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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000376222
Querying Taster for transcript #2: ENST00000364810
Querying Taster for transcript #3: ENST00000399172
Querying Taster for transcript #4: ENST00000449934
MT speed 0 s - this script 5.113542 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MICApolymorphism_automatic7.20820070299055e-11simple_aaeaffectedR190Wsingle base exchangers1051798show file
MICApolymorphism_automatic7.20820070299055e-11simple_aaeaffectedR95Wsingle base exchangers1051798show file
MICApolymorphism_automatic8.89539553128316e-11simple_aaeaffectedR233Wsingle base exchangers1051798show file
MICApolymorphism_automatic8.89539553128316e-11simple_aaeaffectedR233Wsingle base exchangers1051798show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999927918 (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) chr6:31379807C>TN/A show variant in all transcripts   IGV
HGNC symbol MICA
Ensembl transcript ID ENST00000399172
Genbank transcript ID N/A
UniProt peptide Q29983
alteration type single base exchange
alteration region CDS
DNA changes c.568C>T
cDNA.662C>T
g.12247C>T
AA changes R190W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 190
frameshift no
known variant Reference ID: rs1051798
databasehomozygous (T/T)heterozygousallele carriers
1000G34811271475
ExAC52982217127469
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0940.001
-2.6730
(flanking)-0.6630
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased12249wt: 0.44 / mu: 0.52wt: GCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGCG
mu: GCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGCG		 ccgg|AATA
Acc increased12245wt: 0.25 / mu: 0.56wt: CAGGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCT
mu: CAGGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCT		 atcc|CCGG
Acc marginally increased12248wt: 0.8416 / mu: 0.8428 (marginal change - not scored)wt: GGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGC
mu: GGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGC		 cccg|GAAT
Acc marginally increased12247wt: 0.6265 / mu: 0.6347 (marginal change - not scored)wt: GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
mu: GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG		 cccc|GGAA
Donor marginally increased12245wt: 0.2960 / mu: 0.3063 (marginal change - not scored)wt: CTATCCCCGGAATAT
mu: CTATCCCTGGAATAT		 ATCC|ccgg
distance from splice site 84
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      190TVTCRASSFYPRNIILTWRQDGVS
mutated  not conserved    190TCRASSFYPWNIILTWRQDGV
Ptroglodytes  all identical  ENSPTRG00000017957  233TVTCWASSFYPRNITLTWR
Mmulatta  not conserved  ENSMMUG00000006609  233TVTCRASGFYPGNITLTWRQD
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000030689  225KLHCRVYGFYPRDVEVKWIK
protein features
start (aa)end (aa)featuredetails 
24307TOPO_DOMExtracellular (Potential).lost
177196HELIXlost
207296DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
208213STRANDmight get lost (downstream of altered splice site)
210210CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
217233STRANDmight get lost (downstream of altered splice site)
220220CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
225225DISULFIDmight get lost (downstream of altered splice site)
236241STRANDmight get lost (downstream of altered splice site)
248250TURNmight get lost (downstream of altered splice site)
251253STRANDmight get lost (downstream of altered splice site)
260262STRANDmight get lost (downstream of altered splice site)
261261CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
264273STRANDmight get lost (downstream of altered splice site)
277279HELIXmight get lost (downstream of altered splice site)
280286STRANDmight get lost (downstream of altered splice site)
282282DISULFIDmight get lost (downstream of altered splice site)
289294STRANDmight get lost (downstream of altered splice site)
308328TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
329383TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 870 / 870
position (AA) of stopcodon in wt / mu AA sequence 290 / 290
position of stopcodon in wt / mu cDNA 964 / 964
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 95 / 95
chromosome 6
strand 1
last intron/exon boundary 994
theoretical NMD boundary in CDS 849
length of CDS 870
coding sequence (CDS) position 568
cDNA position
(for ins/del: last normal base / first normal base)		 662
gDNA position
(for ins/del: last normal base / first normal base)		 12247
chromosomal position
(for ins/del: last normal base / first normal base)		 31379807
original gDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered gDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
original cDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered cDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
wildtype AA sequence MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEVP QSSRAQTLAM
NVRNFLKEDA MKTKTHYHAM HADCLQELRR YLESGVVLRR TVPPMVNVTR SEASEGNITV
TCRASSFYPR NIILTWRQDG VSLSHDTQQW GDVLPDGNGT YQTWVATRIC RGEEQRFTCY
MEHSGNHSTH PVPSGKVLVL QSHWQTFHVS AVAAGCCYFC YYYFLCPLL*
mutated AA sequence MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEVP QSSRAQTLAM
NVRNFLKEDA MKTKTHYHAM HADCLQELRR YLESGVVLRR TVPPMVNVTR SEASEGNITV
TCRASSFYPW NIILTWRQDG VSLSHDTQQW GDVLPDGNGT YQTWVATRIC RGEEQRFTCY
MEHSGNHSTH PVPSGKVLVL QSHWQTFHVS AVAAGCCYFC YYYFLCPLL*
speed 0.56 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: 0.999999999927918 (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) chr6:31379807C>TN/A show variant in all transcripts   IGV
HGNC symbol MICA
Ensembl transcript ID ENST00000376222
Genbank transcript ID N/A
UniProt peptide Q29983
alteration type single base exchange
alteration region CDS
DNA changes c.283C>T
cDNA.1435C>T
g.12247C>T
AA changes R95W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 95
frameshift no
known variant Reference ID: rs1051798
databasehomozygous (T/T)heterozygousallele carriers
1000G34811271475
ExAC52982217127469
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0940.001
-2.6730
(flanking)-0.6630
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased12249wt: 0.44 / mu: 0.52wt: GCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGCG
mu: GCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGCG		 ccgg|AATA
Acc increased12245wt: 0.25 / mu: 0.56wt: CAGGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCT
mu: CAGGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCT		 atcc|CCGG
Acc marginally increased12248wt: 0.8416 / mu: 0.8428 (marginal change - not scored)wt: GGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGC
mu: GGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGC		 cccg|GAAT
Acc marginally increased12247wt: 0.6265 / mu: 0.6347 (marginal change - not scored)wt: GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
mu: GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG		 cccc|GGAA
Donor marginally increased12245wt: 0.2960 / mu: 0.3063 (marginal change - not scored)wt: CTATCCCCGGAATAT
mu: CTATCCCTGGAATAT		 ATCC|ccgg
distance from splice site 84
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      95TVTCRASSFYPRNIILTWRQDGVS
mutated  not conserved    95TVTCRASSFYPWNIILTWRQDGV
Ptroglodytes  all identical  ENSPTRG00000017957  233TVTCWASSFYPRNITLTWRQDGI
Mmulatta  not conserved  ENSMMUG00000006609  233ASGFYPGNITLTWRQDGV
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000030689  225KLHCRVYGFYPRDVEVKWIK
protein features
start (aa)end (aa)featuredetails 
24307TOPO_DOMExtracellular (Potential).lost
82101HELIXlost
109121STRANDmight get lost (downstream of altered splice site)
119119DISULFIDmight get lost (downstream of altered splice site)
127135STRANDmight get lost (downstream of altered splice site)
138144STRANDmight get lost (downstream of altered splice site)
145148TURNmight get lost (downstream of altered splice site)
149151STRANDmight get lost (downstream of altered splice site)
156170HELIXmight get lost (downstream of altered splice site)
177196HELIXmight get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
207296DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
208213STRANDmight get lost (downstream of altered splice site)
210210CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
217233STRANDmight get lost (downstream of altered splice site)
220220CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
225225DISULFIDmight get lost (downstream of altered splice site)
236241STRANDmight get lost (downstream of altered splice site)
248250TURNmight get lost (downstream of altered splice site)
251253STRANDmight get lost (downstream of altered splice site)
260262STRANDmight get lost (downstream of altered splice site)
261261CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
264273STRANDmight get lost (downstream of altered splice site)
277279HELIXmight get lost (downstream of altered splice site)
280286STRANDmight get lost (downstream of altered splice site)
282282DISULFIDmight get lost (downstream of altered splice site)
289294STRANDmight get lost (downstream of altered splice site)
308328TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
329383TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 585 / 585
position (AA) of stopcodon in wt / mu AA sequence 195 / 195
position of stopcodon in wt / mu cDNA 1737 / 1737
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 1153 / 1153
chromosome 6
strand 1
last intron/exon boundary 1767
theoretical NMD boundary in CDS 564
length of CDS 585
coding sequence (CDS) position 283
cDNA position
(for ins/del: last normal base / first normal base)		 1435
gDNA position
(for ins/del: last normal base / first normal base)		 12247
chromosomal position
(for ins/del: last normal base / first normal base)		 31379807
original gDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered gDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
original cDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered cDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
wildtype AA sequence MGQRDQGLDR ERKGPQDDPG SYQGPERRNF LKEDAMKTKT HYHAMHADCL QELRRYLESG
VVLRRTVPPM VNVTRSEASE GNITVTCRAS SFYPRNIILT WRQDGVSLSH DTQQWGDVLP
DGNGTYQTWV ATRICRGEEQ RFTCYMEHSG NHSTHPVPSG KVLVLQSHWQ TFHVSAVAAG
CCYFCYYYFL CPLL*
mutated AA sequence MGQRDQGLDR ERKGPQDDPG SYQGPERRNF LKEDAMKTKT HYHAMHADCL QELRRYLESG
VVLRRTVPPM VNVTRSEASE GNITVTCRAS SFYPWNIILT WRQDGVSLSH DTQQWGDVLP
DGNGTYQTWV ATRICRGEEQ RFTCYMEHSG NHSTHPVPSG KVLVLQSHWQ TFHVSAVAAG
CCYFCYYYFL CPLL*
speed 1.40 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: 0.999999999911046 (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) chr6:31379807C>TN/A show variant in all transcripts   IGV
HGNC symbol MICA
Ensembl transcript ID ENST00000364810
Genbank transcript ID NM_001177519
UniProt peptide Q29983
alteration type single base exchange
alteration region CDS
DNA changes c.697C>T
cDNA.1100C>T
g.12247C>T
AA changes R233W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 233
frameshift no
known variant Reference ID: rs1051798
databasehomozygous (T/T)heterozygousallele carriers
1000G34811271475
ExAC52982217127469
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0940.001
-2.6730
(flanking)-0.6630
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased12249wt: 0.44 / mu: 0.52wt: GCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGCG
mu: GCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGCG		 ccgg|AATA
Acc increased12245wt: 0.25 / mu: 0.56wt: CAGGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCT
mu: CAGGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCT		 atcc|CCGG
Acc marginally increased12248wt: 0.8416 / mu: 0.8428 (marginal change - not scored)wt: GGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGC
mu: GGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGC		 cccg|GAAT
Acc marginally increased12247wt: 0.6265 / mu: 0.6347 (marginal change - not scored)wt: GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
mu: GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG		 cccc|GGAA
Donor marginally increased12245wt: 0.2960 / mu: 0.3063 (marginal change - not scored)wt: CTATCCCCGGAATAT
mu: CTATCCCTGGAATAT		 ATCC|ccgg
distance from splice site 84
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      233TVTCRASSFYPRNIILTWRQDGVS
mutated  not conserved    233TVTCRASSFYPWNIILTWR
Ptroglodytes  all identical  ENSPTRG00000017957  233TVTCWASSFYPRNITLTWR
Mmulatta  not conserved  ENSMMUG00000006609  233TVTCRASGFYPGNITLTWRQD
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000030689  226KLHCRVYGFYPRDVEVKWIKNGR
protein features
start (aa)end (aa)featuredetails 
24307TOPO_DOMExtracellular (Potential).lost
207296DOMAINIg-like C1-type.lost
217233STRANDlost
236241STRANDmight get lost (downstream of altered splice site)
248250TURNmight get lost (downstream of altered splice site)
251253STRANDmight get lost (downstream of altered splice site)
260262STRANDmight get lost (downstream of altered splice site)
261261CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
264273STRANDmight get lost (downstream of altered splice site)
277279HELIXmight get lost (downstream of altered splice site)
280286STRANDmight get lost (downstream of altered splice site)
282282DISULFIDmight get lost (downstream of altered splice site)
289294STRANDmight get lost (downstream of altered splice site)
308328TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
329383TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 999 / 999
position (AA) of stopcodon in wt / mu AA sequence 333 / 333
position of stopcodon in wt / mu cDNA 1402 / 1402
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 404 / 404
chromosome 6
strand 1
last intron/exon boundary 1432
theoretical NMD boundary in CDS 978
length of CDS 999
coding sequence (CDS) position 697
cDNA position
(for ins/del: last normal base / first normal base)		 1100
gDNA position
(for ins/del: last normal base / first normal base)		 12247
chromosomal position
(for ins/del: last normal base / first normal base)		 31379807
original gDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered gDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
original cDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered cDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
wildtype AA sequence MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEGL HSLQEIRVCE
IHEDNSTRSS QHFYYDGELF LSQNLETEEW TVPQSSRAQT LAMNVRNFLK EDAMKTKTHY
HAMHADCLQE LRRYLESGVV LRRTVPPMVN VTRSEASEGN ITVTCRASSF YPRNIILTWR
QDGVSLSHDT QQWGDVLPDG NGTYQTWVAT RICRGEEQRF TCYMEHSGNH STHPVPSGKV
LVLQSHWQTF HVSAVAAGCC YFCYYYFLCP LL*
mutated AA sequence MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEGL HSLQEIRVCE
IHEDNSTRSS QHFYYDGELF LSQNLETEEW TVPQSSRAQT LAMNVRNFLK EDAMKTKTHY
HAMHADCLQE LRRYLESGVV LRRTVPPMVN VTRSEASEGN ITVTCRASSF YPWNIILTWR
QDGVSLSHDT QQWGDVLPDG NGTYQTWVAT RICRGEEQRF TCYMEHSGNH STHPVPSGKV
LVLQSHWQTF HVSAVAAGCC YFCYYYFLCP LL*
speed 0.44 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: 0.999999999911046 (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) chr6:31379807C>TN/A show variant in all transcripts   IGV
HGNC symbol MICA
Ensembl transcript ID ENST00000449934
Genbank transcript ID NM_001177519
UniProt peptide Q29983
alteration type single base exchange
alteration region CDS
DNA changes c.697C>T
cDNA.736C>T
g.12247C>T
AA changes R233W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 233
frameshift no
known variant Reference ID: rs1051798
databasehomozygous (T/T)heterozygousallele carriers
1000G34811271475
ExAC52982217127469
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0940.001
-2.6730
(flanking)-0.6630
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased12249wt: 0.44 / mu: 0.52wt: GCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGCG
mu: GCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGCG		 ccgg|AATA
Acc increased12245wt: 0.25 / mu: 0.56wt: CAGGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCT
mu: CAGGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCT		 atcc|CCGG
Acc marginally increased12248wt: 0.8416 / mu: 0.8428 (marginal change - not scored)wt: GGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGC
mu: GGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGC		 cccg|GAAT
Acc marginally increased12247wt: 0.6265 / mu: 0.6347 (marginal change - not scored)wt: GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
mu: GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG		 cccc|GGAA
Donor marginally increased12245wt: 0.2960 / mu: 0.3063 (marginal change - not scored)wt: CTATCCCCGGAATAT
mu: CTATCCCTGGAATAT		 ATCC|ccgg
distance from splice site 84
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      233TVTCRASSFYPRNIILTWRQDGVS
mutated  not conserved    233TVTCRASSFYPWNIILTWR
Ptroglodytes  all identical  ENSPTRG00000017957  233TVTCWASSFYPRNITLTWR
Mmulatta  not conserved  ENSMMUG00000006609  233TVTCRASGFYPGNITLTWRQD
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000030689  226KLHCRVYGFYPRDVEVKWIKNGR
protein features
start (aa)end (aa)featuredetails 
24307TOPO_DOMExtracellular (Potential).lost
207296DOMAINIg-like C1-type.lost
217233STRANDlost
236241STRANDmight get lost (downstream of altered splice site)
248250TURNmight get lost (downstream of altered splice site)
251253STRANDmight get lost (downstream of altered splice site)
260262STRANDmight get lost (downstream of altered splice site)
261261CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
264273STRANDmight get lost (downstream of altered splice site)
277279HELIXmight get lost (downstream of altered splice site)
280286STRANDmight get lost (downstream of altered splice site)
282282DISULFIDmight get lost (downstream of altered splice site)
289294STRANDmight get lost (downstream of altered splice site)
308328TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
329383TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 999 / 999
position (AA) of stopcodon in wt / mu AA sequence 333 / 333
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 40 / 40
chromosome 6
strand 1
last intron/exon boundary 1068
theoretical NMD boundary in CDS 978
length of CDS 999
coding sequence (CDS) position 697
cDNA position
(for ins/del: last normal base / first normal base)		 736
gDNA position
(for ins/del: last normal base / first normal base)		 12247
chromosomal position
(for ins/del: last normal base / first normal base)		 31379807
original gDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered gDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
original cDNA sequence snippet GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
altered cDNA sequence snippet GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG
wildtype AA sequence MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEGL HSLQEIRVCE
IHEDNSTRSS QHFYYDGELF LSQNLETEEW TVPQSSRAQT LAMNVRNFLK EDAMKTKTHY
HAMHADCLQE LRRYLESGVV LRRTVPPMVN VTRSEASEGN ITVTCRASSF YPRNIILTWR
QDGVSLSHDT QQWGDVLPDG NGTYQTWVAT RICRGEEQRF TCYMEHSGNH STHPVPSGKV
LVLQSHWQTF HVSAVAAGCC YFCYYYFLCP LL*
mutated AA sequence MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEGL HSLQEIRVCE
IHEDNSTRSS QHFYYDGELF LSQNLETEEW TVPQSSRAQT LAMNVRNFLK EDAMKTKTHY
HAMHADCLQE LRRYLESGVV LRRTVPPMVN VTRSEASEGN ITVTCRASSF YPWNIILTWR
QDGVSLSHDT QQWGDVLPDG NGTYQTWVAT RICRGEEQRF TCYMEHSGNH STHPVPSGKV
LVLQSHWQTF HVSAVAAGCC YFCYYYFLCP LL*
speed 0.92 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