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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000380701
Querying Taster for transcript #2: ENST00000297641
MT speed 1.2 s - this script 3.451057 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CCDC171	polymorphism_automatic	1.43273441000069e-07	simple_aae		affected		K1069R	single base exchange	rs1539172		show file
CCDC171	polymorphism_automatic	1.43273441000069e-07	simple_aae		affected		K1069R	single base exchange	rs1539172		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999856726559 (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)

chr9:15784631A>GN/A show variant in all transcripts IGV

HGNC symbol

CCDC171

Ensembl transcript ID

ENST00000380701

Genbank transcript ID

NM_173550

UniProt peptide

Q6TFL3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3206A>G
cDNA.3534A>G
g.231737A>G

AA changes

K1069R Score: 26 explain score(s)

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

1069

frameshift

known variant

Reference ID: rs1539172

database	homozygous (G/G)	heterozygous	allele carriers
1000G	575	1226	1801
ExAC	14192	4383	18575

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.386	1
	1.128	1
(flanking)	0.501	1

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	231736	0.40	mu: ATTATAGACTTGAAT	TATA\|gact

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1069

mutated

all conserved

1069

Ptroglodytes

all conserved

ENSPTRG00000020787

1069

Mmulatta

all conserved

ENSMMUG00000016731

1068

Fcatus

no alignment

ENSFCAG00000000682

n/a

Mmusculus

all conserved

ENSMUSG00000052407

1071

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000009178

1054

protein features

start (aa)	end (aa)	feature	details
979	1143	COILED	Potential.	lost
1217	1241	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3981 / 3981

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

1327 / 1327

position of stopcodon in wt / mu cDNA

4309 / 4309

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

329 / 329

chromosome

strand

last intron/exon boundary

4082

theoretical NMD boundary in CDS

3703

length of CDS

3981

coding sequence (CDS) position

3206

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

3534

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

231737

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

15784631

original gDNA sequence snippet

ACTACAGGAATTGAATTATAAACTTGAATTGCACTCCAGTG

altered gDNA sequence snippet

ACTACAGGAATTGAATTATAGACTTGAATTGCACTCCAGTG

original cDNA sequence snippet

ACTACAGGAATTGAATTATAAACTTGAATTGCACTCCAGTG

altered cDNA sequence snippet

ACTACAGGAATTGAATTATAGACTTGAATTGCACTCCAGTG

wildtype AA sequence

MNLNTSSNTG DTQRLKIASL DVKQILKNET ELDITDNLRK KLHWAKKEKL EITTKHNAEL
ASYESQIAKL RSEVEKGEAL RQSLEYDLAV ARKEAGLGRR AAEERLAEAH RIQEKLCAQN
SELQAKTNET EKAFQTSQQK WKEECRRFEH DLEERDNMIQ NCNREYDLLM KEKSRLEKTL
QEALEKHQRE KNEMESHIRE TALEEFRLQE EQWEAERREL QFIVQEQDTA VQNMHKKVEK
LETEHMDCSD LLRRQTSELE FSTQREERLR KEFEATTLRV RKLEENIEAE RAAHLESKFN
SEIIQLRIRD LEGALQVEKA SQAEAVADLE IIKNEFKEVE SAYEREKHNA QESFAKLNLL
EKEYFSKNKK LNEDIEEQKK VIIDLSKRLQ YNEKSCSELQ EELVMAKKHQ AFLVETCENN
VKELESILDS FTVSGQWTSG IHKDKDKPPS FSVVLERLRR TLTDYQNKLE DASNEEKACN
ELDSTKQKID SHTKNIKELQ DKLADVNKEL SHLHTKCADR EALISTLKVE LQNVLHCWEK
EKAQAAQSES ELQKLSQAFH KDAEEKLTFL HTLYQHLVAG CVLIKQPEGM LDKFSWSELC
AVLQENVDAL IADLNRANEK IRHLEYICKN KSDTMRELQQ TQEDTFTKVA EQIKAQESCW
HRQKKELELQ YSELFLEVQK RAQKFQEIAE KNMEKLNHIE KSHEQLVLEN SHFKKLLSQT
QREQMSLLAA CALMAGALYP LYSRSCALST QRDFLQEQVN TFELFKLEIR TLAQALSTVE
EKKQEEAKMK KKTFKGLIRI FRKGVIAVLA ANRLKILGQS CASLFTWMES FKEGIGMLVC
TGEPQDKHKF PKHQKEQLRC LQALSWLTSS DLLAAIISSM AELQDVIGKA DPNSRICGHL
LIGAAKNSFA KLMDKISLVM ECIPLHSSRS ITYVEKDSLV QRLAHGLHKV NTLALKYGLR
GHVPITKSTA SLQKQILGFT QRLHAAEVER RSLRLEVTEF KRSVNEMKKE LDKAQGLQMQ
LNEFKQSKLI THEKFESACE ELNNALLREE QAQMLLNEQA QQLQELNYKL ELHSSEEADK
NQTLGEAVKS LSEAKMELRR KDQSLRQLNR HLTQLEQDKR RLEENIHDAE SALRMAAKDK
ECVANHMRAV ENTLHKVRDQ ISLSWSAASR NDFTLQLPKL HLETFAMEGL KGGPEVVACQ
AMIKSFMDVY QLASTRIMTL EKEMTSHRSH IAALKSELHT ACLRENASLQ SIGSRDHSNL
SIPSRAPLPA DTTGIGDFLP LKAELDTTYT FLKETFINTV PHALTSSHSS PVTMSANANR
PTQIGL*

mutated AA sequence

MNLNTSSNTG DTQRLKIASL DVKQILKNET ELDITDNLRK KLHWAKKEKL EITTKHNAEL
ASYESQIAKL RSEVEKGEAL RQSLEYDLAV ARKEAGLGRR AAEERLAEAH RIQEKLCAQN
SELQAKTNET EKAFQTSQQK WKEECRRFEH DLEERDNMIQ NCNREYDLLM KEKSRLEKTL
QEALEKHQRE KNEMESHIRE TALEEFRLQE EQWEAERREL QFIVQEQDTA VQNMHKKVEK
LETEHMDCSD LLRRQTSELE FSTQREERLR KEFEATTLRV RKLEENIEAE RAAHLESKFN
SEIIQLRIRD LEGALQVEKA SQAEAVADLE IIKNEFKEVE SAYEREKHNA QESFAKLNLL
EKEYFSKNKK LNEDIEEQKK VIIDLSKRLQ YNEKSCSELQ EELVMAKKHQ AFLVETCENN
VKELESILDS FTVSGQWTSG IHKDKDKPPS FSVVLERLRR TLTDYQNKLE DASNEEKACN
ELDSTKQKID SHTKNIKELQ DKLADVNKEL SHLHTKCADR EALISTLKVE LQNVLHCWEK
EKAQAAQSES ELQKLSQAFH KDAEEKLTFL HTLYQHLVAG CVLIKQPEGM LDKFSWSELC
AVLQENVDAL IADLNRANEK IRHLEYICKN KSDTMRELQQ TQEDTFTKVA EQIKAQESCW
HRQKKELELQ YSELFLEVQK RAQKFQEIAE KNMEKLNHIE KSHEQLVLEN SHFKKLLSQT
QREQMSLLAA CALMAGALYP LYSRSCALST QRDFLQEQVN TFELFKLEIR TLAQALSTVE
EKKQEEAKMK KKTFKGLIRI FRKGVIAVLA ANRLKILGQS CASLFTWMES FKEGIGMLVC
TGEPQDKHKF PKHQKEQLRC LQALSWLTSS DLLAAIISSM AELQDVIGKA DPNSRICGHL
LIGAAKNSFA KLMDKISLVM ECIPLHSSRS ITYVEKDSLV QRLAHGLHKV NTLALKYGLR
GHVPITKSTA SLQKQILGFT QRLHAAEVER RSLRLEVTEF KRSVNEMKKE LDKAQGLQMQ
LNEFKQSKLI THEKFESACE ELNNALLREE QAQMLLNEQA QQLQELNYRL ELHSSEEADK
NQTLGEAVKS LSEAKMELRR KDQSLRQLNR HLTQLEQDKR RLEENIHDAE SALRMAAKDK
ECVANHMRAV ENTLHKVRDQ ISLSWSAASR NDFTLQLPKL HLETFAMEGL KGGPEVVACQ
AMIKSFMDVY QLASTRIMTL EKEMTSHRSH IAALKSELHT ACLRENASLQ SIGSRDHSNL
SIPSRAPLPA DTTGIGDFLP LKAELDTTYT FLKETFINTV PHALTSSHSS PVTMSANANR
PTQIGL*

speed

0.47 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: 0.999999856726559 (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)

chr9:15784631A>GN/A show variant in all transcripts IGV

HGNC symbol

CCDC171

Ensembl transcript ID

ENST00000297641

Genbank transcript ID

N/A

UniProt peptide

Q6TFL3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3206A>G
cDNA.3613A>G
g.231737A>G

AA changes

K1069R Score: 26 explain score(s)

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

1069

frameshift

known variant

Reference ID: rs1539172

database	homozygous (G/G)	heterozygous	allele carriers
1000G	575	1226	1801
ExAC	14192	4383	18575

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.386	1
	1.128	1
(flanking)	0.501	1

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	231736	0.40	mu: ATTATAGACTTGAAT	TATA\|gact

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1069

mutated

all conserved

1069

Ptroglodytes

all conserved

ENSPTRG00000020787

1069

Mmulatta

all conserved

ENSMMUG00000016731

1068

Fcatus

no alignment

ENSFCAG00000000682

n/a

Mmusculus

all conserved

ENSMUSG00000052407

1071

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000009178

1054

protein features

start (aa)	end (aa)	feature	details
979	1143	COILED	Potential.	lost
1217	1241	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3690 / 3690

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

1230 / 1230

position of stopcodon in wt / mu cDNA

4097 / 4097

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

408 / 408

chromosome

strand

last intron/exon boundary

4008

theoretical NMD boundary in CDS

3550

length of CDS

3690

coding sequence (CDS) position

3206

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

3613

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

231737

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

15784631

original gDNA sequence snippet

ACTACAGGAATTGAATTATAAACTTGAATTGCACTCCAGTG

altered gDNA sequence snippet

ACTACAGGAATTGAATTATAGACTTGAATTGCACTCCAGTG

original cDNA sequence snippet

ACTACAGGAATTGAATTATAAACTTGAATTGCACTCCAGTG

altered cDNA sequence snippet

ACTACAGGAATTGAATTATAGACTTGAATTGCACTCCAGTG

wildtype AA sequence

mutated AA sequence

MNLNTSSNTG DTQRLKIASL DVKQILKNET ELDITDNLRK KLHWAKKEKL EITTKHNAEL
ASYESQIAKL RSEVEKGEAL RQSLEYDLAV ARKEAGLGRR AAEERLAEAH RIQEKLCAQN
SELQAKTNET EKAFQTSQQK WKEECRRFEH DLEERDNMIQ NCNREYDLLM KEKSRLEKTL
QEALEKHQRE KNEMESHIRE TALEEFRLQE EQWEAERREL QFIVQEQDTA VQNMHKKVEK
LETEHMDCSD LLRRQTSELE FSTQREERLR KEFEATTLRV RKLEENIEAE RAAHLESKFN
SEIIQLRIRD LEGALQVEKA SQAEAVADLE IIKNEFKEVE SAYEREKHNA QESFAKLNLL
EKEYFSKNKK LNEDIEEQKK VIIDLSKRLQ YNEKSCSELQ EELVMAKKHQ AFLVETCENN
VKELESILDS FTVSGQWTSG IHKDKDKPPS FSVVLERLRR TLTDYQNKLE DASNEEKACN
ELDSTKQKID SHTKNIKELQ DKLADVNKEL SHLHTKCADR EALISTLKVE LQNVLHCWEK
EKAQAAQSES ELQKLSQAFH KDAEEKLTFL HTLYQHLVAG CVLIKQPEGM LDKFSWSELC
AVLQENVDAL IADLNRANEK IRHLEYICKN KSDTMRELQQ TQEDTFTKVA EQIKAQESCW
HRQKKELELQ YSELFLEVQK RAQKFQEIAE KNMEKLNHIE KSHEQLVLEN SHFKKLLSQT
QREQMSLLAA CALMAGALYP LYSRSCALST QRDFLQEQVN TFELFKLEIR TLAQALSTVE
EKKQEEAKMK KKTFKGLIRI FRKGVIAVLA ANRLKILGQS CASLFTWMES FKEGIGMLVC
TGEPQDKHKF PKHQKEQLRC LQALSWLTSS DLLAAIISSM AELQDVIGKA DPNSRICGHL
LIGAAKNSFA KLMDKISLVM ECIPLHSSRS ITYVEKDSLV QRLAHGLHKV NTLALKYGLR
GHVPITKSTA SLQKQILGFT QRLHAAEVER RSLRLEVTEF KRSVNEMKKE LDKAQGLQMQ
LNEFKQSKLI THEKFESACE ELNNALLREE QAQMLLNEQA QQLQELNYRL ELHSSEEADK
NQTLGEAVKS LSEAKMELRR KDQSLRQLNR HLTQLEQDKR RLEENIHDAE SALRMAAKDK
ECVANHMRAV ENTLHKVRDQ ISLSWSAASR NDFTLQLPKL HLETFAMEGL KGGPEVVACQ
VRVQWCDHSS LQSQMPGLKQ SSCLSLLST*

speed

0.73 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems