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: ENST00000555265
Querying Taster for transcript #2: ENST00000281129
MT speed 1.89 s - this script 3.929304 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CEP128	polymorphism_automatic	0.923005980882013	simple_aae		affected		H732R	single base exchange	rs327463		show file
CEP128	polymorphism_automatic	0.923005980882013	simple_aae		affected		H732R	single base exchange	rs327463		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0769940191179865 (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)

chr14:81251255T>CN/A show variant in all transcripts IGV

HGNC symbol

CEP128

Ensembl transcript ID

ENST00000555265

Genbank transcript ID

N/A

UniProt peptide

Q6ZU80

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2195A>G
cDNA.2571A>G
g.174607A>G

AA changes

H732R Score: 29 explain score(s)

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

732

frameshift

known variant

Reference ID: rs327463

database	homozygous (C/C)	heterozygous	allele carriers
1000G	316	1032	1348
ExAC	9130	14507	23637

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.137	0.984
	1.72	0.999
(flanking)	5.015	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	174601	0.98	mu: GGCTGAGAATCGTAT	CTGA\|gaat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

732

mutated

not conserved

732

Ptroglodytes

all identical

ENSPTRG00000006594

732

Mmulatta

all identical

ENSMMUG00000019710

733

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000061533

731

Ggallus

all identical

ENSGALG00000010562

363

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000062898

615

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
190	827	COILED	Potential.	lost
879	959	COILED	Potential.	might get lost (downstream of altered splice site)
941	941	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
950	950	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
973	973	CONFLICT	P -> A (in Ref. 3; BAB71273).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3285 / 3285

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

1095 / 1095

position of stopcodon in wt / mu cDNA

3661 / 3661

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

377 / 377

chromosome

strand

-1

last intron/exon boundary

3558

theoretical NMD boundary in CDS

3131

length of CDS

3285

coding sequence (CDS) position

2195

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

2571

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

174607

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

81251255

original gDNA sequence snippet

AAAGAGTGAGGCTGAGAATCATATCAGGACTCTGAAGGTAC

altered gDNA sequence snippet

AAAGAGTGAGGCTGAGAATCGTATCAGGACTCTGAAGGTAC

original cDNA sequence snippet

AAAGAGTGAGGCTGAGAATCATATCAGGACTCTGAAGGCTG

altered cDNA sequence snippet

AAAGAGTGAGGCTGAGAATCGTATCAGGACTCTGAAGGCTG

wildtype AA sequence

MAESSSESDH FRCRDRLSPW AARSTHRGTR SLPTVEVTEK VNTITSTLQD TSRNLRQVDQ
MLGRYREYSN GQAGAIEHLK ESLEQSIDQL RSQRLLRNSG GRSISVTSLS ASDLDGGTGS
ELHHFPPTSP LKDYGDPQGI KRMRSRTGVR FVQETDDMTQ LHGFHQSLRD LSSEQIRLGD
DFNRELSRRS RSDAETKRAL EELTEKLNEA QKQEVVSDRV ERRLQELERE MRTERELVER
RQDQLGLMSL QLQEALKKQE AKADEHEGAI KNKLRQTETE KNQLEQELEL SRRLLNQSEG
SRETLLHQVE ELRTQLTKAE GDRKGLQHQV SQISKQQSNY QDEQGEDWRF RRGVEREKQD
LEKQMSDLRV QLNFSAMASE LEEVKRCMER KDKEKAHLAS QVENLTRELE NGEKQQLQML
DRLKEIQNHF DTCEAERKHA DLQISELTRH AEDATKQAER YLSELQQSEA LKEEAEKRRE
DLKLKAQESI RQWKLKHKKL ERALEKQSET VDELTGKNNQ ILKEKDELKT QLYAALQQIE
NLRKELNDVL TKRALQEEEL HSKEEKLRDI KSHQADLELE VKNSLDTIHR LESELKKQSK
IQSQMKVEKA HLEEEIAELK KSQAQDKAKL LEMQESIKDL SAIRADLANK LAEEERAKKA
VLKDLSDLTA QAKSRDEETA TIITQLKLER DVHQRELKDL TSSLQSVKTK HEQNIQELMK
HFKKEKSEAE NHIRTLKAES LEEKNMAKIH RGQLEKLKSQ CDRLTEELTQ NENENKKLKL
KYQCLKDQLE EREKHISIEE EHLRRMEEAR LQLKDQLLCL ETEQESILGV IGKEIDAACK
TFSKDSVEKL KVFSSGPDIH YDPHRWLAES KTKLQWLCEE LKERENREKN LRHQLMLCRQ
QLRNLTENKE SELQCLFQQI ERQEQLLDEI HREKRDLLEE TQRKDEEMGS LQDRVIALET
STQVALDHLE SVPEKLSLLE DFKDFRDSCS SSERTDGRYS KYRVRRNSLQ HHQDDTKYRT
KSFKGDRTFL EGSHTRGLDH SSSWQDHSRF LSSPRFSYVN SFTKRTVAPD SASNKEDATM
NGTSSQPKKE EYGS*

mutated AA sequence

MAESSSESDH FRCRDRLSPW AARSTHRGTR SLPTVEVTEK VNTITSTLQD TSRNLRQVDQ
MLGRYREYSN GQAGAIEHLK ESLEQSIDQL RSQRLLRNSG GRSISVTSLS ASDLDGGTGS
ELHHFPPTSP LKDYGDPQGI KRMRSRTGVR FVQETDDMTQ LHGFHQSLRD LSSEQIRLGD
DFNRELSRRS RSDAETKRAL EELTEKLNEA QKQEVVSDRV ERRLQELERE MRTERELVER
RQDQLGLMSL QLQEALKKQE AKADEHEGAI KNKLRQTETE KNQLEQELEL SRRLLNQSEG
SRETLLHQVE ELRTQLTKAE GDRKGLQHQV SQISKQQSNY QDEQGEDWRF RRGVEREKQD
LEKQMSDLRV QLNFSAMASE LEEVKRCMER KDKEKAHLAS QVENLTRELE NGEKQQLQML
DRLKEIQNHF DTCEAERKHA DLQISELTRH AEDATKQAER YLSELQQSEA LKEEAEKRRE
DLKLKAQESI RQWKLKHKKL ERALEKQSET VDELTGKNNQ ILKEKDELKT QLYAALQQIE
NLRKELNDVL TKRALQEEEL HSKEEKLRDI KSHQADLELE VKNSLDTIHR LESELKKQSK
IQSQMKVEKA HLEEEIAELK KSQAQDKAKL LEMQESIKDL SAIRADLANK LAEEERAKKA
VLKDLSDLTA QAKSRDEETA TIITQLKLER DVHQRELKDL TSSLQSVKTK HEQNIQELMK
HFKKEKSEAE NRIRTLKAES LEEKNMAKIH RGQLEKLKSQ CDRLTEELTQ NENENKKLKL
KYQCLKDQLE EREKHISIEE EHLRRMEEAR LQLKDQLLCL ETEQESILGV IGKEIDAACK
TFSKDSVEKL KVFSSGPDIH YDPHRWLAES KTKLQWLCEE LKERENREKN LRHQLMLCRQ
QLRNLTENKE SELQCLFQQI ERQEQLLDEI HREKRDLLEE TQRKDEEMGS LQDRVIALET
STQVALDHLE SVPEKLSLLE DFKDFRDSCS SSERTDGRYS KYRVRRNSLQ HHQDDTKYRT
KSFKGDRTFL EGSHTRGLDH SSSWQDHSRF LSSPRFSYVN SFTKRTVAPD SASNKEDATM
NGTSSQPKKE EYGS*

speed

0.79 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: 0.0769940191179865 (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)

chr14:81251255T>CN/A show variant in all transcripts IGV

HGNC symbol

CEP128

Ensembl transcript ID

ENST00000281129

Genbank transcript ID

NM_152446

UniProt peptide

Q6ZU80

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2195A>G
cDNA.2366A>G
g.174607A>G

AA changes

H732R Score: 29 explain score(s)

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

732

frameshift

known variant

Reference ID: rs327463

database	homozygous (C/C)	heterozygous	allele carriers
1000G	316	1032	1348
ExAC	9130	14507	23637

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.137	0.984
	1.72	0.999
(flanking)	5.015	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	174601	0.98	mu: GGCTGAGAATCGTAT	CTGA\|gaat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

732

mutated

not conserved

732

Ptroglodytes

all identical

ENSPTRG00000006594

732

Mmulatta

all identical

ENSMMUG00000019710

733

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000061533

731

Ggallus

all identical

ENSGALG00000010562

363

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000062898

615

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
190	827	COILED	Potential.	lost
879	959	COILED	Potential.	might get lost (downstream of altered splice site)
941	941	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
950	950	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
973	973	CONFLICT	P -> A (in Ref. 3; BAB71273).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3285 / 3285

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

1095 / 1095

position of stopcodon in wt / mu cDNA

3456 / 3456

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

172 / 172

chromosome

strand

-1

last intron/exon boundary

3353

theoretical NMD boundary in CDS

3131

length of CDS

3285

coding sequence (CDS) position

2195

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

2366

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

174607

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

81251255

original gDNA sequence snippet

AAAGAGTGAGGCTGAGAATCATATCAGGACTCTGAAGGTAC

altered gDNA sequence snippet

AAAGAGTGAGGCTGAGAATCGTATCAGGACTCTGAAGGTAC

original cDNA sequence snippet

AAAGAGTGAGGCTGAGAATCATATCAGGACTCTGAAGGCTG

altered cDNA sequence snippet

AAAGAGTGAGGCTGAGAATCGTATCAGGACTCTGAAGGCTG

wildtype AA sequence

mutated AA sequence

MAESSSESDH FRCRDRLSPW AARSTHRGTR SLPTVEVTEK VNTITSTLQD TSRNLRQVDQ
MLGRYREYSN GQAGAIEHLK ESLEQSIDQL RSQRLLRNSG GRSISVTSLS ASDLDGGTGS
ELHHFPPTSP LKDYGDPQGI KRMRSRTGVR FVQETDDMTQ LHGFHQSLRD LSSEQIRLGD
DFNRELSRRS RSDAETKRAL EELTEKLNEA QKQEVVSDRV ERRLQELERE MRTERELVER
RQDQLGLMSL QLQEALKKQE AKADEHEGAI KNKLRQTETE KNQLEQELEL SRRLLNQSEG
SRETLLHQVE ELRTQLTKAE GDRKGLQHQV SQISKQQSNY QDEQGEDWRF RRGVEREKQD
LEKQMSDLRV QLNFSAMASE LEEVKRCMER KDKEKAHLAS QVENLTRELE NGEKQQLQML
DRLKEIQNHF DTCEAERKHA DLQISELTRH AEDATKQAER YLSELQQSEA LKEEAEKRRE
DLKLKAQESI RQWKLKHKKL ERALEKQSET VDELTGKNNQ ILKEKDELKT QLYAALQQIE
NLRKELNDVL TKRALQEEEL HSKEEKLRDI KSHQADLELE VKNSLDTIHR LESELKKQSK
IQSQMKVEKA HLEEEIAELK KSQAQDKAKL LEMQESIKDL SAIRADLANK LAEEERAKKA
VLKDLSDLTA QAKSRDEETA TIITQLKLER DVHQRELKDL TSSLQSVKTK HEQNIQELMK
HFKKEKSEAE NRIRTLKAES LEEKNMAKIH RGQLEKLKSQ CDRLTEELTQ NENENKKLKL
KYQCLKDQLE EREKHISIEE EHLRRMEEAR LQLKDQLLCL ETEQESILGV IGKEIDAACK
TFSKDSVEKL KVFSSGPDIH YDPHRWLAES KTKLQWLCEE LKERENREKN LRHQLMLCRQ
QLRNLTENKE SELQCLFQQI ERQEQLLDEI HREKRDLLEE TQRKDEEMGS LQDRVIALET
STQVALDHLE SVPEKLSLLE DFKDFRDSCS SSERTDGRYS KYRVRRNSLQ HHQDDTKYRT
KSFKGDRTFL EGSHTRGLDH SSSWQDHSRF LSSPRFSYVN SFTKRTVAPD SASNKEDATM
NGTSSQPKKE EYGS*

speed

1.10 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems