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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000369287
Querying Taster for transcript #2: ENST00000369286
Querying Taster for transcript #3: ENST00000369285
MT speed 0 s - this script 3.046236 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CCDC186	polymorphism_automatic	4.66959804157341e-13	simple_aae		affected		T85I	single base exchange	rs1061159		show file
CCDC186	polymorphism_automatic	4.66959804157341e-13	simple_aae		affected		T85I	single base exchange	rs1061159		show file
CCDC186	polymorphism_automatic	5.17030862567935e-13	simple_aae		affected		T85I	single base exchange	rs1061159		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999533 (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)

chr10:115922774G>AN/A show variant in all transcripts IGV

HGNC symbol

CCDC186

Ensembl transcript ID

ENST00000369286

Genbank transcript ID

N/A

UniProt peptide

Q7Z3E2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.254C>T
cDNA.521C>T
g.11206C>T

AA changes

T85I Score: 89 explain score(s)

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

frameshift

known variant

Reference ID: rs1061159

database	homozygous (A/A)	heterozygous	allele carriers
1000G	157	724	881
ExAC	2853	19262	22115

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.063	0
	-1.687	0
(flanking)	0.054	0.022

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 increased	11199	wt: 0.46 / mu: 0.76	wt: CCAAAACAGACACAG mu: CCAAAACAGACATAG	AAAA\|caga
Donor gained	11202	0.38	mu: AAACAGACATAGGCT	ACAG\|acat

distance from splice site

315

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000002957

Mmulatta

not conserved

ENSMMUG00000022514

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035173

103

Ggallus

all identical

ENSGALG00000008956

TCSERRVEGSM

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000061020

468

SHKETKDRL

Dmelanogaster

no alignment

FBgn0036614

n/a

Celegans

no alignment

Y49E10.23

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
201	712	COILED	Potential.	might get lost (downstream of altered splice site)
209	209	CONFLICT	I -> T (in Ref. 2; AAH70368).	might get lost (downstream of altered splice site)
614	614	CONFLICT	D -> I (in Ref. 4; BAA91480).	might get lost (downstream of altered splice site)
710	747	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
745	745	CONFLICT	G -> E (in Ref. 1; CAD39031).	might get lost (downstream of altered splice site)
759	803	COILED	Potential.	might get lost (downstream of altered splice site)
855	894	COILED	Potential.	might get lost (downstream of altered splice site)
857	857	CONFLICT	Q -> L (in Ref. 1; CAD97928).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

636 / 636

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

212 / 212

position of stopcodon in wt / mu cDNA

903 / 903

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

268 / 268

chromosome

strand

-1

last intron/exon boundary

207

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

636

coding sequence (CDS) position

254

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

521

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

11206

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

115922774

original gDNA sequence snippet

TTCTTGTGCCAAAACAGACACAGGCTCAGAAAATTCTGAAC

altered gDNA sequence snippet

TTCTTGTGCCAAAACAGACATAGGCTCAGAAAATTCTGAAC

original cDNA sequence snippet

TTCTTGTGCCAAAACAGACACAGGCTCAGAAAATTCTGAAC

altered cDNA sequence snippet

TTCTTGTGCCAAAACAGACATAGGCTCAGAAAATTCTGAAC

wildtype AA sequence

mutated AA sequence

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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999533 (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)

chr10:115922774G>AN/A show variant in all transcripts IGV

HGNC symbol

CCDC186

Ensembl transcript ID

ENST00000369285

Genbank transcript ID

N/A

UniProt peptide

Q7Z3E2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.254C>T
cDNA.628C>T
g.11206C>T

AA changes

T85I Score: 89 explain score(s)

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

frameshift

known variant

Reference ID: rs1061159

database	homozygous (A/A)	heterozygous	allele carriers
1000G	157	724	881
ExAC	2853	19262	22115

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.063	0
	-1.687	0
(flanking)	0.054	0.022

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 increased	11199	wt: 0.46 / mu: 0.76	wt: CCAAAACAGACACAG mu: CCAAAACAGACATAG	AAAA\|caga
Donor gained	11202	0.38	mu: AAACAGACATAGGCT	ACAG\|acat

distance from splice site

315

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000002957

Mmulatta

not conserved

ENSMMUG00000022514

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035173

103

Ggallus

all identical

ENSGALG00000008956

TCSERRVEGSM

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000061020

468

SHKETKDRL

Dmelanogaster

no alignment

FBgn0036614

n/a

Celegans

no alignment

Y49E10.23

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
201	712	COILED	Potential.	might get lost (downstream of altered splice site)
209	209	CONFLICT	I -> T (in Ref. 2; AAH70368).	might get lost (downstream of altered splice site)
614	614	CONFLICT	D -> I (in Ref. 4; BAA91480).	might get lost (downstream of altered splice site)
710	747	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
745	745	CONFLICT	G -> E (in Ref. 1; CAD39031).	might get lost (downstream of altered splice site)
759	803	COILED	Potential.	might get lost (downstream of altered splice site)
855	894	COILED	Potential.	might get lost (downstream of altered splice site)
857	857	CONFLICT	Q -> L (in Ref. 1; CAD97928).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

636 / 636

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

212 / 212

position of stopcodon in wt / mu cDNA

1010 / 1010

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

375 / 375

chromosome

strand

-1

last intron/exon boundary

314

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

636

coding sequence (CDS) position

254

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

628

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

11206

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

115922774

original gDNA sequence snippet

TTCTTGTGCCAAAACAGACACAGGCTCAGAAAATTCTGAAC

altered gDNA sequence snippet

TTCTTGTGCCAAAACAGACATAGGCTCAGAAAATTCTGAAC

original cDNA sequence snippet

TTCTTGTGCCAAAACAGACACAGGCTCAGAAAATTCTGAAC

altered cDNA sequence snippet

TTCTTGTGCCAAAACAGACATAGGCTCAGAAAATTCTGAAC

wildtype AA sequence

mutated AA sequence

speed

0.45 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999483 (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)

chr10:115922774G>AN/A show variant in all transcripts IGV

HGNC symbol

CCDC186

Ensembl transcript ID

ENST00000369287

Genbank transcript ID

NM_018017

UniProt peptide

Q7Z3E2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.254C>T
cDNA.521C>T
g.11206C>T

AA changes

T85I Score: 89 explain score(s)

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

frameshift

known variant

Reference ID: rs1061159

database	homozygous (A/A)	heterozygous	allele carriers
1000G	157	724	881
ExAC	2853	19262	22115

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.063	0
	-1.687	0
(flanking)	0.054	0.022

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 increased	11199	wt: 0.46 / mu: 0.76	wt: CCAAAACAGACACAG mu: CCAAAACAGACATAG	AAAA\|caga
Donor gained	11202	0.38	mu: AAACAGACATAGGCT	ACAG\|acat

distance from splice site

315

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000002957

Mmulatta

not conserved

ENSMMUG00000022514

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035173

103

Ggallus

all identical

ENSGALG00000008956

TCSERRVEGSM

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000061020

n/a

Dmelanogaster

no alignment

FBgn0036614

n/a

Celegans

no alignment

Y49E10.23

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
201	712	COILED	Potential.	might get lost (downstream of altered splice site)
209	209	CONFLICT	I -> T (in Ref. 2; AAH70368).	might get lost (downstream of altered splice site)
614	614	CONFLICT	D -> I (in Ref. 4; BAA91480).	might get lost (downstream of altered splice site)
710	747	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
745	745	CONFLICT	G -> E (in Ref. 1; CAD39031).	might get lost (downstream of altered splice site)
759	803	COILED	Potential.	might get lost (downstream of altered splice site)
855	894	COILED	Potential.	might get lost (downstream of altered splice site)
857	857	CONFLICT	Q -> L (in Ref. 1; CAD97928).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2697 / 2697

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

899 / 899

position of stopcodon in wt / mu cDNA

2964 / 2964

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

268 / 268

chromosome

strand

-1

last intron/exon boundary

2881

theoretical NMD boundary in CDS

2563

length of CDS

2697

coding sequence (CDS) position

254

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

521

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

11206

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

115922774

original gDNA sequence snippet

TTCTTGTGCCAAAACAGACACAGGCTCAGAAAATTCTGAAC

altered gDNA sequence snippet

TTCTTGTGCCAAAACAGACATAGGCTCAGAAAATTCTGAAC

original cDNA sequence snippet

TTCTTGTGCCAAAACAGACACAGGCTCAGAAAATTCTGAAC

altered cDNA sequence snippet

TTCTTGTGCCAAAACAGACATAGGCTCAGAAAATTCTGAAC

wildtype AA sequence

MSETDHIAST SSDKNVGKTP ELKEDSCNLF SGNESSKLEN ESKLLSLNTD KTLCQPNEHN
NRIEAQENYI PDHGGGEDSC AKTDTGSENS EQIANFPSGN FAKHISKTNE TEQKVTQILV
ELRSSTFPES ANEKTYSESP YDTDCTKKFI SKIKSVSASE DLLEEIESEL LSTEFAEHRV
PNGMNKGEHA LVLFEKCVQD KYLQQEHIIK KLIKENKKHQ ELFVDICSEK DNLREELKKR
TETEKQHMNT IKQLESRIEE LNKEVKASRD QLIAQDVTAK NAVQQLHKEM AQRMEQANKK
CEEARQEKEA MVMKYVRGEK ESLDLRKEKE TLEKKLRDAN KELEKNTNKI KQLSQEKGRL
HQLYETKEGE TTRLIREIDK LKEDINSHVI KVKWAQNKLK AEMDSHKETK DKLKETTTKL
TQAKEEADQI RKNCQDMIKT YQESEEIKSN ELDAKLRVTK GELEKQMQEK SDQLEMHHAK
IKELEDLKRT FKEGMDELRT LRTKVKCLED ERLRTEDELS KYKEIINRQK AEIQNLLDKV
KTADQLQEQL QRGKQEIENL KEEVESLNSL INDLQKDIEG SRKRESELLL FTERLTSKNA
QLQSESNSLQ SQFDKVSCSE SQLQSQCEQM KQTNINLESR LLKEEELRKE EVQTLQAELA
CRQTEVKALS TQVEELKDEL VTQRRKHASS IKDLTKQLQQ ARRKLDQVES GSYDKEVSSM
GSRSSSSGSL NARSSAEDRS PENTGSSVAV DNFPQVDKAM LIERIVRLQK AHARKNEKIE
FMEDHIKQLV EEIRKKTKII QSYILREESG TLSSEASDFN KVHLSRRGGI MASLYTSHPA
DNGLTLELSL EINRKLQAVL EDTLLKNITL KENLQTLGTE IERLIKHQHE LEQRTKKT*

mutated AA sequence

MSETDHIAST SSDKNVGKTP ELKEDSCNLF SGNESSKLEN ESKLLSLNTD KTLCQPNEHN
NRIEAQENYI PDHGGGEDSC AKTDIGSENS EQIANFPSGN FAKHISKTNE TEQKVTQILV
ELRSSTFPES ANEKTYSESP YDTDCTKKFI SKIKSVSASE DLLEEIESEL LSTEFAEHRV
PNGMNKGEHA LVLFEKCVQD KYLQQEHIIK KLIKENKKHQ ELFVDICSEK DNLREELKKR
TETEKQHMNT IKQLESRIEE LNKEVKASRD QLIAQDVTAK NAVQQLHKEM AQRMEQANKK
CEEARQEKEA MVMKYVRGEK ESLDLRKEKE TLEKKLRDAN KELEKNTNKI KQLSQEKGRL
HQLYETKEGE TTRLIREIDK LKEDINSHVI KVKWAQNKLK AEMDSHKETK DKLKETTTKL
TQAKEEADQI RKNCQDMIKT YQESEEIKSN ELDAKLRVTK GELEKQMQEK SDQLEMHHAK
IKELEDLKRT FKEGMDELRT LRTKVKCLED ERLRTEDELS KYKEIINRQK AEIQNLLDKV
KTADQLQEQL QRGKQEIENL KEEVESLNSL INDLQKDIEG SRKRESELLL FTERLTSKNA
QLQSESNSLQ SQFDKVSCSE SQLQSQCEQM KQTNINLESR LLKEEELRKE EVQTLQAELA
CRQTEVKALS TQVEELKDEL VTQRRKHASS IKDLTKQLQQ ARRKLDQVES GSYDKEVSSM
GSRSSSSGSL NARSSAEDRS PENTGSSVAV DNFPQVDKAM LIERIVRLQK AHARKNEKIE
FMEDHIKQLV EEIRKKTKII QSYILREESG TLSSEASDFN KVHLSRRGGI MASLYTSHPA
DNGLTLELSL EINRKLQAVL EDTLLKNITL KENLQTLGTE IERLIKHQHE LEQRTKKT*

speed

0.54 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