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: ENST00000409914
Querying Taster for transcript #2: ENST00000357462
MT speed 0 s - this script 3.502192 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
POTEF	polymorphism_automatic	8.87973432894817e-06	simple_aae		affected		H896R	single base exchange	rs201946437		show file
POTEF	polymorphism_automatic	8.87973432894817e-06	simple_aae		affected		H896R	single base exchange	rs201946437		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999991120265671 (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)

chr2:130832358T>CN/A show variant in all transcripts IGV

HGNC symbol

POTEF

Ensembl transcript ID

ENST00000357462

Genbank transcript ID

NM_001099771

UniProt peptide

A5A3E0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2687A>G
cDNA.2781A>G
g.54438A>G

AA changes

H896R Score: 29 explain score(s)

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

896

frameshift

known variant

Reference ID: rs201946437

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	4604	8884	13488

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.252	0.999
	1.74	1
(flanking)	0.496	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 marginally increased	54447	wt: 0.5769 / mu: 0.6308 (marginal change - not scored)	wt: CCTCACCGAGCATGGCTATAGGTTCACCACCATGGCCGAGC mu: CCTCACCGAGCGTGGCTATAGGTTCACCACCATGGCCGAGC	atag\|GTTC
Donor gained	54430	0.38	mu: ATCCTCACCGAGCGT	CCTC\|accg

distance from splice site

788

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

896

mutated

not conserved

896

Ptroglodytes

not conserved

ENSPTRG00000024298

896

Mmulatta

no alignment

ENSMMUG00000031128

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000016302

n/a

Drerio

no alignment

ENSDARG00000013015

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000021831

n/a

protein features

start (aa)	end (aa)	feature	details
702	1075	REGION	Actin-like.	lost
930	930	CONFLICT	V -> A (in Ref. 1; ABP57734).	might get lost (downstream of altered splice site)
1006	1006	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3228 / 3228

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

1076 / 1076

position of stopcodon in wt / mu cDNA

3322 / 3322

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

95 / 95

chromosome

strand

-1

last intron/exon boundary

1994

theoretical NMD boundary in CDS

1849

length of CDS

3228

coding sequence (CDS) position

2687

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

2781

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

54438

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

130832358

original gDNA sequence snippet

CATGAAGATCCTCACCGAGCATGGCTATAGGTTCACCACCA

altered gDNA sequence snippet

CATGAAGATCCTCACCGAGCGTGGCTATAGGTTCACCACCA

original cDNA sequence snippet

CATGAAGATCCTCACCGAGCATGGCTATAGGTTCACCACCA

altered cDNA sequence snippet

CATGAAGATCCTCACCGAGCGTGGCTATAGGTTCACCACCA

wildtype AA sequence

MVVEVDSMPA ASSVKKPFGL RSKMGKWCCR CFPCCRESGK SNVGTSGDHD DSAMKTLRSK
MGKWCRHCFP CCRGSGKSNV GASGDHDDSA MKTLRNKMGK WCCHCFPCCR GSSKSKVGAW
GDYDDSAFME PRYHVRGEDL DKLHRAAWWG KVPRKDLIVM LRDTDVNKQD KQKRTALHLA
SANGNSEVVK LLLDRRCQLN VLDNKKRTAL IKAVQCQEDE CALMLLEHGT DPNIPDEYGN
TTLHYAIYNE DKLMAKALLL YGADIESKNK HGLTPLLLGV HEQKQQVVKF LIKKKANLNA
LDRYGRTALI LAVCCGSASI VSLLLEQNID VSSQDLSGQT AREYAVSSHH HVICQLLSDY
KEKQMLKISS ENSNPEQDLK LTSEEESQRF KGSENSQPEK MSQEPEINKD GDREVEEEMK
KHESNNVGLL ENLTNGVTAG NGDNGLIPQR KSRTPENQQF PDNESEEYHR ICELLSDYKE
KQMPKYSSEN SNPEQDLKLT SEEESQRLKG SENGQPEKRS QEPEINKDGD RELENFMAIE
EMKKHRSTHV GFPENLTNGA TAGNGDDGLI PPRKSRTPES QQFPDTENEE YHSDEQNDTQ
KQFCEEQNTG ILHDEILIHE EKQIEVVEKM NSELSLSCKK EKDILHENST LREEIAMLRL
ELDTMKHQSQ LREKKYLEDI ESVKKRNDNL LKALQLNELT MDDDTAVLVI DNGSGMCKAG
FAGDDAPRAV FPSIVGRPRQ QGMMGGMHQK ESYVGKEAQS KRGILTLKYP MEHGIITNWD
DMEKIWHHTF YNELRVAPEE HPVLLTEATL NPKANREKMT QIMFETFNTP AMYVAIQAVL
SLYTSGRTTG IVMDSGDGVT HTVPIYEGNA LPHATLRLDL AGRELPDYLM KILTEHGYRF
TTMAEREIVR DIKEKLCYVA LDFEQEMATV ASSSSLEKSY ELPDGQVITI GNERFRCPEA
LFQPCFLGME SCGIHETTFN SIMKSDVDIR KDLYTNTVLS GGTTMYPGMA HRMQKEIAAL
APSMMKIRII APPKRKYSVW VGGSILASLS TFQQMWISKQ EYDESGPSIV HRKCL*

mutated AA sequence

MVVEVDSMPA ASSVKKPFGL RSKMGKWCCR CFPCCRESGK SNVGTSGDHD DSAMKTLRSK
MGKWCRHCFP CCRGSGKSNV GASGDHDDSA MKTLRNKMGK WCCHCFPCCR GSSKSKVGAW
GDYDDSAFME PRYHVRGEDL DKLHRAAWWG KVPRKDLIVM LRDTDVNKQD KQKRTALHLA
SANGNSEVVK LLLDRRCQLN VLDNKKRTAL IKAVQCQEDE CALMLLEHGT DPNIPDEYGN
TTLHYAIYNE DKLMAKALLL YGADIESKNK HGLTPLLLGV HEQKQQVVKF LIKKKANLNA
LDRYGRTALI LAVCCGSASI VSLLLEQNID VSSQDLSGQT AREYAVSSHH HVICQLLSDY
KEKQMLKISS ENSNPEQDLK LTSEEESQRF KGSENSQPEK MSQEPEINKD GDREVEEEMK
KHESNNVGLL ENLTNGVTAG NGDNGLIPQR KSRTPENQQF PDNESEEYHR ICELLSDYKE
KQMPKYSSEN SNPEQDLKLT SEEESQRLKG SENGQPEKRS QEPEINKDGD RELENFMAIE
EMKKHRSTHV GFPENLTNGA TAGNGDDGLI PPRKSRTPES QQFPDTENEE YHSDEQNDTQ
KQFCEEQNTG ILHDEILIHE EKQIEVVEKM NSELSLSCKK EKDILHENST LREEIAMLRL
ELDTMKHQSQ LREKKYLEDI ESVKKRNDNL LKALQLNELT MDDDTAVLVI DNGSGMCKAG
FAGDDAPRAV FPSIVGRPRQ QGMMGGMHQK ESYVGKEAQS KRGILTLKYP MEHGIITNWD
DMEKIWHHTF YNELRVAPEE HPVLLTEATL NPKANREKMT QIMFETFNTP AMYVAIQAVL
SLYTSGRTTG IVMDSGDGVT HTVPIYEGNA LPHATLRLDL AGRELPDYLM KILTERGYRF
TTMAEREIVR DIKEKLCYVA LDFEQEMATV ASSSSLEKSY ELPDGQVITI GNERFRCPEA
LFQPCFLGME SCGIHETTFN SIMKSDVDIR KDLYTNTVLS GGTTMYPGMA HRMQKEIAAL
APSMMKIRII APPKRKYSVW VGGSILASLS TFQQMWISKQ EYDESGPSIV HRKCL*

speed

0.64 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: 0.999991120265671 (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)

chr2:130832358T>CN/A show variant in all transcripts IGV

HGNC symbol

POTEF

Ensembl transcript ID

ENST00000409914

Genbank transcript ID

N/A

UniProt peptide

A5A3E0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2687A>G
cDNA.3087A>G
g.54438A>G

AA changes

H896R Score: 29 explain score(s)

