MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000299543
Querying Taster for transcript #2: ENST00000075430
MT speed 0 s - this script 3.356576 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CTDP1	polymorphism_automatic	1.47704071196131e-12	simple_aae		affected		S61A	single base exchange	rs17855830		show file
CTDP1	polymorphism_automatic	1.47704071196131e-12	simple_aae		affected		S61A	single base exchange	rs17855830		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998523 (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)

chr18:77440128T>GN/A show variant in all transcripts IGV

HGNC symbol

CTDP1

Ensembl transcript ID

ENST00000299543

Genbank transcript ID

NM_001202504

UniProt peptide

Q9Y5B0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.181T>G
cDNA.328T>G
g.328T>G

AA changes

S61A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs17855830

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1099	1084	2183
ExAC	1836	1819	3655

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
TFIIIC-110, Transcription Factor, TFIIIC-110 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.889	0.007
	-2.044	0.003
(flanking)	2.362	0.345

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	327	0.60	mu: CAGTCCGCCGGGGCC	GTCC\|gccg

distance from splice site

134

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000010133

Mmulatta

all conserved

ENSMMUG00000009151

Fcatus

no alignment

ENSFCAG00000000566

n/a

Mmusculus

all conserved

ENSMUSG00000033323

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000012998

Drerio

not conserved

ENSDARG00000017522

Dmelanogaster

not conserved

FBgn0035026

Celegans

no alignment

F36F2.6

n/a

Xtropicalis

not conserved

ENSXETG00000000856

protein features

start (aa)	end (aa)	feature	details
61	61	CONFLICT	S -> A (in Ref. 2; AAD42088 and 5; AAH63447).	lost
157	157	CONFLICT	P -> A (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
178	344	DOMAIN	FCP1 homology.	might get lost (downstream of altered splice site)
281	281	CONFLICT	F -> I (in Ref. 5; AAH52576).	might get lost (downstream of altered splice site)
305	305	CONFLICT	E -> K (in Ref. 2; AAD42088).	might get lost (downstream of altered splice site)
390	390	CONFLICT	A -> P (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
455	478	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
478	478	CONFLICT	S -> T (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
486	487	CONFLICT	KP -> NA (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
504	505	CONFLICT	EP -> DA (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
513	513	CONFLICT	L -> V (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
577	582	COMPBIAS	Poly-Glu.	might get lost (downstream of altered splice site)
586	598	HELIX		might get lost (downstream of altered splice site)
629	728	DOMAIN	BRCT.	might get lost (downstream of altered splice site)
656	657	CONFLICT	EH -> DD (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
674	674	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
740	740	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
780	780	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
869	869	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
872	872	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
896	900	CONFLICT	ERTLG -> GADAR (in Ref. 2; AAD42088).	might get lost (downstream of altered splice site)
945	956	HELIX		might get lost (downstream of altered splice site)
957	959	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2886 / 2886

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

962 / 962

position of stopcodon in wt / mu cDNA

3033 / 3033

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

148 / 148

chromosome

strand

last intron/exon boundary

2895

theoretical NMD boundary in CDS

2697

length of CDS

2886

coding sequence (CDS) position

181

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

328

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

328

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

77440128

original gDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCTCCGGGGCCTCTCAGTCCCGT

altered gDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCGCCGGGGCCTCTCAGTCCCGT

original cDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCTCCGGGGCCTCTCAGTCCCGT

altered cDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCGCCGGGGCCTCTCAGTCCCGT

wildtype AA sequence

MEVPAAGRVP AEGAPTAAVA EVRCPGPAPL RLLEWRVAAG AAVRIGSVLA VFEAAASAQS
SGASQSRVAS GGCVRPARPE RRLRSERAGV VRELCAQPGQ VVAPGAVLVR LEGCSHPVVM
KGLCAECGQD LTQLQSKNGK QQVPLSTATV SMVHSVPELM VSSEQAEQLG REDQQRLHRN
RKLVLMVDLD QTLIHTTEQH CQQMSNKGIF HFQLGRGEPM LHTRLRPHCK DFLEKIAKLY
ELHVFTFGSR LYAHTIAGFL DPEKKLFSHR ILSRDECIDP FSKTGNLRNL FPCGDSMVCI
IDDREDVWKF APNLITVKKY VYFQGTGDMN APPGSRESQT RKKVNHSRGT EVSEPSPPVR
DPEGVTQAPG VEPSNGLEKP ARELNGSEAA TPRDSPRPGK PDERDIWPPA QAPTSSQELA
GAPEPQGSCA QGGRVAPGQR PAQGATGTDL DFDLSSDSES SSESEGTKSS SSASDGESEG
KRGRQKPKAA PEGAGALAQG SSLEPGRPAA PSLPGEAEPG AHAPDKEPEL GGQEEGERDG
LCGLGNGCAD RKEAETESQN SELSGVTAGE SLDQSMEEEE EEDTDEDDHL IYLEEILVRV
HTDYYAKYDR YLNKEIEEAP DIRKIVPELK SKVLADVAII FSGLHPTNFP IEKTREHYHA
TALGAKILTR LVLSPDAPDR ATHLIAARAG TEKVLQAQEC GHLHVVNPDW LWSCLERWDK
VEEQLFPLRD DHTKAQRENS PAAFPDREGV PPTALFHPMP VLPKAQPGPE VRIYDSNTGK
LIRTGARGPP APSSSLPIRQ EPSSFRAVPP PQPQMFGEEL PDAQDGEQPG PSRRKRQPSM
SETMPLYTLC KEDLESMDKE VDDILGEGSD DSDSEKRRPE EQEEEPQPRK PGTRRERTLG
APASSERSAA GGRGPRGHKR KLNEEDAASE SSRESSNEDE GSSSEADEMA KALEAELNDL
M*

mutated AA sequence

MEVPAAGRVP AEGAPTAAVA EVRCPGPAPL RLLEWRVAAG AAVRIGSVLA VFEAAASAQS
AGASQSRVAS GGCVRPARPE RRLRSERAGV VRELCAQPGQ VVAPGAVLVR LEGCSHPVVM
KGLCAECGQD LTQLQSKNGK QQVPLSTATV SMVHSVPELM VSSEQAEQLG REDQQRLHRN
RKLVLMVDLD QTLIHTTEQH CQQMSNKGIF HFQLGRGEPM LHTRLRPHCK DFLEKIAKLY
ELHVFTFGSR LYAHTIAGFL DPEKKLFSHR ILSRDECIDP FSKTGNLRNL FPCGDSMVCI
IDDREDVWKF APNLITVKKY VYFQGTGDMN APPGSRESQT RKKVNHSRGT EVSEPSPPVR
DPEGVTQAPG VEPSNGLEKP ARELNGSEAA TPRDSPRPGK PDERDIWPPA QAPTSSQELA
GAPEPQGSCA QGGRVAPGQR PAQGATGTDL DFDLSSDSES SSESEGTKSS SSASDGESEG
KRGRQKPKAA PEGAGALAQG SSLEPGRPAA PSLPGEAEPG AHAPDKEPEL GGQEEGERDG
LCGLGNGCAD RKEAETESQN SELSGVTAGE SLDQSMEEEE EEDTDEDDHL IYLEEILVRV
HTDYYAKYDR YLNKEIEEAP DIRKIVPELK SKVLADVAII FSGLHPTNFP IEKTREHYHA
TALGAKILTR LVLSPDAPDR ATHLIAARAG TEKVLQAQEC GHLHVVNPDW LWSCLERWDK
VEEQLFPLRD DHTKAQRENS PAAFPDREGV PPTALFHPMP VLPKAQPGPE VRIYDSNTGK
LIRTGARGPP APSSSLPIRQ EPSSFRAVPP PQPQMFGEEL PDAQDGEQPG PSRRKRQPSM
SETMPLYTLC KEDLESMDKE VDDILGEGSD DSDSEKRRPE EQEEEPQPRK PGTRRERTLG
APASSERSAA GGRGPRGHKR KLNEEDAASE SSRESSNEDE GSSSEADEMA KALEAELNDL
M*

speed

0.10 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: 0.999999999998523 (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)

chr18:77440128T>GN/A show variant in all transcripts IGV

HGNC symbol

CTDP1

Ensembl transcript ID

ENST00000075430

Genbank transcript ID

NM_048368

UniProt peptide

Q9Y5B0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.181T>G
cDNA.283T>G
g.328T>G

AA changes

S61A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs17855830

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1099	1084	2183
ExAC	1836	1819	3655

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.889	0.007
	-2.044	0.003
(flanking)	2.362	0.345

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	327	0.60	mu: CAGTCCGCCGGGGCC	GTCC\|gccg

distance from splice site

134

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000010133

Mmulatta

all conserved

ENSMMUG00000009151

Fcatus

no alignment

ENSFCAG00000000566

n/a

Mmusculus

all conserved

ENSMUSG00000033323

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000012998

Drerio

not conserved

ENSDARG00000017522

Dmelanogaster

not conserved

FBgn0035026

Celegans

no alignment

F36F2.6

n/a

Xtropicalis

not conserved

ENSXETG00000000856

protein features

start (aa)	end (aa)	feature	details
61	61	CONFLICT	S -> A (in Ref. 2; AAD42088 and 5; AAH63447).	lost
157	157	CONFLICT	P -> A (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
178	344	DOMAIN	FCP1 homology.	might get lost (downstream of altered splice site)
281	281	CONFLICT	F -> I (in Ref. 5; AAH52576).	might get lost (downstream of altered splice site)
305	305	CONFLICT	E -> K (in Ref. 2; AAD42088).	might get lost (downstream of altered splice site)
390	390	CONFLICT	A -> P (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
455	478	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
478	478	CONFLICT	S -> T (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
486	487	CONFLICT	KP -> NA (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
504	505	CONFLICT	EP -> DA (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
513	513	CONFLICT	L -> V (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
577	582	COMPBIAS	Poly-Glu.	might get lost (downstream of altered splice site)
586	598	HELIX		might get lost (downstream of altered splice site)
629	728	DOMAIN	BRCT.	might get lost (downstream of altered splice site)
656	657	CONFLICT	EH -> DD (in Ref. 1; AAC64549).	might get lost (downstream of altered splice site)
674	674	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
740	740	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
780	780	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
869	869	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
872	872	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
896	900	CONFLICT	ERTLG -> GADAR (in Ref. 2; AAD42088).	might get lost (downstream of altered splice site)
945	956	HELIX		might get lost (downstream of altered splice site)
957	959	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2604 / 2604

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

868 / 868

position of stopcodon in wt / mu cDNA

2706 / 2706

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

103 / 103

chromosome

strand

last intron/exon boundary

2687

theoretical NMD boundary in CDS

2534

length of CDS

2604

coding sequence (CDS) position

181

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

283

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

328

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

77440128

original gDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCTCCGGGGCCTCTCAGTCCCGT

altered gDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCGCCGGGGCCTCTCAGTCCCGT

original cDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCTCCGGGGCCTCTCAGTCCCGT

altered cDNA sequence snippet

CCGCCGCCTCCGCGCAGTCCGCCGGGGCCTCTCAGTCCCGT

wildtype AA sequence

MEVPAAGRVP AEGAPTAAVA EVRCPGPAPL RLLEWRVAAG AAVRIGSVLA VFEAAASAQS
SGASQSRVAS GGCVRPARPE RRLRSERAGV VRELCAQPGQ VVAPGAVLVR LEGCSHPVVM
KGLCAECGQD LTQLQSKNGK QQVPLSTATV SMVHSVPELM VSSEQAEQLG REDQQRLHRN
RKLVLMVDLD QTLIHTTEQH CQQMSNKGIF HFQLGRGEPM LHTRLRPHCK DFLEKIAKLY
ELHVFTFGSR LYAHTIAGFL DPEKKLFSHR ILSRDECIDP FSKTGNLRNL FPCGDSMVCI
IDDREDVWKF APNLITVKKY VYFQGTGDMN APPGSRESQT RKKVNHSRGT EVSEPSPPVR
DPEGVTQAPG VEPSNGLEKP ARELNGSEAA TPRDSPRPGK PDERDIWPPA QAPTSSQELA
GAPEPQGSCA QGGRVAPGQR PAQGATGTDL DFDLSSDSES SSESEGTKSS SSASDGESEG
KRGRQKPKAA PEGAGALAQG SSLEPGRPAA PSLPGEAEPG AHAPDKEPEL GGQEEGERDG
LCGLGNGCAD RKEAETESQN SELSGVTAGE SLDQSMEEEE EEDTDEDDHL IYLEEILVRV
HTDYYAKYDR YLNKEIEEAP DIRKIVPELK SKVLADVAII FSGLHPTNFP IEKTREHYHA
TALGAKILTR LVLSPDAPDR ATHLIAARAG TEKVLQAQEC GHLHVVNPDW LWSCLERWDK
VEEQLFPLRD DHTKAQRENS PAAFPDREGV PPTALFHPMP VLPKAQPGPE VRIYDSNTGK
LIRTGARGPP APSSSLPIRQ EPSSFRWTTS LEKAATTATA RRGGLRSRRR SPSPGSQGPA
GSGRSGHLRP ARGARQGAGG PEATRGS*

mutated AA sequence

MEVPAAGRVP AEGAPTAAVA EVRCPGPAPL RLLEWRVAAG AAVRIGSVLA VFEAAASAQS
AGASQSRVAS GGCVRPARPE RRLRSERAGV VRELCAQPGQ VVAPGAVLVR LEGCSHPVVM
KGLCAECGQD LTQLQSKNGK QQVPLSTATV SMVHSVPELM VSSEQAEQLG REDQQRLHRN
RKLVLMVDLD QTLIHTTEQH CQQMSNKGIF HFQLGRGEPM LHTRLRPHCK DFLEKIAKLY
ELHVFTFGSR LYAHTIAGFL DPEKKLFSHR ILSRDECIDP FSKTGNLRNL FPCGDSMVCI
IDDREDVWKF APNLITVKKY VYFQGTGDMN APPGSRESQT RKKVNHSRGT EVSEPSPPVR
DPEGVTQAPG VEPSNGLEKP ARELNGSEAA TPRDSPRPGK PDERDIWPPA QAPTSSQELA
GAPEPQGSCA QGGRVAPGQR PAQGATGTDL DFDLSSDSES SSESEGTKSS SSASDGESEG
KRGRQKPKAA PEGAGALAQG SSLEPGRPAA PSLPGEAEPG AHAPDKEPEL GGQEEGERDG
LCGLGNGCAD RKEAETESQN SELSGVTAGE SLDQSMEEEE EEDTDEDDHL IYLEEILVRV
HTDYYAKYDR YLNKEIEEAP DIRKIVPELK SKVLADVAII FSGLHPTNFP IEKTREHYHA
TALGAKILTR LVLSPDAPDR ATHLIAARAG TEKVLQAQEC GHLHVVNPDW LWSCLERWDK
VEEQLFPLRD DHTKAQRENS PAAFPDREGV PPTALFHPMP VLPKAQPGPE VRIYDSNTGK
LIRTGARGPP APSSSLPIRQ EPSSFRWTTS LEKAATTATA RRGGLRSRRR SPSPGSQGPA
GSGRSGHLRP ARGARQGAGG PEATRGS*

speed

1.27 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems