MutationTaster - study a chromosomal position

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 4.35 s - this script 5.399262 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MICA	polymorphism_automatic	9.88986670336089e-13	simple_aae				G198S	single base exchange	rs1131896		show file
MICA	polymorphism_automatic	9.88986670336089e-13	simple_aae				G60S	single base exchange	rs1131896		show file
MICA	polymorphism_automatic	9.88986670336089e-13	simple_aae				G155S	single base exchange	rs1131896		show file
MICA	polymorphism_automatic	9.88986670336089e-13	simple_aae				G198S	single base exchange	rs1131896		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999011 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:31379115G>AN/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.592G>A
cDNA.995G>A
g.11555G>A

AA changes

G198S Score: 56 explain score(s)

position(s) of altered AA
if AA alteration in CDS

198

frameshift

known variant

Reference ID: rs1131896

database	homozygous (A/A)	heterozygous	allele carriers
1000G	324	1082	1406
ExAC	2507	12029	14536

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.216	0
	-1.391	0
(flanking)	1.116	0.001

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	11552	wt: 0.4788 / mu: 0.5483 (marginal change - not scored)	wt: TAGAATCCGGCGTAG mu: TAGAATCCAGCGTAG	GAAT\|ccgg
Donor marginally increased	11555	wt: 0.9886 / mu: 0.9983 (marginal change - not scored)	wt: AATCCGGCGTAGTCC mu: AATCCAGCGTAGTCC	TCCG\|gcgt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

198

mutated

not conserved

198

Ptroglodytes

all identical

ENSPTRG00000017957

198

Mmulatta

not conserved

ENSMMUG00000006609

198

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000030689

196

protein features

start (aa)	end (aa)	feature	details
24	307	TOPO_DOM	Extracellular (Potential).	lost

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

strand

last intron/exon boundary

1432

theoretical NMD boundary in CDS

978

length of CDS

999

coding sequence (CDS) position

592

cDNA position
(for ins/del: last normal base / first normal base)

995

gDNA position
(for ins/del: last normal base / first normal base)

11555

chromosomal position
(for ins/del: last normal base / first normal base)

31379115

original gDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered gDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

original cDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered cDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

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 LRRYLESSVV LRRTVPPMVN VTRSEASEGN ITVTCRASSF YPRNIILTWR
QDGVSLSHDT QQWGDVLPDG NGTYQTWVAT RICRGEEQRF TCYMEHSGNH STHPVPSGKV
LVLQSHWQTF HVSAVAAGCC YFCYYYFLCP LL*

speed

1.11 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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999011 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:31379115G>AN/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.178G>A
cDNA.1330G>A
g.11555G>A

AA changes

G60S Score: 56 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs1131896

database	homozygous (A/A)	heterozygous	allele carriers
1000G	324	1082	1406
ExAC	2507	12029	14536

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.216	0
	-1.391	0
(flanking)	1.116	0.001

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	11552	wt: 0.4788 / mu: 0.5483 (marginal change - not scored)	wt: TAGAATCCGGCGTAG mu: TAGAATCCAGCGTAG	GAAT\|ccgg
Donor marginally increased	11555	wt: 0.9886 / mu: 0.9983 (marginal change - not scored)	wt: AATCCGGCGTAGTCC mu: AATCCAGCGTAGTCC	TCCG\|gcgt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000017957

197

Mmulatta

not conserved

ENSMMUG00000006609

198

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000030689

190

protein features

start (aa)	end (aa)	feature	details
24	307	TOPO_DOM	Extracellular (Potential).	lost

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

strand

last intron/exon boundary

1767

theoretical NMD boundary in CDS

564

length of CDS

585

coding sequence (CDS) position

178

cDNA position
(for ins/del: last normal base / first normal base)

1330

gDNA position
(for ins/del: last normal base / first normal base)

11555

chromosomal position
(for ins/del: last normal base / first normal base)

31379115

original gDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered gDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

original cDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered cDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

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 QELRRYLESS
VVLRRTVPPM VNVTRSEASE GNITVTCRAS SFYPRNIILT WRQDGVSLSH DTQQWGDVLP
DGNGTYQTWV ATRICRGEEQ RFTCYMEHSG NHSTHPVPSG KVLVLQSHWQ TFHVSAVAAG
CCYFCYYYFL CPLL*

speed

1.08 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999011 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:31379115G>AN/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.463G>A
cDNA.557G>A
g.11555G>A

AA changes

G155S Score: 56 explain score(s)

position(s) of altered AA
if AA alteration in CDS

155

frameshift

known variant

Reference ID: rs1131896

database	homozygous (A/A)	heterozygous	allele carriers
1000G	324	1082	1406
ExAC	2507	12029	14536

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.216	0
	-1.391	0
(flanking)	1.116	0.001

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	11552	wt: 0.4788 / mu: 0.5483 (marginal change - not scored)	wt: TAGAATCCGGCGTAG mu: TAGAATCCAGCGTAG	GAAT\|ccgg
Donor marginally increased	11555	wt: 0.9886 / mu: 0.9983 (marginal change - not scored)	wt: AATCCGGCGTAGTCC mu: AATCCAGCGTAGTCC	TCCG\|gcgt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

155

mutated

not conserved

155

Ptroglodytes

all identical

ENSPTRG00000017957

198

Mmulatta

not conserved

ENSMMUG00000006609

198

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000030689

190

protein features

start (aa)	end (aa)	feature	details
24	307	TOPO_DOM	Extracellular (Potential).	lost

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

strand

last intron/exon boundary

994

theoretical NMD boundary in CDS

849

length of CDS

870

coding sequence (CDS) position

463

cDNA position
(for ins/del: last normal base / first normal base)

557

gDNA position
(for ins/del: last normal base / first normal base)

11555

chromosomal position
(for ins/del: last normal base / first normal base)

31379115

original gDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered gDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

original cDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered cDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

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 YLESSVVLRR TVPPMVNVTR SEASEGNITV
TCRASSFYPR NIILTWRQDG VSLSHDTQQW GDVLPDGNGT YQTWVATRIC RGEEQRFTCY
MEHSGNHSTH PVPSGKVLVL QSHWQTFHVS AVAAGCCYFC YYYFLCPLL*

speed

1.05 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999011 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:31379115G>AN/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.592G>A
cDNA.631G>A
g.11555G>A

AA changes

G198S Score: 56 explain score(s)

position(s) of altered AA
if AA alteration in CDS

198

frameshift

known variant

Reference ID: rs1131896

database	homozygous (A/A)	heterozygous	allele carriers
1000G	324	1082	1406
ExAC	2507	12029	14536

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.216	0
	-1.391	0
(flanking)	1.116	0.001

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	11552	wt: 0.4788 / mu: 0.5483 (marginal change - not scored)	wt: TAGAATCCGGCGTAG mu: TAGAATCCAGCGTAG	GAAT\|ccgg
Donor marginally increased	11555	wt: 0.9886 / mu: 0.9983 (marginal change - not scored)	wt: AATCCGGCGTAGTCC mu: AATCCAGCGTAGTCC	TCCG\|gcgt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

198

mutated

not conserved

198

Ptroglodytes

all identical

ENSPTRG00000017957

198

Mmulatta

not conserved

ENSMMUG00000006609

198

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000030689

196

protein features

start (aa)	end (aa)	feature	details
24	307	TOPO_DOM	Extracellular (Potential).	lost

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

strand

last intron/exon boundary

1068

theoretical NMD boundary in CDS

978

length of CDS

999

coding sequence (CDS) position

592

cDNA position
(for ins/del: last normal base / first normal base)

631

gDNA position
(for ins/del: last normal base / first normal base)

11555

chromosomal position
(for ins/del: last normal base / first normal base)

31379115

original gDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered gDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

original cDNA sequence snippet

TACGGCGATATCTAGAATCCGGCGTAGTCCTGAGGAGAACA

altered cDNA sequence snippet

TACGGCGATATCTAGAATCCAGCGTAGTCCTGAGGAGAACA

wildtype AA sequence

mutated AA sequence

MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEGL HSLQEIRVCE
IHEDNSTRSS QHFYYDGELF LSQNLETEEW TVPQSSRAQT LAMNVRNFLK EDAMKTKTHY
HAMHADCLQE LRRYLESSVV LRRTVPPMVN VTRSEASEGN ITVTCRASSF YPRNIILTWR
QDGVSLSHDT QQWGDVLPDG NGTYQTWVAT RICRGEEQRF TCYMEHSGNH STHPVPSGKV
LVLQSHWQTF HVSAVAAGCC YFCYYYFLCP LL*

speed

1.11 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems