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: ENST00000278520
Querying Taster for transcript #2: ENST00000423339
Querying Taster for transcript #3: ENST00000542662
MT speed 0 s - this script 3.940271 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CCDC82	polymorphism_automatic	0.01808692284823	simple_aae				Q327R	single base exchange	rs10831519		show file
CCDC82	polymorphism_automatic	0.01808692284823	simple_aae				Q327R	single base exchange	rs10831519		show file
CCDC82	polymorphism_automatic	0.01808692284823	simple_aae				Q327R	single base exchange	rs10831519		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.98191307715177 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:96116444T>CN/A show variant in all transcripts IGV

HGNC symbol

CCDC82

Ensembl transcript ID

ENST00000278520

Genbank transcript ID

NM_024725

UniProt peptide

Q8N4S0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.980A>G
cDNA.1409A>G
g.6644A>G

AA changes

Q327R Score: 43 explain score(s)

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

327

frameshift

known variant

Reference ID: rs10831519

database	homozygous (C/C)	heterozygous	allele carriers
1000G	136	860	996
ExAC	2607	19392	21999

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.23	0.925
	0.442	0.958
(flanking)	3.558	0.999

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	6641	wt: 0.4368 / mu: 0.4697 (marginal change - not scored)	wt: AGTAAAACAGAATTC mu: AGTAAAACGGAATTC	TAAA\|acag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

327

mutated

all conserved

327

Ptroglodytes

all identical

ENSPTRG00000004198

327

Mmulatta

all identical

ENSMMUG00000007999

309

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000079084

303

Ggallus

not conserved

ENSGALG00000013489

206

NIL

VFFPVCH

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000014966

263

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000007073

194

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1635 / 1635

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

545 / 545

position of stopcodon in wt / mu cDNA

2064 / 2064

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

430 / 430

chromosome

strand

-1

last intron/exon boundary

1996

theoretical NMD boundary in CDS

1516

length of CDS

1635

coding sequence (CDS) position

980

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

1409

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

6644

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

96116444

original gDNA sequence snippet

ACAACTGAAATTAGTAAAACAGAATTCTCTTTGTAAGTTCA

altered gDNA sequence snippet

ACAACTGAAATTAGTAAAACGGAATTCTCTTTGTAAGTTCA

original cDNA sequence snippet

ACAACTGAAATTAGTAAAACAGAATTCTCTTTATTCTTTTA

altered cDNA sequence snippet

ACAACTGAAATTAGTAAAACGGAATTCTCTTTATTCTTTTA

wildtype AA sequence

MIHVRRHETR RNSKSHVPEQ KSRVDWRRTK RSSISQLLDS DEELDSEEFD SDEELDSDES
FENDEELDSN KGPDCNKTPG SERELNLSKI QSEGNDSKCL INSGNGSTYE EETNKIKHRN
IDLQDQEKHL SQEDNDLNKQ TGQIIEDDQE KHLSQEDNDL NKQTGQIIED DLEEEDIKRG
KRKRLSSVMC DSDESDDSDI LVRKVGVKRP RRVVEDEGSS VEMEQKTPEK TLAAQKREKL
QKLKELSKQR SRQRRSSGRD FEDSEKESCP SSDEVDEEEE EDNYESDEDG DDYIIDDFVV
QDEEGDEENK NQQGEKLTTS QLKLVKQNSL YSFSDHYTHF ERVVKALLIN ALDESFLGTL
YDGTRQKSYA KDMLTSLHYL DNRFVQPRLE SLVSRSRWKE QYKERVENYS NVSIHLKNPE
NCSCQACGLH RYCKYSVHLS GELYNTRTMQ IDNFMSHDKQ VFTVGRICAS RTRIYHKLKH
FKFKLYQECC TIAMTEEVED EQVKETVERI FRRSKENGWI KEKYGQLEEY LNFADYFQEE
KFEL*