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

896

frameshift

known variant

Reference ID: rs201946437

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	4604	8884	13488

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.252	0.999
	1.74	1
(flanking)	0.496	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 marginally increased	54447	wt: 0.5769 / mu: 0.6308 (marginal change - not scored)	wt: CCTCACCGAGCATGGCTATAGGTTCACCACCATGGCCGAGC mu: CCTCACCGAGCGTGGCTATAGGTTCACCACCATGGCCGAGC	atag\|GTTC
Donor gained	54430	0.38	mu: ATCCTCACCGAGCGT	CCTC\|accg

distance from splice site

756

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

896

mutated

not conserved

896

Ptroglodytes

not conserved

ENSPTRG00000024298

896

Mmulatta

no alignment

ENSMMUG00000031128

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000016302

n/a

Drerio

no alignment

ENSDARG00000013015

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000021831

n/a

protein features

start (aa)	end (aa)	feature	details
702	1075	REGION	Actin-like.	lost
930	930	CONFLICT	V -> A (in Ref. 1; ABP57734).	might get lost (downstream of altered splice site)
1006	1006	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3228 / 3228

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

1076 / 1076

position of stopcodon in wt / mu cDNA

3628 / 3628

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

401 / 401

chromosome

strand

-1

last intron/exon boundary

2300

theoretical NMD boundary in CDS

1849

length of CDS

3228

coding sequence (CDS) position

2687

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

3087

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

54438

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

130832358

original gDNA sequence snippet

CATGAAGATCCTCACCGAGCATGGCTATAGGTTCACCACCA

altered gDNA sequence snippet

CATGAAGATCCTCACCGAGCGTGGCTATAGGTTCACCACCA

original cDNA sequence snippet

CATGAAGATCCTCACCGAGCATGGCTATAGGTTCACCACCA

altered cDNA sequence snippet

CATGAAGATCCTCACCGAGCGTGGCTATAGGTTCACCACCA

wildtype AA sequence

mutated AA sequence

MVVEVDSMPA ASSVKKPFGL RSKMGKWCCR CFPCCRESGK SNVGTSGDHD DSAMKTLRSK
MGKWCRHCFP CCRGSGKSNV GASGDHDDSA MKTLRNKMGK WCCHCFPCCR GSSKSKVGAW
GDYDDSAFME PRYHVRGEDL DKLHRAAWWG KVPRKDLIVM LRDTDVNKQD KQKRTALHLA
SANGNSEVVK LLLDRRCQLN VLDNKKRTAL IKAVQCQEDE CALMLLEHGT DPNIPDEYGN
TTLHYAIYNE DKLMAKALLL YGADIESKNK HGLTPLLLGV HEQKQQVVKF LIKKKANLNA
LDRYGRTALI LAVCCGSASI VSLLLEQNID VSSQDLSGQT AREYAVSSHH HVICQLLSDY
KEKQMLKISS ENSNPEQDLK LTSEEESQRF KGSENSQPEK MSQEPEINKD GDREVEEEMK
KHESNNVGLL ENLTNGVTAG NGDNGLIPQR KSRTPENQQF PDNESEEYHR ICELLSDYKE
KQMPKYSSEN SNPEQDLKLT SEEESQRLKG SENGQPEKRS QEPEINKDGD RELENFMAIE
EMKKHRSTHV GFPENLTNGA TAGNGDDGLI PPRKSRTPES QQFPDTENEE YHSDEQNDTQ
KQFCEEQNTG ILHDEILIHE EKQIEVVEKM NSELSLSCKK EKDILHENST LREEIAMLRL
ELDTMKHQSQ LREKKYLEDI ESVKKRNDNL LKALQLNELT MDDDTAVLVI DNGSGMCKAG
FAGDDAPRAV FPSIVGRPRQ QGMMGGMHQK ESYVGKEAQS KRGILTLKYP MEHGIITNWD
DMEKIWHHTF YNELRVAPEE HPVLLTEATL NPKANREKMT QIMFETFNTP AMYVAIQAVL
SLYTSGRTTG IVMDSGDGVT HTVPIYEGNA LPHATLRLDL AGRELPDYLM KILTERGYRF
TTMAEREIVR DIKEKLCYVA LDFEQEMATV ASSSSLEKSY ELPDGQVITI GNERFRCPEA
LFQPCFLGME SCGIHETTFN SIMKSDVDIR KDLYTNTVLS GGTTMYPGMA HRMQKEIAAL
APSMMKIRII APPKRKYSVW VGGSILASLS TFQQMWISKQ EYDESGPSIV HRKCL*

speed

0.81 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems