)heterozygousallele carriers
1000G12478912138
ExAC17217-166715550
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3010.008
-0.0640.003
(flanking)-0.1580.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased10509wt: 0.9085 / mu: 0.9765 (marginal change - not scored)wt: AAGCTGTCCAAGCCC
mu: AAGCTGCCCAAGCCC		 GCTG|tcca
Donor gained105050.57mu: AGCAAAGCTGCCCAA CAAA|gctg
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      240DPVTLNLLPKLSKPYITINNLNPR
mutated  not conserved    240DPVTLNLLPKLPKPYITINNLNP
Ptroglodytes  not conserved  ENSPTRG00000040468  240DPVTLNLLPKLPKPYITINNLNP
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
start (aa)end (aa)featuredetails 
237327DOMAINIg-like C2-type 2.lost
262262DISULFIDProbable.might get lost (downstream of altered splice site)
268268CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
299299CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
310310DISULFIDProbable.might get lost (downstream of altered splice site)
332410DOMAINIg-like C2-type 3.might get lost (downstream of altered splice site)
352352CONFLICTL -> F (in Ref. 3; CAA34956).might get lost (downstream of altered splice site)
354354DISULFIDProbable.might get lost (downstream of altered splice site)
356356CONFLICTA -> G (in Ref. 3; CAA34956).might get lost (downstream of altered splice site)
394394DISULFIDProbable.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1498 / 1498
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 239 / 239
chromosome 19
strand -1
last intron/exon boundary 1482
theoretical NMD boundary in CDS 1193
length of CDS 1260
coding sequence (CDS) position 718
cDNA position
(for ins/del: last normal base / first normal base)		 956
gDNA position
(for ins/del: last normal base / first normal base)		 10510
chromosomal position
(for ins/del: last normal base / first normal base)		 43699417
original gDNA sequence snippet TTATCCACACAGCAAAGCTGTCCAAGCCCTACATCACAATC
altered gDNA sequence snippet TTATCCACACAGCAAAGCTGCCCAAGCCCTACATCACAATC
original cDNA sequence snippet TGAATCTCCTCCCAAAGCTGTCCAAGCCCTACATCACAATC
altered cDNA sequence snippet TGAATCTCCTCCCAAAGCTGCCCAAGCCCTACATCACAATC
wildtype AA sequence MGPLSAPPCT QRITWKGVLL TASLLNFWNP PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLAGYIWYKG QMTYLYHYIT SYVVDGQRII YGPAYSGRER VYSNASLLIQ NVTQEDAGSY
TLHIIKRRDG TGGVTGHFTF TLHLETPKPS ISSSNLNPRE AMEAVILTCD PATPAASYQW
WMNGQSLPMT HRLQLSKTNR TLFIFGVTKY IAGPYECEIR NPVSASRSDP VTLNLLPKLS
KPYITINNLN PRENKDVLTF TCEPKSKNYT YIWWLNGQSL PVSPRVKRPI ENRILILPNV
TRNETGPYQC EIRDRYGGIR SDPVTLNVLY GPDLPSIYPS FTYYRSGENL YLSCFAESNP
RAQYSWTING KFQLSGQKLS IPQITTKHSG LYACSVRNSA TGKESSKSIT VKVSDWILP*
mutated AA sequence MGPLSAPPCT QRITWKGVLL TASLLNFWNP PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLAGYIWYKG QMTYLYHYIT SYVVDGQRII YGPAYSGRER VYSNASLLIQ NVTQEDAGSY
TLHIIKRRDG TGGVTGHFTF TLHLETPKPS ISSSNLNPRE AMEAVILTCD PATPAASYQW
WMNGQSLPMT HRLQLSKTNR TLFIFGVTKY IAGPYECEIR NPVSASRSDP VTLNLLPKLP
KPYITINNLN PRENKDVLTF TCEPKSKNYT YIWWLNGQSL PVSPRVKRPI ENRILILPNV
TRNETGPYQC EIRDRYGGIR SDPVTLNVLY GPDLPSIYPS FTYYRSGENL YLSCFAESNP
RAQYSWTING KFQLSGQKLS IPQITTKHSG LYACSVRNSA TGKESSKSIT VKVSDWILP*
speed 1.10 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