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: ENST00000421127
Querying Taster for transcript #2: ENST00000528266
Querying Taster for transcript #3: ENST00000445048
Querying Taster for transcript #4: ENST00000343901
MT speed 0 s - this script 4.768375 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CCDC17	polymorphism_automatic	2.17269535696119e-11	simple_aae		affected		S580N	single base exchange	rs3014246		show file
CCDC17	polymorphism_automatic	2.17269535696119e-11	simple_aae		affected		S571N	single base exchange	rs3014246		show file
CCDC17	polymorphism_automatic	2.17269535696119e-11	simple_aae		affected		S548N	single base exchange	rs3014246		show file
CCDC17	polymorphism_automatic	6.07319750045576e-11	simple_aae		affected		S68N	single base exchange	rs3014246		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999978273 (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)

chr1:46086077C>TN/A show variant in all transcripts IGV

HGNC symbol

CCDC17

Ensembl transcript ID

ENST00000528266

Genbank transcript ID

NM_001114938

UniProt peptide

Q96LX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1739G>A
cDNA.1887G>A
g.3653G>A

AA changes

S580N Score: 46 explain score(s)

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

580

frameshift

known variant

Reference ID: rs3014246

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1217	1004	2221
ExAC	24817	-16867	7950

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.169	0.06
	-0.334	0.065
(flanking)	1.225	0.477

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	3648	wt: 0.73 / mu: 0.98	wt: CTGGAAGCCAGCTTC mu: CTGGAAGCCAACTTC	GGAA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

580

mutated

all conserved

580

Ptroglodytes

all conserved

ENSPTRG00000000679

580

Mmulatta

all conserved

ENSMMUG00000023432

401

Fcatus

not conserved

ENSFCAG00000002862

303

Mmusculus

all identical

ENSMUSG00000034035

532

Ggallus

no alignment

ENSGALG00000010272

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000090480

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
615	615	CONFLICT	S -> F (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1869 / 1869

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

623 / 623

position of stopcodon in wt / mu cDNA

2017 / 2017

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

149 / 149

chromosome

strand

-1

last intron/exon boundary

1859

theoretical NMD boundary in CDS

1660

length of CDS

1869

coding sequence (CDS) position

1739

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

1887

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

3653

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

46086077

original gDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered gDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

original cDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered cDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

wildtype AA sequence

MDSHSGEPAL LPCGTCDMVF RSSALLATHT QRFCIGHPTQ EMTFGAQASV ATEPQRAAVV
PQEHQGVPQE PQGLPDQQAS RSALKRLTEE VQWLRLSLQE MRPWITEVPR VFAGPWTRSE
ARPQSPMSEA VGSPSERLRA LFRTRARRVA EMEAQSRALQ LRGEELSRRL QVVACTRGGM
SRLFGLEQEI RELQAEAGRT RGALEVLGAR IQELQAEPGN PLSSRREAEL YSPVQKANPG
TLAAEIRALR EAYIRDGGRD PGVLGQIWQL QVEASALELQ RSQTRRGRAG ATSGELPVVE
AENRRLEAEI LALQMQRGRA PLGPQDLRLL GDASLQPKGR RDPPLLPPPV APPLPPLPGF
SEPQLPGTMT RNLGLDSHFL LPTSDMLGPA PYDPGAGLVI FYDFLRGLEA SWIWVQLRTG
LARDGRDTGR TTALPPALCL PPPPAPGPMG NCAILASRQP VPRLPPSSSV SLVCELQVWQ
GLAWARAPQP KAWVSLGLFD QDQRVLSGRW RLPLRALPLD PSLSLGQLNG IPQAGQAELF
LRLVNARDAA VQTLAEINPA SVHEYQYPPP VSSTSSLEAS FLTPAVGFAD PPPRTEEPLS
GVKDRDEGLG PHHSSDLPPV SF*

mutated AA sequence

speed

1.10 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: 0.999999999978273 (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)

chr1:46086077C>TN/A show variant in all transcripts IGV

HGNC symbol

CCDC17

Ensembl transcript ID

ENST00000421127

Genbank transcript ID

NM_001190182

UniProt peptide

Q96LX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1712G>A
cDNA.1856G>A
g.3653G>A

AA changes

S571N Score: 46 explain score(s)

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

571

frameshift

known variant

Reference ID: rs3014246

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1217	1004	2221
ExAC	24817	-16867	7950

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.169	0.06
	-0.334	0.065
(flanking)	1.225	0.477

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	3648	wt: 0.73 / mu: 0.98	wt: CTGGAAGCCAGCTTC mu: CTGGAAGCCAACTTC	GGAA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

571

mutated

all conserved

571

Ptroglodytes

all conserved

ENSPTRG00000000679

580

Mmulatta

all conserved

ENSMMUG00000023432

401

Fcatus

not conserved

ENSFCAG00000002862

303

Mmusculus

all identical

ENSMUSG00000034035

532

Ggallus

no alignment

ENSGALG00000010272

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000090480

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
615	615	CONFLICT	S -> F (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1842 / 1842

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

614 / 614

position of stopcodon in wt / mu cDNA

1986 / 1986

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

145 / 145

chromosome

strand

-1

last intron/exon boundary

1828

theoretical NMD boundary in CDS

1633

length of CDS

1842

coding sequence (CDS) position

1712

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

1856

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

3653

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

46086077

original gDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered gDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

original cDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered cDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

wildtype AA sequence

MDSHSGEPAL LPCGTCDMVF RSSALLATHT QRFCIGHPTQ EMTFGAQASV ATEPQRAAVV
PQEHQGVPQE PQGLPDQQAS RSALKRLTEE EMRPWITEVP RVFAGPWTRS EARPQSPMSE
AVGSPSERLR ALFRTRARRV AEMEAQSRAL QLRGEELSRR LQVVACTRGG MSRLFGLEQE
IRELQAEAGR TRGALEVLGA RIQELQAEPG NPLSSRREAE LYSPVQKANP GTLAAEIRAL
REAYIRDGGR DPGVLGQIWQ LQVEASALEL QRSQTRRGRA GATSGELPVV EAENRRLEAE
ILALQMQRGR APLGPQDLRL LGDASLQPKG RRDPPLLPPP VAPPLPPLPG FSEPQLPGTM
TRNLGLDSHF LLPTSDMLGP APYDPGAGLV IFYDFLRGLE ASWIWVQLRT GLARDGRDTG
RTTALPPALC LPPPPAPGPM GNCAILASRQ PVPRLPPSSS VSLVCELQVW QGLAWARAPQ
PKAWVSLGLF DQDQRVLSGR WRLPLRALPL DPSLSLGQLN GIPQAGQAEL FLRLVNARDA
AVQTLAEINP ASVHEYQYPP PVSSTSSLEA SFLTPAVGFA DPPPRTEEPL SGVKDRDEGL
GPHHSSDLPP VSF*

mutated AA sequence

speed

1.01 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999978273 (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)

chr1:46086077C>TN/A show variant in all transcripts IGV

HGNC symbol

CCDC17

Ensembl transcript ID

ENST00000343901

Genbank transcript ID

N/A

UniProt peptide

Q96LX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1643G>A
cDNA.1791G>A
g.3653G>A

AA changes

S548N Score: 46 explain score(s)

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

548

frameshift

known variant

Reference ID: rs3014246

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1217	1004	2221
ExAC	24817	-16867	7950

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.169	0.06
	-0.334	0.065
(flanking)	1.225	0.477

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	3648	wt: 0.73 / mu: 0.98	wt: CTGGAAGCCAGCTTC mu: CTGGAAGCCAACTTC	GGAA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

548

mutated

all conserved

548

Ptroglodytes

all conserved

ENSPTRG00000000679

580

Mmulatta

all conserved

ENSMMUG00000023432

401

Fcatus

not conserved

ENSFCAG00000002862

303

Mmusculus

all identical

ENSMUSG00000034035

532

Ggallus

no alignment

ENSGALG00000010272

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000090480

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
615	615	CONFLICT	S -> F (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1773 / 1773

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

591 / 591

position of stopcodon in wt / mu cDNA

1921 / 1921

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

149 / 149

chromosome

strand

-1

last intron/exon boundary

1763

theoretical NMD boundary in CDS

1564

length of CDS

1773

coding sequence (CDS) position

1643

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

1791

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

3653

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

46086077

original gDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered gDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

original cDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered cDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

wildtype AA sequence

MDSHSGEPAL LPCGTCDMVF RSSALLATHT QRFCIGHPTQ EMTFGAQASV ATEPQRAAVQ
WLRLSLQEMR PWITEVPRVF AGPWTRSEAR PQSPMSEAVG SPSERLRALF RTRARRVAEM
EAQSRALQLR GEELSRRLQV VACTRGGMSR LFGLEQEIRE LQAEAGRTRG ALEVLGARIQ
ELQAEPGNPL SSRREAELYS PVQKANPGTL AAEIRALREA YIRDGGRDPG VLGQIWQLQV
EASALELQRS QTRRGRAGAT SGELPVVEAE NRRLEAEILA LQMQRGRAPL GPQDLRLLGD
ASLQPKGRRD PPLLPPPVAP PLPPLPGFSE PQLPGTMTRN LGLDSHFLLP TSDMLGPAPY
DPGAGLVIFY DFLRGLEASW IWVQLRTGLA RDGRDTGRTT ALPPALCLPP PPAPGPMGNC
AILASRQPVP RLPPSSSVSL VCELQVWQGL AWARAPQPKA WVSLGLFDQD QRVLSGRWRL
PLRALPLDPS LSLGQLNGIP QAGQAELFLR LVNARDAAVQ TLAEINPASV HEYQYPPPVS
STSSLEASFL TPAVGFADPP PRTEEPLSGV KDRDEGLGPH HSSDLPPVSF *

mutated AA sequence

speed

0.81 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999939268 (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)

chr1:46086077C>TN/A show variant in all transcripts IGV

HGNC symbol

CCDC17

Ensembl transcript ID

ENST00000445048

Genbank transcript ID

N/A

UniProt peptide

Q96LX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.203G>A
cDNA.261G>A
g.3653G>A

AA changes

S68N Score: 46 explain score(s)

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

frameshift

known variant

Reference ID: rs3014246

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1217	1004	2221
ExAC	24817	-16867	7950

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.169	0.06
	-0.334	0.065
(flanking)	1.225	0.477

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	3648	wt: 0.73 / mu: 0.98	wt: CTGGAAGCCAGCTTC mu: CTGGAAGCCAACTTC	GGAA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000000679

580

Mmulatta

all conserved

ENSMMUG00000023432

401

Fcatus

no alignment

ENSFCAG00000002862

n/a

Mmusculus

all identical

ENSMUSG00000034035

531

Ggallus

no alignment

ENSGALG00000010272

n/a

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000090480

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
74	74	CONFLICT	L -> P (in Ref. 1; BAG64867).	might get lost (downstream of altered splice site)
81	102	COILED	Potential.	might get lost (downstream of altered splice site)
146	207	COILED	Potential.	might get lost (downstream of altered splice site)
294	320	COILED	Potential.	might get lost (downstream of altered splice site)
343	366	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
417	417	CONFLICT	L -> E (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)
420	421	CONFLICT	GL -> AS (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)
423	425	CONFLICT	RDG -> HAA (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)
439	439	CONFLICT	C -> F (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)
450	450	CONFLICT	G -> S (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)
615	615	CONFLICT	S -> F (in Ref. 3; AAH29888).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

333 / 333

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

111 / 111

position of stopcodon in wt / mu cDNA

391 / 391

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

59 / 59

chromosome

strand

-1

last intron/exon boundary

233

theoretical NMD boundary in CDS

124

length of CDS

333

coding sequence (CDS) position

203

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

261

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

3653

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

46086077

original gDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered gDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

original cDNA sequence snippet

CACATCTTCACTGGAAGCCAGCTTCCTCACCCCCGCAGTTG

altered cDNA sequence snippet

CACATCTTCACTGGAAGCCAACTTCCTCACCCCCGCAGTTG

wildtype AA sequence

MDSHSGEPAL LPCGTCDMVF RSSALLATHT QRFCIGHPTQ EMTFGAQASV ATEPQRAAVS
STSSLEASFL TPAVGFADPP PRTEEPLSGV KDRDEGLGPH HSSDLPPVSF *

mutated AA sequence

MDSHSGEPAL LPCGTCDMVF RSSALLATHT QRFCIGHPTQ EMTFGAQASV ATEPQRAAVS
STSSLEANFL TPAVGFADPP PRTEEPLSGV KDRDEGLGPH HSSDLPPVSF *

speed

0.81 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