mutated AA sequence

MIHVRRHETR RNSKSHVPEQ KSRVDWRRTK RSSISQLLDS DEELDSEEFD SDEELDSDES
FENDEELDSN KGPDCNKTPG SERELNLSKI QSEGNDSKCL INSGNGSTYE EETNKIKHRN
IDLQDQEKHL SQEDNDLNKQ TGQIIEDDQE KHLSQEDNDL NKQTGQIIED DLEEEDIKRG
KRKRLSSVMC DSDESDDSDI LVRKVGVKRP RRVVEDEGSS VEMEQKTPEK TLAAQKREKL
QKLKELSKQR SRQRRSSGRD FEDSEKESCP SSDEVDEEEE EDNYESDEDG DDYIIDDFVV
QDEEGDEENK NQQGEKLTTS QLKLVKRNSL YSFSDHYTHF ERVVKALLIN ALDESFLGTL
YDGTRQKSYA KDMLTSLHYL DNRFVQPRLE SLVSRSRWKE QYKERVENYS NVSIHLKNPE
NCSCQACGLH RYCKYSVHLS GELYNTRTMQ IDNFMSHDKQ VFTVGRICAS RTRIYHKLKH
FKFKLYQECC TIAMTEEVED EQVKETVERI FRRSKENGWI KEKYGQLEEY LNFADYFQEE
KFEL*

speed

0.78 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: 0.98191307715177 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:96116444T>CN/A show variant in all transcripts IGV

HGNC symbol

CCDC82

Ensembl transcript ID

ENST00000423339

Genbank transcript ID

N/A

UniProt peptide

Q8N4S0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.980A>G
cDNA.1223A>G
g.6644A>G

AA changes

Q327R Score: 43 explain score(s)

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

327

frameshift

known variant

Reference ID: rs10831519

database	homozygous (C/C)	heterozygous	allele carriers
1000G	136	860	996
ExAC	2607	19392	21999

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.23	0.925
	0.442	0.958
(flanking)	3.558	0.999

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	6641	wt: 0.4368 / mu: 0.4697 (marginal change - not scored)	wt: AGTAAAACAGAATTC mu: AGTAAAACGGAATTC	TAAA\|acag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

327

mutated

all conserved

327

Ptroglodytes

all identical

ENSPTRG00000004198

327

Mmulatta

all identical

ENSMMUG00000007999

309

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000079084

303

Ggallus

not conserved

ENSGALG00000013489

206

NIL

VFFPVCH

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000014966

263

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000007073

194

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1635 / 1635

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

545 / 545

position of stopcodon in wt / mu cDNA

1878 / 1878

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

244 / 244

chromosome

strand

-1

last intron/exon boundary

1810

theoretical NMD boundary in CDS

1516

length of CDS

1635

coding sequence (CDS) position

980

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

1223

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

6644

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

96116444

original gDNA sequence snippet

ACAACTGAAATTAGTAAAACAGAATTCTCTTTGTAAGTTCA

altered gDNA sequence snippet

ACAACTGAAATTAGTAAAACGGAATTCTCTTTGTAAGTTCA

original cDNA sequence snippet

ACAACTGAAATTAGTAAAACAGAATTCTCTTTATTCTTTTA

altered cDNA sequence snippet

ACAACTGAAATTAGTAAAACGGAATTCTCTTTATTCTTTTA

wildtype AA sequence

mutated AA sequence

MIHVRRHETR RNSKSHVPEQ KSRVDWRRTK RSSISQLLDS DEELDSEEFD SDEELDSDES
FENDEELDSN KGPDCNKTPG SERELNLSKI QSEGNDSKCL INSGNGSTYE EETNKIKHRN
IDLQDQEKHL SQEDNDLNKQ TGQIIEDDQE KHLSQEDNDL NKQTGQIIED DLEEEDIKRG
KRKRLSSVMC DSDESDDSDI LVRKVGVKRP RRVVEDEGSS VEMEQKTPEK TLAAQKREKL
QKLKELSKQR SRQRRSSGRD FEDSEKESCP SSDEVDEEEE EDNYESDEDG DDYIIDDFVV
QDEEGDEENK NQQGEKLTTS QLKLVKRNSL YSFSDHYTHF ERVVKALLIN ALDESFLGTL
YDGTRQKSYA KDMLTSLHYL DNRFVQPRLE SLVSRSRWKE QYKERVENYS NVSIHLKNPE
NCSCQACGLH RYCKYSVHLS GELYNTRTMQ IDNFMSHDKQ VFTVGRICAS RTRIYHKLKH
FKFKLYQECC TIAMTEEVED EQVKETVERI FRRSKENGWI KEKYGQLEEY LNFADYFQEE
KFEL*

speed

0.92 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.98191307715177 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:96116444T>CN/A show variant in all transcripts IGV

HGNC symbol

CCDC82

Ensembl transcript ID

ENST00000542662

Genbank transcript ID

N/A

UniProt peptide

Q8N4S0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.980A>G
cDNA.1322A>G
g.6644A>G

AA changes

Q327R Score: 43 explain score(s)

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

327

frameshift

known variant

Reference ID: rs10831519

database	homozygous (C/C)	heterozygous	allele carriers
1000G	136	860	996
ExAC	2607	19392	21999

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.23	0.925
	0.442	0.958
(flanking)	3.558	0.999

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	6641	wt: 0.4368 / mu: 0.4697 (marginal change - not scored)	wt: AGTAAAACAGAATTC mu: AGTAAAACGGAATTC	TAAA\|acag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

327

mutated

all conserved

327

Ptroglodytes

all identical

ENSPTRG00000004198

327

Mmulatta

all identical

ENSMMUG00000007999

309

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000079084

303

Ggallus

not conserved

ENSGALG00000013489

206

NIL

VFFPVCH

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000014966

263

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000007073

194

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1635 / 1635

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

545 / 545

position of stopcodon in wt / mu cDNA

1977 / 1977

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

343 / 343

chromosome

strand

-1

last intron/exon boundary

1909

theoretical NMD boundary in CDS

1516

length of CDS

1635

coding sequence (CDS) position

980

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

1322

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

6644

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

96116444

original gDNA sequence snippet

ACAACTGAAATTAGTAAAACAGAATTCTCTTTGTAAGTTCA

altered gDNA sequence snippet

ACAACTGAAATTAGTAAAACGGAATTCTCTTTGTAAGTTCA

original cDNA sequence snippet

ACAACTGAAATTAGTAAAACAGAATTCTCTTTATTCTTTTA

altered cDNA sequence snippet

ACAACTGAAATTAGTAAAACGGAATTCTCTTTATTCTTTTA

wildtype AA sequence

mutated AA sequence

MIHVRRHETR RNSKSHVPEQ KSRVDWRRTK RSSISQLLDS DEELDSEEFD SDEELDSDES
FENDEELDSN KGPDCNKTPG SERELNLSKI QSEGNDSKCL INSGNGSTYE EETNKIKHRN
IDLQDQEKHL SQEDNDLNKQ TGQIIEDDQE KHLSQEDNDL NKQTGQIIED DLEEEDIKRG
KRKRLSSVMC DSDESDDSDI LVRKVGVKRP RRVVEDEGSS VEMEQKTPEK TLAAQKREKL
QKLKELSKQR SRQRRSSGRD FEDSEKESCP SSDEVDEEEE EDNYESDEDG DDYIIDDFVV
QDEEGDEENK NQQGEKLTTS QLKLVKRNSL YSFSDHYTHF ERVVKALLIN ALDESFLGTL
YDGTRQKSYA KDMLTSLHYL DNRFVQPRLE SLVSRSRWKE QYKERVENYS NVSIHLKNPE
NCSCQACGLH RYCKYSVHLS GELYNTRTMQ IDNFMSHDKQ VFTVGRICAS RTRIYHKLKH
FKFKLYQECC TIAMTEEVED EQVKETVERI FRRSKENGWI KEKYGQLEEY LNFADYFQEE
KFEL*

speed

1.04 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems