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: ENST00000361413
Querying Taster for transcript #2: ENST00000572370
Querying Taster for transcript #3: ENST00000542606
MT speed 0 s - this script 4.661079 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KIAA0753	polymorphism_automatic	0.842601792607032	simple_aae		affected		E375D	single base exchange	rs9889363		show file
KIAA0753	polymorphism_automatic	0.842601792607032	simple_aae		affected		E76D	single base exchange	rs9889363		show file
KIAA0753	polymorphism_automatic	0.842601792607032	simple_aae		affected		E76D	single base exchange	rs9889363		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.157398207392968 (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)

chr17:6524298T>AN/A show variant in all transcripts IGV

HGNC symbol

KIAA0753

Ensembl transcript ID

ENST00000361413

Genbank transcript ID

NM_014804

UniProt peptide

Q2KHM9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1125A>T
cDNA.1484A>T
g.19950A>T

AA changes

E375D Score: 45 explain score(s)

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

375

frameshift

known variant

Reference ID: rs9889363

database	homozygous (A/A)	heterozygous	allele carriers
1000G	251	1040	1291
ExAC	8426	15915	24341

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.587	1
	1.322	1
(flanking)	2.587	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
Acc gained	19948	0.54	mu: AGGCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAA	ctgg\|ATAA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

375

mutated

all conserved

375

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000003784

383

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020807

367

Ggallus

all identical

ENSGALG00000006011

376

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031158

326

protein features

start (aa)	end (aa)	feature	details
616	642	COILED	Potential.	might get lost (downstream of altered splice site)
821	821	CONFLICT	S -> G (in Ref. 1; BAA34473).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2904 / 2904

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

968 / 968

position of stopcodon in wt / mu cDNA

3263 / 3263

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

360 / 360

chromosome

strand

-1

last intron/exon boundary

3146

theoretical NMD boundary in CDS

2736

length of CDS

2904

coding sequence (CDS) position

1125

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

1484

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

19950

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

6524298

original gDNA sequence snippet

GCTTTGGAATCTCTCCTGGAAAAGAAACTGTCACCAAAAAA

altered gDNA sequence snippet

GCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAAAA

original cDNA sequence snippet

GCTTTGGAATCTCTCCTGGAAAAGAAACTGTCACCAAAAAA

altered cDNA sequence snippet

GCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAAAA

wildtype AA sequence

MGPGQPASTC VHLAPRTQLD GRSDPKVLQT QNQLQFNRNV PTHSSNLAIR YSCPHAIRIE
KLKHSYNESY HCKDADCRVG PDLGSSVSFS VISQERLSYA VHLARRDVKR RQFEKHIKEH
HLRSQPQSSQ KCGHTKYKIP DHRVERKESK SQAACQCSHQ PSKVEISSSG AKVYLYSSHP
GQSDLTVPNS PPTHDPGLQP HPRIGDHKNI SEQKSLLEVQ RLQKELSSCI HKIEEVTKKD
RLEEALDPDE ERRIRIRRQE QAARSARMLY VLQQQVKEIQ EELDKLSPHK IKHTKKSWAM
SKLAAAHRGA IRALQMFVTQ FTDRGEHPLP ARCKELGSLI RQLSLCSVKL DADPSVPDVV
IDILQQIEAL ESLLEKKLSP KKVKKCFSEI RSRFPIGSQK ALERWPSTSP KGERRPLTAK
DTFPQETSRP SVAKQLLADK YQPDTELPET QRLQSELDVL DADIVLEEGP FILDQSASFK
DEVLAVAKTK AGKKKPVTEN VPFRKKDTLA PARQQGLRKA ERGRQSQPHS KSRVQQTTVS
SRLKMNRQPV KDRKAPWIPP NPTSPPASPK CAAWLKVKTS PRDATKEPLQ QEDPQEESHL
TGAVEHEAAR LAWLDAETSK RLKELEELKA KEIDSMQKQR LDWLDAETSR RTKELNELKA
EEMYRLQQLS VSATHLADKV EEAVLDRLKP LLVKAQRVNS TTEANIHLKD GSSVNTAKAQ
PAQEVAAVDF ESNNIRQLDD FLEDCASELW AVTHAKILGS ETLATVEDSK DSPDLEIMMR
RMEEMEKYQE SVRQRYNKIA YADPRLWMQE ENNDQKISAI SEKPLSPHPI RITKTVDRKD
PAVNIMLERP CNGNSLDESV GTEEGSEKRE APLLSLAEDS QQKEGRAPLF VPPGMQHSIG
DYCSRFEQYL RIISHEAVGS FNPWLIAESF SEELVDEALG AVAAELQDMC EDYAEAVFTS
EFLEAAT*

mutated AA sequence

MGPGQPASTC VHLAPRTQLD GRSDPKVLQT QNQLQFNRNV PTHSSNLAIR YSCPHAIRIE
KLKHSYNESY HCKDADCRVG PDLGSSVSFS VISQERLSYA VHLARRDVKR RQFEKHIKEH
HLRSQPQSSQ KCGHTKYKIP DHRVERKESK SQAACQCSHQ PSKVEISSSG AKVYLYSSHP
GQSDLTVPNS PPTHDPGLQP HPRIGDHKNI SEQKSLLEVQ RLQKELSSCI HKIEEVTKKD
RLEEALDPDE ERRIRIRRQE QAARSARMLY VLQQQVKEIQ EELDKLSPHK IKHTKKSWAM
SKLAAAHRGA IRALQMFVTQ FTDRGEHPLP ARCKELGSLI RQLSLCSVKL DADPSVPDVV
IDILQQIEAL ESLLDKKLSP KKVKKCFSEI RSRFPIGSQK ALERWPSTSP KGERRPLTAK
DTFPQETSRP SVAKQLLADK YQPDTELPET QRLQSELDVL DADIVLEEGP FILDQSASFK
DEVLAVAKTK AGKKKPVTEN VPFRKKDTLA PARQQGLRKA ERGRQSQPHS KSRVQQTTVS
SRLKMNRQPV KDRKAPWIPP NPTSPPASPK CAAWLKVKTS PRDATKEPLQ QEDPQEESHL
TGAVEHEAAR LAWLDAETSK RLKELEELKA KEIDSMQKQR LDWLDAETSR RTKELNELKA
EEMYRLQQLS VSATHLADKV EEAVLDRLKP LLVKAQRVNS TTEANIHLKD GSSVNTAKAQ
PAQEVAAVDF ESNNIRQLDD FLEDCASELW AVTHAKILGS ETLATVEDSK DSPDLEIMMR
RMEEMEKYQE SVRQRYNKIA YADPRLWMQE ENNDQKISAI SEKPLSPHPI RITKTVDRKD
PAVNIMLERP CNGNSLDESV GTEEGSEKRE APLLSLAEDS QQKEGRAPLF VPPGMQHSIG
DYCSRFEQYL RIISHEAVGS FNPWLIAESF SEELVDEALG AVAAELQDMC EDYAEAVFTS
EFLEAAT*

speed

1.54 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: 0.157398207392968 (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)

chr17:6524298T>AN/A show variant in all transcripts IGV

HGNC symbol

KIAA0753

Ensembl transcript ID

ENST00000572370

Genbank transcript ID

N/A

UniProt peptide

Q2KHM9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.228A>T
cDNA.1126A>T
g.19950A>T

AA changes

E76D Score: 45 explain score(s)

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

frameshift

known variant

Reference ID: rs9889363

database	homozygous (A/A)	heterozygous	allele carriers
1000G	251	1040	1291
ExAC	8426	15915	24341

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.587	1
	1.322	1
(flanking)	2.587	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
Acc gained	19948	0.54	mu: AGGCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAA	ctgg\|ATAA

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

no homologue

Mmulatta

all identical

ENSMMUG00000003784

385

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020807

367

Ggallus

all identical

ENSGALG00000006011

376

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031158

328

protein features

start (aa)	end (aa)	feature	details
250	250	CONFLICT	E -> K (in Ref. 3; BAF85565).	might get lost (downstream of altered splice site)
616	642	COILED	Potential.	might get lost (downstream of altered splice site)
821	821	CONFLICT	S -> G (in Ref. 1; BAA34473).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2007 / 2007

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

669 / 669

position of stopcodon in wt / mu cDNA

2905 / 2905

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

899 / 899

chromosome

strand

-1

last intron/exon boundary

2788

theoretical NMD boundary in CDS

1839

length of CDS

2007

coding sequence (CDS) position

228

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

1126

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

19950

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

6524298

original gDNA sequence snippet

GCTTTGGAATCTCTCCTGGAAAAGAAACTGTCACCAAAAAA

altered gDNA sequence snippet

GCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAAAA

original cDNA sequence snippet

GCTTTGGAATCTCTCCTGGAAAAGAAACTGTCACCAAAAAA

altered cDNA sequence snippet

GCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAAAA

wildtype AA sequence

MSKLAAAHRG AIRALQMFVT QFTDRGEHPL PARCKELGSL IRQLSLCSVK LDADPSVPDV
VIDILQQIEA LESLLEKKLS PKKVKKCFSE IRSRFPIGSQ KALERWPSTS PKGERRPLTA
KDTFPQETSR PSVAKQLLAD KYQPDTELPE TQRLQSELDV LDADIVLEEG PFILDQSASF
KDEVLAVAKT KAGKKKPVTE NVPFRKKDTL APARQQGLRK AERGRQSQPH SKSRVQQTTV
SSRLKMNRQP VKDRKAPWIP PNPTSPPASP KCAAWLKVKT SPRDATKEPL QQEDPQEESH
LTGAVEHEAA RLAWLDAETS KRLKELEELK AKEIDSMQKQ RLDWLDAETS RRTKELNELK
AEEMYRLQQL SVSATHLADK VEEAVLDRLK PLLVKAQRVN STTEANIHLK DGSSVNTAKA
QPAQEVAAVD FESNNIRQLD DFLEDCASEL WAVTHAKILG SETLATVEDS KDSPDLEIMM
RRMEEMEKYQ ESVRQRYNKI AYADPRLWMQ EENNDQKISA ISEKPLSPHP IRITKTVDRK
DPAVNIMLER PCNGNSLDES VGTEEGSEKR EAPLLSLAED SQQKEGRAPL FVPPGMQHSI
GDYCSRFEQY LRIISHEAVG SFNPWLIAES FSEELVDEAL GAVAAELQDM CEDYAEAVFT
SEFLEAAT*

mutated AA sequence

MSKLAAAHRG AIRALQMFVT QFTDRGEHPL PARCKELGSL IRQLSLCSVK LDADPSVPDV
VIDILQQIEA LESLLDKKLS PKKVKKCFSE IRSRFPIGSQ KALERWPSTS PKGERRPLTA
KDTFPQETSR PSVAKQLLAD KYQPDTELPE TQRLQSELDV LDADIVLEEG PFILDQSASF
KDEVLAVAKT KAGKKKPVTE NVPFRKKDTL APARQQGLRK AERGRQSQPH SKSRVQQTTV
SSRLKMNRQP VKDRKAPWIP PNPTSPPASP KCAAWLKVKT SPRDATKEPL QQEDPQEESH
LTGAVEHEAA RLAWLDAETS KRLKELEELK AKEIDSMQKQ RLDWLDAETS RRTKELNELK
AEEMYRLQQL SVSATHLADK VEEAVLDRLK PLLVKAQRVN STTEANIHLK DGSSVNTAKA
QPAQEVAAVD FESNNIRQLD DFLEDCASEL WAVTHAKILG SETLATVEDS KDSPDLEIMM
RRMEEMEKYQ ESVRQRYNKI AYADPRLWMQ EENNDQKISA ISEKPLSPHP IRITKTVDRK
DPAVNIMLER PCNGNSLDES VGTEEGSEKR EAPLLSLAED SQQKEGRAPL FVPPGMQHSI
GDYCSRFEQY LRIISHEAVG SFNPWLIAES FSEELVDEAL GAVAAELQDM CEDYAEAVFT
SEFLEAAT*

speed

1.59 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.157398207392968 (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)

chr17:6524298T>AN/A show variant in all transcripts IGV

HGNC symbol

KIAA0753

Ensembl transcript ID

ENST00000542606

Genbank transcript ID

N/A

UniProt peptide

Q2KHM9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.228A>T
cDNA.1088A>T
g.19950A>T

AA changes

E76D Score: 45 explain score(s)

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

frameshift

known variant

Reference ID: rs9889363

database	homozygous (A/A)	heterozygous	allele carriers
1000G	251	1040	1291
ExAC	8426	15915	24341

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.587	1
	1.322	1
(flanking)	2.587	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
Acc gained	19948	0.54	mu: AGGCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAA	ctgg\|ATAA

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

no homologue

Mmulatta

all identical

ENSMMUG00000003784

385

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020807

367

Ggallus

all identical

ENSGALG00000006011

376

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031158

328

protein features

start (aa)	end (aa)	feature	details
250	250	CONFLICT	E -> K (in Ref. 3; BAF85565).	might get lost (downstream of altered splice site)
616	642	COILED	Potential.	might get lost (downstream of altered splice site)
821	821	CONFLICT	S -> G (in Ref. 1; BAA34473).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2007 / 2007

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

669 / 669

position of stopcodon in wt / mu cDNA

2867 / 2867

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

861 / 861

chromosome

strand

-1

last intron/exon boundary

2750

theoretical NMD boundary in CDS

1839

length of CDS

2007

coding sequence (CDS) position

228

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

1088

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

19950

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

6524298

original gDNA sequence snippet

GCTTTGGAATCTCTCCTGGAAAAGAAACTGTCACCAAAAAA

altered gDNA sequence snippet

GCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAAAA

original cDNA sequence snippet

GCTTTGGAATCTCTCCTGGAAAAGAAACTGTCACCAAAAAA

altered cDNA sequence snippet

GCTTTGGAATCTCTCCTGGATAAGAAACTGTCACCAAAAAA

wildtype AA sequence

mutated AA sequence

speed

0.94 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