Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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...
found 10 transcript(s)...
Querying Taster for transcript #1: ENST00000553728
Querying Taster for transcript #2: ENST00000341749
Querying Taster for transcript #3: ENST00000557038
Querying Taster for transcript #4: ENST00000396165
Querying Taster for transcript #5: ENST00000280083
Querying Taster for transcript #6: ENST00000556148
Querying Taster for transcript #7: ENST00000348007
Querying Taster for transcript #8: ENST00000553352
Querying Taster for transcript #9: ENST00000341502
Querying Taster for transcript #10: ENST00000396158
MT speed 0 s - this script 7.17964 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MIA2polymorphism_automatic8.40438829641244e-14simple_aaeaffectedI699Vsingle base exchangers1140952show file
MIA2polymorphism_automatic1.51989532071184e-13simple_aaeaffectedI687Vsingle base exchangers1140952show file
MIA2polymorphism_automatic1.51989532071184e-13simple_aaeaffectedI619Vsingle base exchangers1140952show file
MIA2polymorphism_automatic1.51989532071184e-13simple_aaeaffectedI670Vsingle base exchangers1140952show file
MIA2polymorphism_automatic1.51989532071184e-13simple_aaeaffectedI699Vsingle base exchangers1140952show file
MIA2polymorphism_automatic1.51989532071184e-13simple_aaeaffectedI624Vsingle base exchangers1140952show file
MIA2polymorphism_automatic1.51989532071184e-13simple_aaeaffectedI670Vsingle base exchangers1140952show file
MIA2polymorphism_automatic1.51989532071184e-13simple_aaeaffectedI704Vsingle base exchangers1140952show file
MIA2polymorphism_automatic5.71986902286881e-13simple_aaeaffectedI656Vsingle base exchangers1140952show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999916 (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 ENST00000341502
Genbank transcript ID N/A
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2095A>G
cDNA.2431A>G
g.83541A>G
AA changes I699V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 699
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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      699GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    699GPGFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1220SSGFGPPPFPPVRPPTMPMDPRG
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000023516  600PPGPPLMSMPPPMDP-RDPHFP--HRG
Dmelanogaster  no alignment  FBgn0031842  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
502804COMPBIASPro-rich.lost
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 2316 / 2316
position (AA) of stopcodon in wt / mu AA sequence 772 / 772
position of stopcodon in wt / mu cDNA 2652 / 2652
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 337 / 337
chromosome 14
strand 1
last intron/exon boundary 2585
theoretical NMD boundary in CDS 2198
length of CDS 2316
coding sequence (CDS) position 2095
cDNA position
(for ins/del: last normal base / first normal base)		 2431
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 MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL
LEGPLRLSPL LPGGGGRGSR GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD
QDRRMMFPPP GQSYPDSALP PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME
SSRNDTKDDL GNLNVPDSSL PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP
PPPPGAMFGA SRDYFPPGDF PGPPPAPFAS ARSPPGAGAP ASGRGLGGPQ K*
mutated AA sequence MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL
LEGPLRLSPL LPGGGGRGSR GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD
QDRRMMFPPP GQSYPDSALP PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME
SSRNDTKDDL GNLNVPDSSL PAENEATGPG FVPPPLAPVR GPLFPVDARG PFLRRGPPFP
PPPPGAMFGA SRDYFPPGDF PGPPPAPFAS ARSPPGAGAP ASGRGLGGPQ K*
speed 0.97 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
back to results table
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 ENST00000341749
Genbank transcript ID NM_203354
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2059A>G
cDNA.2162A>G
g.83541A>G
AA changes I687V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 687
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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      687GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    687GPGFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
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
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 2379 / 2379
position (AA) of stopcodon in wt / mu AA sequence 793 / 793
position of stopcodon in wt / mu cDNA 2482 / 2482
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 104 / 104
chromosome 14
strand 1
last intron/exon boundary 2316
theoretical NMD boundary in CDS 2162
length of CDS 2379
coding sequence (CDS) position 2059
cDNA position
(for ins/del: last normal base / first normal base)		 2162
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 MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPIRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPGDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*
mutated AA sequence MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPVRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPGDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*
speed 0.89 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
back to results table
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 ENST00000557038
Genbank transcript ID N/A
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.1855A>G
cDNA.2123A>G
g.83541A>G
AA changes I619V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 619
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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      619GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    619GPGFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1222SSGFGPPPFPPVRPPTMPMDPRG
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000023516  597GP--LPPPGPPLMSMPPPMDPRD
Dmelanogaster  no alignment  FBgn0031842  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
502804COMPBIASPro-rich.lost
635635MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
647647MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
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 2175 / 2175
position (AA) of stopcodon in wt / mu AA sequence 725 / 725
position of stopcodon in wt / mu cDNA 2443 / 2443
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 269 / 269
chromosome 14
strand 1
last intron/exon boundary 2277
theoretical NMD boundary in CDS 1958
length of CDS 2175
coding sequence (CDS) position 1855
cDNA position
(for ins/del: last normal base / first normal base)		 2123
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 MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEAT CEKLNRSNSE
LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES KSLKSQVAEA KMTFKIFQMN
EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN KQKVTFEDSK VHAEQVLNDK
ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE NGAYLDNPPK GALKKLIHAA
KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE QASLQSENTH FENENQKLQQ
KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK ISHATEELET YRKRAKDLEE
ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE NAHNRQKLTE TELKFELLEK
DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL LEGPLRLSPL LPGGGGRGSR
GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD QDRRMMFPPP GQSYPDSALP
PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME SSRNDTKDDL GNLNVPDSSL
PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP PPPPGAMFGA SRDYFPPGDF
PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS EFPSGLIPPS NEPATEHPEP
QQET*
mutated AA sequence MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEAT CEKLNRSNSE
LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES KSLKSQVAEA KMTFKIFQMN
EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN KQKVTFEDSK VHAEQVLNDK
ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE NGAYLDNPPK GALKKLIHAA
KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE QASLQSENTH FENENQKLQQ
KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK ISHATEELET YRKRAKDLEE
ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE NAHNRQKLTE TELKFELLEK
DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL LEGPLRLSPL LPGGGGRGSR
GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD QDRRMMFPPP GQSYPDSALP
PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME SSRNDTKDDL GNLNVPDSSL
PAENEATGPG FVPPPLAPVR GPLFPVDARG PFLRRGPPFP PPPPGAMFGA SRDYFPPGDF
PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS EFPSGLIPPS NEPATEHPEP
QQET*
speed 0.87 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
back to results table
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 ENST00000396165
Genbank transcript ID N/A
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2008A>G
cDNA.2592A>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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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 2912 / 2912
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 585 / 585
chromosome 14
strand 1
last intron/exon boundary 2746
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)		 2592
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 0.68 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
back to results table
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 ENST00000280083
Genbank transcript ID NM_005930
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2095A>G
cDNA.2409A>G
g.83541A>G
AA changes I699V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 699
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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      699GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    699GPGFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1220SSGFGPPPFPPVRPPTMPMDPRG
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
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 2415 / 2415
position (AA) of stopcodon in wt / mu AA sequence 805 / 805
position of stopcodon in wt / mu cDNA 2729 / 2729
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 315 / 315
chromosome 14
strand 1
last intron/exon boundary 2563
theoretical NMD boundary in CDS 2198
length of CDS 2415
coding sequence (CDS) position 2095
cDNA position
(for ins/del: last normal base / first normal base)		 2409
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 MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL
LEGPLRLSPL LPGGGGRGSR GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD
QDRRMMFPPP GQSYPDSALP PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME
SSRNDTKDDL GNLNVPDSSL PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP
PPPPGAMFGA SRDYFPPGDF PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS
EFPSGLIPPS NEPATEHPEP QQET*
mutated AA sequence MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL
LEGPLRLSPL LPGGGGRGSR GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD
QDRRMMFPPP GQSYPDSALP PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME
SSRNDTKDDL GNLNVPDSSL PAENEATGPG FVPPPLAPVR GPLFPVDARG PFLRRGPPFP
PPPPGAMFGA SRDYFPPGDF PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS
EFPSGLIPPS NEPATEHPEP QQET*
speed 1.02 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
back to results table
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 ENST00000556148
Genbank transcript ID N/A
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.1870A>G
cDNA.2049A>G
g.83541A>G
AA changes I624V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 624
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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      624GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    624GPGFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1220SSGFGPPPFPPVRPPTMPMDPRG
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
635635MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
647647MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
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 2190 / 2190
position (AA) of stopcodon in wt / mu AA sequence 730 / 730
position of stopcodon in wt / mu cDNA 2369 / 2369
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 180 / 180
chromosome 14
strand 1
last intron/exon boundary 2203
theoretical NMD boundary in CDS 1973
length of CDS 2190
coding sequence (CDS) position 1870
cDNA position
(for ins/del: last normal base / first normal base)		 2049
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 MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEVE NQMATCEKLN
RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS LEDESKSLKS QVAEAKMTFK
IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ VSELNKQKVT FEDSKVHAEQ
VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM NSESENGAYL DNPPKGALKK
LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK NLQTEQASLQ SENTHFENEN
QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS KVDEKISHAT EELETYRKRA
KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN DLRKENAHNR QKLTETELKF
ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL SPPTLLEGPL RLSPLLPGGG
GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL SPPWDQDRRM MFPPPGQSYP
DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM PSEMESSRND TKDDLGNLNV
PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR GPPFPPPPPG AMFGASRDYF
PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH SEGRSEFPSG LIPPSNEPAT
EHPEPQQET*
mutated AA sequence MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEVE NQMATCEKLN
RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS LEDESKSLKS QVAEAKMTFK
IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ VSELNKQKVT FEDSKVHAEQ
VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM NSESENGAYL DNPPKGALKK
LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK NLQTEQASLQ SENTHFENEN
QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS KVDEKISHAT EELETYRKRA
KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN DLRKENAHNR QKLTETELKF
ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL SPPTLLEGPL RLSPLLPGGG
GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL SPPWDQDRRM MFPPPGQSYP
DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM PSEMESSRND TKDDLGNLNV
PDSSLPAENE ATGPGFVPPP LAPVRGPLFP VDARGPFLRR GPPFPPPPPG AMFGASRDYF
PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH SEGRSEFPSG LIPPSNEPAT
EHPEPQQET*
speed 0.98 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
back to results table
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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 1.20 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
back to results table
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 ENST00000396158
Genbank transcript ID NM_001247989
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2110A>G
cDNA.2446A>G
g.83541A>G
AA changes I704V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 704
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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      704GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    704GPGFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1220SSGFGPPPFPPVRPPTMPMDPRG
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
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 2430 / 2430
position (AA) of stopcodon in wt / mu AA sequence 810 / 810
position of stopcodon in wt / mu cDNA 2766 / 2766
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 337 / 337
chromosome 14
strand 1
last intron/exon boundary 2600
theoretical NMD boundary in CDS 2213
length of CDS 2430
coding sequence (CDS) position 2110
cDNA position
(for ins/del: last normal base / first normal base)		 2446
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 MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEVE NQMATCEKLN RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS
LEDESKSLKS QVAEAKMTFK IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ
VSELNKQKVT FEDSKVHAEQ VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM
NSESENGAYL DNPPKGALKK LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK
NLQTEQASLQ SENTHFENEN QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS
KVDEKISHAT EELETYRKRA KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN
DLRKENAHNR QKLTETELKF ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL
SPPTLLEGPL RLSPLLPGGG GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL
SPPWDQDRRM MFPPPGQSYP DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM
PSEMESSRND TKDDLGNLNV PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR
GPPFPPPPPG AMFGASRDYF PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH
SEGRSEFPSG LIPPSNEPAT EHPEPQQET*
mutated AA sequence MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEVE NQMATCEKLN RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS
LEDESKSLKS QVAEAKMTFK IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ
VSELNKQKVT FEDSKVHAEQ VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM
NSESENGAYL DNPPKGALKK LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK
NLQTEQASLQ SENTHFENEN QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS
KVDEKISHAT EELETYRKRA KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN
DLRKENAHNR QKLTETELKF ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL
SPPTLLEGPL RLSPLLPGGG GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL
SPPWDQDRRM MFPPPGQSYP DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM
PSEMESSRND TKDDLGNLNV PDSSLPAENE ATGPGFVPPP LAPVRGPLFP VDARGPFLRR
GPPFPPPPPG AMFGASRDYF PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH
SEGRSEFPSG LIPPSNEPAT EHPEPQQET*
speed 1.22 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999428 (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 ENST00000348007
Genbank transcript ID NM_001247988
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.1966A>G
cDNA.2012A>G
g.83541A>G
AA changes I656V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 656
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 increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
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
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
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      656GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    656GPGFVPPPLAPVRGPL
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1220SSGFGPPPFPPVRPPTMPMDPRG
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000023516  596GP--LPPPGPPLMSMPPPMDPRD
Dmelanogaster  all conserved  FBgn0031842  1290PLLNMPNPL-------
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 2286 / 2286
position (AA) of stopcodon in wt / mu AA sequence 762 / 762
position of stopcodon in wt / mu cDNA 2332 / 2332
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 47 / 47
chromosome 14
strand 1
last intron/exon boundary 2166
theoretical NMD boundary in CDS 2069
length of CDS 2286
coding sequence (CDS) position 1966
cDNA position
(for ins/del: last normal base / first normal base)		 2012
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 MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGRGSRGPG NPLDHQITNE RGESSCDRLT
DPHRAPSDTG SLSPPWDQDR RMMFPPPGQS YPDSALPPQR QDRFCSNSGR LSGPAELRSF
NMPSLDKMDG SMPSEMESSR NDTKDDLGNL NVPDSSLPAE NEATGPGFVP PPLAPIRGPL
FPVDARGPFL RRGPPFPPPP PGAMFGASRD YFPPGDFPGP PPAPFAMRNV YPPRGFPPYL
PPRPGFFPPP PHSEGRSEFP SGLIPPSNEP ATEHPEPQQE T*
mutated AA sequence MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGRGSRGPG NPLDHQITNE RGESSCDRLT
DPHRAPSDTG SLSPPWDQDR RMMFPPPGQS YPDSALPPQR QDRFCSNSGR LSGPAELRSF
NMPSLDKMDG SMPSEMESSR NDTKDDLGNL NVPDSSLPAE NEATGPGFVP PPLAPVRGPL
FPVDARGPFL RRGPPFPPPP PGAMFGASRD YFPPGDFPGP PPAPFAMRNV YPPRGFPPYL
PPRPGFFPPP PHSEGRSEFP SGLIPPSNEP ATEHPEPQQE T*
speed 0.96 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
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Problems

data problem

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