MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000320741
Querying Taster for transcript #2: ENST00000444204
Querying Taster for transcript #3: ENST00000412955
MT speed 0 s - this script 3.653639 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADIPOQ	disease_causing_automatic	0.999982883481217	simple_aae		affected	0	R112C	single base exchange	rs121917815		show file
ADIPOQ	disease_causing_automatic	0.999982883481217	simple_aae		affected	0	R112C	single base exchange	rs121917815		show file
ADIPOQ	disease_causing_automatic	0.999982883481217	simple_aae		affected	0	R112C	single base exchange	rs121917815		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999982883481217 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004346)
known disease mutation: rs4990 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:186572092C>TN/A show variant in all transcripts IGV

HGNC symbol

ADIPOQ

Ensembl transcript ID

ENST00000320741

Genbank transcript ID

NM_004797

UniProt peptide

Q15848

alteration type

single base exchange

alteration region

CDS

DNA changes

c.334C>T
cDNA.402C>T
g.11630C>T

AA changes

R112C Score: 180 explain score(s)

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

112

frameshift

known variant

Reference ID: rs121917815

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs4990 (pathogenic for Hypoadiponectinemia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM004346)

known disease mutation at this position, please check HGMD for details (HGMD ID CM004346)
known disease mutation at this position, please check HGMD for details (HGMD ID CM004346)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.034	0.419
	1.791	0.861
(flanking)	1.785	0.885

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 gained	11623	0.33	mu: GCCTATGTATACTGC	CTAT\|gtat

distance from splice site

120

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

112

mutated

not conserved

112

Ptroglodytes

all identical

ENSPTRG00000015720

112

Mmulatta

all identical

ENSMMUG00000002684

111

Fcatus

all identical

ENSFCAG00000013885

112

Mmusculus

all identical

ENSMUSG00000022878

115

Ggallus

all identical

ENSGALG00000005554

110

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000056411

139

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003033

113

protein features

start (aa)	end (aa)	feature	details
108	244	DOMAIN	C1q.	lost
114	118	STRAND		might get lost (downstream of altered splice site)
134	137	STRAND		might get lost (downstream of altered splice site)
145	147	TURN		might get lost (downstream of altered splice site)
156	177	STRAND		might get lost (downstream of altered splice site)
180	187	STRAND		might get lost (downstream of altered splice site)
195	205	STRAND		might get lost (downstream of altered splice site)
210	216	STRAND		might get lost (downstream of altered splice site)
220	225	STRAND		might get lost (downstream of altered splice site)
230	230	SITE	Not glycosylated.	might get lost (downstream of altered splice site)
233	241	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

735 / 735

position (AA) of stopcodon in wt / mu AA sequence

245 / 245

position of stopcodon in wt / mu cDNA

803 / 803

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

69 / 69

chromosome

strand

last intron/exon boundary

283

theoretical NMD boundary in CDS

164

length of CDS

735

coding sequence (CDS) position

334

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

402

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

11630

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

186572092

original gDNA sequence snippet

GAGAAGGTGCCTATGTATACCGCTCAGCATTCAGTGTGGGA

altered gDNA sequence snippet

GAGAAGGTGCCTATGTATACTGCTCAGCATTCAGTGTGGGA

original cDNA sequence snippet

GAGAAGGTGCCTATGTATACCGCTCAGCATTCAGTGTGGGA

altered cDNA sequence snippet

GAGAAGGTGCCTATGTATACTGCTCAGCATTCAGTGTGGGA

wildtype AA sequence

MLLLGAVLLL LALPGHDQET TTQGPGVLLP LPKGACTGWM AGIPGHPGHN GAPGRDGRDG
TPGEKGEKGD PGLIGPKGDI GETGVPGAEG PRGFPGIQGR KGEPGEGAYV YRSAFSVGLE
TYVTIPNMPI RFTKIFYNQQ NHYDGSTGKF HCNIPGLYYF AYHITVYMKD VKVSLFKKDK
AMLFTYDQYQ ENNVDQASGS VLLHLEVGDQ VWLQVYGEGE RNGLYADNDN DSTFTGFLLY
HDTN*

mutated AA sequence

MLLLGAVLLL LALPGHDQET TTQGPGVLLP LPKGACTGWM AGIPGHPGHN GAPGRDGRDG
TPGEKGEKGD PGLIGPKGDI GETGVPGAEG PRGFPGIQGR KGEPGEGAYV YCSAFSVGLE
TYVTIPNMPI RFTKIFYNQQ NHYDGSTGKF HCNIPGLYYF AYHITVYMKD VKVSLFKKDK
AMLFTYDQYQ ENNVDQASGS VLLHLEVGDQ VWLQVYGEGE RNGLYADNDN DSTFTGFLLY
HDTN*

speed

0.42 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

disease causing

Model: simple_aae, prob: 0.999982883481217 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004346)
known disease mutation: rs4990 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:186572092C>TN/A show variant in all transcripts IGV

HGNC symbol

ADIPOQ

Ensembl transcript ID

ENST00000444204

Genbank transcript ID

NM_001177800

UniProt peptide

Q15848

alteration type

single base exchange

alteration region

CDS

DNA changes

c.334C>T
cDNA.439C>T
g.11630C>T

AA changes

R112C Score: 180 explain score(s)

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

112

frameshift

known variant

Reference ID: rs121917815

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.034	0.419
	1.791	0.861
(flanking)	1.785	0.885

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 gained	11623	0.33	mu: GCCTATGTATACTGC	CTAT\|gtat

distance from splice site

120

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

112

mutated

not conserved

112

Ptroglodytes

all identical

ENSPTRG00000015720

112

Mmulatta

all identical

ENSMMUG00000002684

111

Fcatus

all identical

ENSFCAG00000013885

112

Mmusculus

all identical

ENSMUSG00000022878

115

Ggallus

all identical

ENSGALG00000005554

110

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000056411

139

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003033

113

protein features

start (aa)	end (aa)	feature	details
108	244	DOMAIN	C1q.	lost
114	118	STRAND		might get lost (downstream of altered splice site)
134	137	STRAND		might get lost (downstream of altered splice site)
145	147	TURN		might get lost (downstream of altered splice site)
156	177	STRAND		might get lost (downstream of altered splice site)
180	187	STRAND		might get lost (downstream of altered splice site)
195	205	STRAND		might get lost (downstream of altered splice site)
210	216	STRAND		might get lost (downstream of altered splice site)
220	225	STRAND		might get lost (downstream of altered splice site)
230	230	SITE	Not glycosylated.	might get lost (downstream of altered splice site)
233	241	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

735 / 735

position (AA) of stopcodon in wt / mu AA sequence

245 / 245

position of stopcodon in wt / mu cDNA

840 / 840

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

106 / 106

chromosome

strand

last intron/exon boundary

320

theoretical NMD boundary in CDS

164

length of CDS

735

coding sequence (CDS) position

334

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

439

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

11630

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

186572092

original gDNA sequence snippet

GAGAAGGTGCCTATGTATACCGCTCAGCATTCAGTGTGGGA

altered gDNA sequence snippet

GAGAAGGTGCCTATGTATACTGCTCAGCATTCAGTGTGGGA

original cDNA sequence snippet

GAGAAGGTGCCTATGTATACCGCTCAGCATTCAGTGTGGGA

altered cDNA sequence snippet

GAGAAGGTGCCTATGTATACTGCTCAGCATTCAGTGTGGGA

wildtype AA sequence

mutated AA sequence

speed

0.84 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999982883481217 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004346)
known disease mutation: rs4990 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:186572092C>TN/A show variant in all transcripts IGV

HGNC symbol

ADIPOQ

Ensembl transcript ID

ENST00000412955

Genbank transcript ID

N/A

UniProt peptide

Q15848

alteration type

single base exchange

alteration region

CDS

DNA changes

c.334C>T
cDNA.475C>T
g.11630C>T

AA changes

R112C Score: 180 explain score(s)

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

112

frameshift

known variant

Reference ID: rs121917815

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.034	0.419
	1.791	0.861
(flanking)	1.785	0.885

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 gained	11623	0.33	mu: GCCTATGTATACTGC	CTAT\|gtat

distance from splice site

120

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

112

mutated

not conserved

112

Ptroglodytes

all identical

ENSPTRG00000015720

112

Mmulatta

all identical

ENSMMUG00000002684

111

Fcatus

all identical

ENSFCAG00000013885

112

Mmusculus

all identical

ENSMUSG00000022878

115

Ggallus

all identical

ENSGALG00000005554

110

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000056411

139

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003033

113

protein features

start (aa)	end (aa)	feature	details
108	244	DOMAIN	C1q.	lost
114	118	STRAND		might get lost (downstream of altered splice site)
134	137	STRAND		might get lost (downstream of altered splice site)
145	147	TURN		might get lost (downstream of altered splice site)
156	177	STRAND		might get lost (downstream of altered splice site)
180	187	STRAND		might get lost (downstream of altered splice site)
195	205	STRAND		might get lost (downstream of altered splice site)
210	216	STRAND		might get lost (downstream of altered splice site)
220	225	STRAND		might get lost (downstream of altered splice site)
230	230	SITE	Not glycosylated.	might get lost (downstream of altered splice site)
233	241	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

735 / 735

position (AA) of stopcodon in wt / mu AA sequence

245 / 245

position of stopcodon in wt / mu cDNA

876 / 876

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

142 / 142

chromosome

strand

last intron/exon boundary

356

theoretical NMD boundary in CDS

164

length of CDS

735

coding sequence (CDS) position

334

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

475

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

11630

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

186572092

original gDNA sequence snippet

GAGAAGGTGCCTATGTATACCGCTCAGCATTCAGTGTGGGA

altered gDNA sequence snippet

GAGAAGGTGCCTATGTATACTGCTCAGCATTCAGTGTGGGA

original cDNA sequence snippet

GAGAAGGTGCCTATGTATACCGCTCAGCATTCAGTGTGGGA

altered cDNA sequence snippet

GAGAAGGTGCCTATGTATACTGCTCAGCATTCAGTGTGGGA

wildtype AA sequence

mutated AA sequence

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems