Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999848 (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) chr14:39818028A>GN/A show variant in all transcripts   IGV
HGNC symbol MIA2
Ensembl transcript ID ENST00000553352
Genbank transcript ID N/A
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2008A>G
cDNA.2740A>G
g.83541A>G
AA changes I670V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 670
frameshift no
known variant Reference ID: rs1140952
databasehomozygous (G/G)heterozygousallele carriers
1000G41910881507
ExAC95161373523251
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3810
-0.3470
(flanking)0.9680.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
Acc marginally increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83531wt: 0.9921 / mu: 0.9928 (marginal change - not scored)wt: CCTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCC
mu: CCTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCC		 acct|CTTG
Acc increased83533wt: 0.70 / mu: 0.86wt: TGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCAT
mu: TGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCAT		 ctct|TGCT
Donor gained835400.85mu: GCTCCAGTCAGAGGT TCCA|gtca
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      670GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    670GFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1221SSGFGPPPFPPVRPPTMPMDPRG
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000023516  600GP--LPPPGPPLMSMPPPMDPRD
Dmelanogaster  no alignment  FBgn0031842  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
502804COMPBIASPro-rich.lost
678678MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
776776CONFLICTS -> F (in Ref. 2; AAN77610).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2328 / 2328
position (AA) of stopcodon in wt / mu AA sequence 776 / 776
position of stopcodon in wt / mu cDNA 3060 / 3060
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 733 / 733
chromosome 14
strand 1
last intron/exon boundary 2894
theoretical NMD boundary in CDS 2111
length of CDS 2328
coding sequence (CDS) position 2008
cDNA position
(for ins/del: last normal base / first normal base)		 2740
gDNA position
(for ins/del: last normal base / first normal base)		 83541
chromosomal position
(for ins/del: last normal base / first normal base)		 39818028
original gDNA sequence snippet TTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCA
altered gDNA sequence snippet TTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCCA
original cDNA sequence snippet TTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCA
altered cDNA sequence snippet TTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCCA
wildtype AA sequence MRPDSNLYGF PWELVICAAV VGFFAVLFFL WRSFRSVRSR LYVGREKKLA LMLSGLIEEK
SKLLEKFSLV QKEYEGYEVE SSLKDASFEK EATEAQSLEA TCEKLNRSNS ELEDEILCLE
KELKEEKSKH SEQDELMADI SKRIQSLEDE SKSLKSQVAE AKMTFKIFQM NEERLKIAIK
DALNENSQLQ ESQKQLLQEA EVWKEQVSEL NKQKVTFEDS KVHAEQVLND KESHIKTLTE
RLLKMKDWAA MLGEDITDDD NLELEMNSES ENGAYLDNPP KGALKKLIHA AKLNASLKTL
EGERNQIYIQ LSEVDKTKEE LTEHIKNLQT EQASLQSENT HFENENQKLQ QKLKVMTELY
QENEMKLHRK LTVEENYRLE KEEKLSKVDE KISHATEELE TYRKRAKDLE EELERTIHSY
QGQIISHEKK AHDNWLAARN AERNLNDLRK ENAHNRQKLT ETELKFELLE KDPYALDVPN
TAFGREHSPY GPSPLGWPSS ETRAFLSPPT LLEGPLRLSP LLPGGGGRGS RGPGNPLDHQ
ITNERGESSC DRLTDPHRAP SDTGSLSPPW DQDRRMMFPP PGQSYPDSAL PPQRQDRFCS
NSGRLSGPAE LRSFNMPSLD KMDGSMPSEM ESSRNDTKDD LGNLNVPDSS LPAENEATGP
GFVPPPLAPI RGPLFPVDAR GPFLRRGPPF PPPPPGAMFG ASRDYFPPGD FPGPPPAPFA
MRNVYPPRGF PPYLPPRPGF FPPPPHSEGR SEFPSGLIPP SNEPATEHPE PQQET*
mutated AA sequence MRPDSNLYGF PWELVICAAV VGFFAVLFFL WRSFRSVRSR LYVGREKKLA LMLSGLIEEK
SKLLEKFSLV QKEYEGYEVE SSLKDASFEK EATEAQSLEA TCEKLNRSNS ELEDEILCLE
KELKEEKSKH SEQDELMADI SKRIQSLEDE SKSLKSQVAE AKMTFKIFQM NEERLKIAIK
DALNENSQLQ ESQKQLLQEA EVWKEQVSEL NKQKVTFEDS KVHAEQVLND KESHIKTLTE
RLLKMKDWAA MLGEDITDDD NLELEMNSES ENGAYLDNPP KGALKKLIHA AKLNASLKTL
EGERNQIYIQ LSEVDKTKEE LTEHIKNLQT EQASLQSENT HFENENQKLQ QKLKVMTELY
QENEMKLHRK LTVEENYRLE KEEKLSKVDE KISHATEELE TYRKRAKDLE EELERTIHSY
QGQIISHEKK AHDNWLAARN AERNLNDLRK ENAHNRQKLT ETELKFELLE KDPYALDVPN
TAFGREHSPY GPSPLGWPSS ETRAFLSPPT LLEGPLRLSP LLPGGGGRGS RGPGNPLDHQ
ITNERGESSC DRLTDPHRAP SDTGSLSPPW DQDRRMMFPP PGQSYPDSAL PPQRQDRFCS
NSGRLSGPAE LRSFNMPSLD KMDGSMPSEM ESSRNDTKDD LGNLNVPDSS LPAENEATGP
GFVPPPLAPV RGPLFPVDAR GPFLRRGPPF PPPPPGAMFG ASRDYFPPGD FPGPPPAPFA
MRNVYPPRGF PPYLPPRPGF FPPPPHSEGR SEFPSGLIPP SNEPATEHPE PQQET*
speed 1.33 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