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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000264956
Querying Taster for transcript #2: ENST00000509451
Querying Taster for transcript #3: ENST00000382674
MT speed 3.06 s - this script 4.120506 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EVC	polymorphism_automatic	5.11860039908996e-08	simple_aae		affected		Y258H	single base exchange	rs6414624		show file
EVC	polymorphism_automatic	5.11860039908996e-08	simple_aae		affected		Y258H	single base exchange	rs6414624		show file
EVC	polymorphism_automatic	5.11860039908996e-08	simple_aae		affected		Y258H	single base exchange	rs6414624		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999948813996 (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)

chr4:5743512T>CN/A show variant in all transcripts IGV

HGNC symbol

EVC

Ensembl transcript ID

ENST00000264956

Genbank transcript ID

NM_153717

UniProt peptide

P57679

alteration type

single base exchange

alteration region

CDS

DNA changes

c.772T>C
cDNA.956T>C
g.30589T>C

AA changes

Y258H Score: 83 explain score(s)

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

258

frameshift

known variant

Reference ID: rs6414624

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1437	856	2293
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.469	0.086
	1.064	0.235
(flanking)	0.017	0.269

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 marginally increased	30580	wt: 0.6887 / mu: 0.7245 (marginal change - not scored)	wt: CAGATGATGAACTAT mu: CAGATGATGAACTAC	GATG\|atga
Donor marginally increased	30593	wt: 0.9099 / mu: 0.9814 (marginal change - not scored)	wt: ATACCAGAAGATCCT mu: ACACCAGAAGATCCT	ACCA\|gaag
Donor gained	30590	0.38	mu: ACTACACCAGAAGAT	TACA\|ccag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

258

mutated

all conserved

258

Ptroglodytes

all identical

ENSPTRG00000015877

258

Mmulatta

all identical

ENSMMUG00000020861

258

Fcatus

all identical

ENSFCAG00000004076

198

Mmusculus

not conserved

ENSMUSG00000029122

258

Ggallus

all conserved

ENSGALG00000015037

252

Trubripes

not conserved

ENSTRUG00000016087

249

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000033121

256

protein features

start (aa)	end (aa)	feature	details
49	992	TOPO_DOM	Cytoplasmic (Potential).	lost
966	966	CONFLICT	Missing (in Ref. 3; AAF44682).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2979 / 2979

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

993 / 993

position of stopcodon in wt / mu cDNA

3163 / 3163

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

185 / 185

chromosome

strand

last intron/exon boundary

3079

theoretical NMD boundary in CDS

2844

length of CDS

2979

coding sequence (CDS) position

772

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

956

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

30589

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

5743512

original gDNA sequence snippet

AGAAGTCAGATGATGAACTATACCAGAAGATCCTTTCAAAA

altered gDNA sequence snippet

AGAAGTCAGATGATGAACTACACCAGAAGATCCTTTCAAAA

original cDNA sequence snippet

AGAAGTCAGATGATGAACTATACCAGAAGATCCTTTCAAAA

altered cDNA sequence snippet

AGAAGTCAGATGATGAACTACACCAGAAGATCCTTTCAAAA

wildtype AA sequence

MARGGAACKS DARLLLGRDA LRPAPALLAP AVLLGAALGL GLGLWLGCRA GRQRTRHQKD
DTQNLLKNLE SNAQTPSETG SPSRRRKREV QMSKDKEAVD ECEPPSNSNI TAFALKAKVI
YPINQKFRPL ADGSSNPSLH ENLKQAVLPH QPVEASPSSS LGSLSQGEKD DCSSSSSVHS
ATSDDRFLSR TFLRVNAFPE VLACESVDVD LCIYSLHLKD LLHLDTALRQ EKHMMFIQIF
KMCLLDLLPK KKSDDELYQK ILSKQEKDLE ELEKGLQVKL SNTEMSGAGD SEYITLADVE
KKEREYSEQL IDNMEAFWKQ MANIQHFLVD QFKCSSSKAR QLMMTLTERM IAAEGLLCDS
QELQALDALE RTMGRAHMAK VIEFLKLQVQ EETRCRLAAI SHGLELLAGE GKLSGRQKEE
LLTQQHKAFW QEAERFSREF VQRGKDLVTA SLAHQVEGTA KLTLAQEEEQ RSFLAEAQPT
ADPEKFLEAF HEVLERQRLM QCDLEEEENV RATEAVVALC QELYFSTVDT FQKFVDALFL
QTLPGMTGLP PEECDYLRQE VQENAAWQLG KSNRFRRQQW KLFQELLEQD QQVWMEECAL
SSVLQTHLRE DHEGTIRGVL GRLGGLTEES TRCVLQGHDL LLRSALRRLA LRGNALATLT
QMRLSGKKHL LQELREQRAL EQGSSQCLDE HQWQLLRALE ARVLEEASRL EEEAQQTRLQ
LQQRLLAEAQ EVGQLLQQHM ECAIGQALLV HARNAATKSR AKDRDDFKRT LMEAAVESVY
VTSAGVSRLV QAYYQQIGRI MEDHEERKLQ HLKTLQGERM ENYKLRKKQE LSNPSSGSRT
AGGAHETSQA VHQRMLSQQK RFLAQFPVHQ QMRLHAQQQQ AGVMDLLEAQ LETQLQEAEQ
NFISELAALA RVPLAESKLL PAKRGLLEKP LRTKRKKPLP QERGDLGVPN NEDLASGDQT
SGSLSSKRLS QQESEAGDSG NSKKMLKRRS NL*

mutated AA sequence

MARGGAACKS DARLLLGRDA LRPAPALLAP AVLLGAALGL GLGLWLGCRA GRQRTRHQKD
DTQNLLKNLE SNAQTPSETG SPSRRRKREV QMSKDKEAVD ECEPPSNSNI TAFALKAKVI
YPINQKFRPL ADGSSNPSLH ENLKQAVLPH QPVEASPSSS LGSLSQGEKD DCSSSSSVHS
ATSDDRFLSR TFLRVNAFPE VLACESVDVD LCIYSLHLKD LLHLDTALRQ EKHMMFIQIF
KMCLLDLLPK KKSDDELHQK ILSKQEKDLE ELEKGLQVKL SNTEMSGAGD SEYITLADVE
KKEREYSEQL IDNMEAFWKQ MANIQHFLVD QFKCSSSKAR QLMMTLTERM IAAEGLLCDS
QELQALDALE RTMGRAHMAK VIEFLKLQVQ EETRCRLAAI SHGLELLAGE GKLSGRQKEE
LLTQQHKAFW QEAERFSREF VQRGKDLVTA SLAHQVEGTA KLTLAQEEEQ RSFLAEAQPT
ADPEKFLEAF HEVLERQRLM QCDLEEEENV RATEAVVALC QELYFSTVDT FQKFVDALFL
QTLPGMTGLP PEECDYLRQE VQENAAWQLG KSNRFRRQQW KLFQELLEQD QQVWMEECAL
SSVLQTHLRE DHEGTIRGVL GRLGGLTEES TRCVLQGHDL LLRSALRRLA LRGNALATLT
QMRLSGKKHL LQELREQRAL EQGSSQCLDE HQWQLLRALE ARVLEEASRL EEEAQQTRLQ
LQQRLLAEAQ EVGQLLQQHM ECAIGQALLV HARNAATKSR AKDRDDFKRT LMEAAVESVY
VTSAGVSRLV QAYYQQIGRI MEDHEERKLQ HLKTLQGERM ENYKLRKKQE LSNPSSGSRT
AGGAHETSQA VHQRMLSQQK RFLAQFPVHQ QMRLHAQQQQ AGVMDLLEAQ LETQLQEAEQ
NFISELAALA RVPLAESKLL PAKRGLLEKP LRTKRKKPLP QERGDLGVPN NEDLASGDQT
SGSLSSKRLS QQESEAGDSG NSKKMLKRRS NL*

speed

0.95 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: 0.999999948813996 (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)

chr4:5743512T>CN/A show variant in all transcripts IGV

HGNC symbol

EVC

Ensembl transcript ID

ENST00000509451

Genbank transcript ID

N/A

UniProt peptide

P57679

alteration type

single base exchange

alteration region

CDS

DNA changes

c.772T>C
cDNA.938T>C
g.30589T>C

AA changes

Y258H Score: 83 explain score(s)

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

258

frameshift

known variant

Reference ID: rs6414624

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1437	856	2293
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.469	0.086
	1.064	0.235
(flanking)	0.017	0.269

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 marginally increased	30580	wt: 0.6887 / mu: 0.7245 (marginal change - not scored)	wt: CAGATGATGAACTAT mu: CAGATGATGAACTAC	GATG\|atga
Donor marginally increased	30593	wt: 0.9099 / mu: 0.9814 (marginal change - not scored)	wt: ATACCAGAAGATCCT mu: ACACCAGAAGATCCT	ACCA\|gaag
Donor gained	30590	0.38	mu: ACTACACCAGAAGAT	TACA\|ccag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

258

mutated

all conserved

258

Ptroglodytes

all identical

ENSPTRG00000015877

258

Mmulatta

all identical

ENSMMUG00000020861

258

Fcatus

all identical

ENSFCAG00000004076

198

Mmusculus

not conserved

ENSMUSG00000029122

258

Ggallus

all conserved

ENSGALG00000015037

252

Trubripes

not conserved

ENSTRUG00000016087

249

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000033121

256

protein features

start (aa)	end (aa)	feature	details
49	992	TOPO_DOM	Cytoplasmic (Potential).	lost
966	966	CONFLICT	Missing (in Ref. 3; AAF44682).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1608 / 1608

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

536 / 536

position of stopcodon in wt / mu cDNA

1774 / 1774

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

167 / 167

chromosome

strand

last intron/exon boundary

1730

theoretical NMD boundary in CDS

1513

length of CDS

1608

coding sequence (CDS) position

772

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

938

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

30589

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

5743512

original gDNA sequence snippet

AGAAGTCAGATGATGAACTATACCAGAAGATCCTTTCAAAA

altered gDNA sequence snippet

AGAAGTCAGATGATGAACTACACCAGAAGATCCTTTCAAAA

original cDNA sequence snippet

AGAAGTCAGATGATGAACTATACCAGAAGATCCTTTCAAAA

altered cDNA sequence snippet

AGAAGTCAGATGATGAACTACACCAGAAGATCCTTTCAAAA

wildtype AA sequence

mutated AA sequence

speed

1.13 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999948813996 (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)

chr4:5743512T>CN/A show variant in all transcripts IGV

HGNC symbol

EVC

Ensembl transcript ID

ENST00000382674

Genbank transcript ID

N/A

UniProt peptide

P57679

alteration type

single base exchange

alteration region

CDS

DNA changes

c.772T>C
cDNA.956T>C
g.30589T>C

AA changes

Y258H Score: 83 explain score(s)

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

258

frameshift

known variant

Reference ID: rs6414624

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1437	856	2293
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.469	0.086
	1.064	0.235
(flanking)	0.017	0.269

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 marginally increased	30580	wt: 0.6887 / mu: 0.7245 (marginal change - not scored)	wt: CAGATGATGAACTAT mu: CAGATGATGAACTAC	GATG\|atga
Donor marginally increased	30593	wt: 0.9099 / mu: 0.9814 (marginal change - not scored)	wt: ATACCAGAAGATCCT mu: ACACCAGAAGATCCT	ACCA\|gaag
Donor gained	30590	0.38	mu: ACTACACCAGAAGAT	TACA\|ccag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

258

mutated

all conserved

258

Ptroglodytes

all identical

ENSPTRG00000015877

258

Mmulatta

all identical

ENSMMUG00000020861

258

Fcatus

all identical

ENSFCAG00000004076

198

Mmusculus

not conserved

ENSMUSG00000029122

258

Ggallus

all conserved

ENSGALG00000015037

252

Trubripes

not conserved

ENSTRUG00000016087

249

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000033121

256

protein features

start (aa)	end (aa)	feature	details
49	992	TOPO_DOM	Cytoplasmic (Potential).	lost
966	966	CONFLICT	Missing (in Ref. 3; AAF44682).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2979 / 2979

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

993 / 993

position of stopcodon in wt / mu cDNA

3163 / 3163

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

185 / 185

chromosome

strand

last intron/exon boundary

6537

theoretical NMD boundary in CDS

6302

length of CDS

2979

coding sequence (CDS) position

772

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

956

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

30589

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

5743512

original gDNA sequence snippet

AGAAGTCAGATGATGAACTATACCAGAAGATCCTTTCAAAA

altered gDNA sequence snippet

AGAAGTCAGATGATGAACTACACCAGAAGATCCTTTCAAAA

original cDNA sequence snippet

AGAAGTCAGATGATGAACTATACCAGAAGATCCTTTCAAAA

altered cDNA sequence snippet

AGAAGTCAGATGATGAACTACACCAGAAGATCCTTTCAAAA

wildtype AA sequence

mutated AA sequence

MARGGAACKS DARLLLGRDA LRPAPALLAP AVLLGAALGL GLGLWLGCRA GRQRTRHQKD
DTQNLLKNLE SNAQTPSETG SPSRRRKREV QMSKDKEAVD ECEPPSNSNI TAFALKAKVI
YPINQKFRPL ADGSSNPSLH ENLKQAVLPH QPVEASPSSS LGSLSQGEKD DCSSSSSVHS
ATSDDRFLSR TFLRVNAFPE VLACESVDVD LCIYSLHLKD LLHLDTALRQ EKHMMFIQIF
KMCLLDLLPK KKSDDELHQK ILSKQEKDLE ELEKGLQVKL SNTEMSGAGD SEYITLADVE
KKEREYSEQL IDNMEAFWKQ MANIQHFLVD QFKCSSSKAR QLMMTLTERM IAAEGLLCDS
QELQALDALE RTMGRAHMAK VIEFLKLQVQ EETRCRLAAI SHGLELLAGE GKLSGRQKEE
LLTQQHKAFW QEAERFSREF VQRGKDLVTA SLAHQVEGTA KLTLAQEEEQ RSFLAEAQPT
ADPEKFLEAF HEVLERQRLM QCDLEEEENV RATEAVVALC QELYFSTVDT FQKFVDALFL
QTLPGMTGLP PEECDYLRQE VQENAAWQLG KSNRFRRQQW KLFQELLEQD QQVWMEECAL
SSVLQTHLRE DHEGTIRGVL GRLGGLTEES TRCVLQGHDL LLRSALRRLA LRGNALATLT
QMRLSGKKHL LQELREQRAL EQGSSQCLDE HQWQLLRALE ARVLEEASRL EEEAQQTRLQ
LQQRLLAEAQ EVGQLLQQHM ECAIGQALLV HARNAATKSR AKDRDDFKRT LMEAAVESVY
VTSAGVSRLV QAYYQQIGRI MEDHEERKLQ HLKTLQGERM ENYKLRKKQE LSNPSSGSRT
AGGAHETSQA VHQRMLSQQK RFLAQFPVHQ QMRLHAQQQQ AGVMDLLEAQ LETQLQEAEQ
NFISELAALA RVPLAESKLL PAKRGLLEKP LRTKRKKPLP QERGDLGVPN NEDLASGDQT
SGSLSSKRLS QQESEAGDSG NSKKMLKRRS NL*

speed

0.98 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