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: ENST00000300215
Querying Taster for transcript #2: ENST00000540029
Querying Taster for transcript #3: ENST00000441366
MT speed 0 s - this script 3.839498 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPB42	disease_causing	0.99984978881091	simple_aae				A142T	single base exchange	rs104894487		show file
EPB42	disease_causing	0.99984978881091	simple_aae				A112T	single base exchange	rs104894487		show file
EPB42	disease_causing	1	without_aae					single base exchange	rs104894487		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99984978881091 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM920241)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:43507389C>TN/A show variant in all transcripts IGV

HGNC symbol

EPB42

Ensembl transcript ID

ENST00000300215

Genbank transcript ID

NM_000119

UniProt peptide

P16452

alteration type

single base exchange

alteration region

CDS

DNA changes

c.424G>A
cDNA.882G>A
g.6093G>A

AA changes

A142T Score: 58 explain score(s)

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

142

frameshift

known variant

Reference ID: rs104894487

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	9	9

known disease mutation at this position, please check HGMD for details (HGMD ID CM920241)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920241)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920241)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.209	0.996
	4.209	0.993
(flanking)	-1.244	0.113

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	6086	wt: 0.2089 / mu: 0.2396 (marginal change - not scored)	wt: ACACCTGCGGACGCT mu: ACACCTGCGGACACT	ACCT\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

142

mutated

not conserved

142

Ptroglodytes

all identical

ENSPTRG00000006988

112

Mmulatta

all identical

ENSMMUG00000022255

142

Fcatus

all identical

ENSFCAG00000013219

139

Mmusculus

all identical

ENSMUSG00000023216

112

Ggallus

all identical

ENSGALG00000021230

112

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2166 / 2166

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

722 / 722

position of stopcodon in wt / mu cDNA

2624 / 2624

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

459 / 459

chromosome

strand

-1

last intron/exon boundary

2462

theoretical NMD boundary in CDS

1953

length of CDS

2166

coding sequence (CDS) position

424

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

882

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

6093

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

43507389

original gDNA sequence snippet

CTGTGACCACACCTGCGGACGCTGTCATTGGCCACTACTCG

altered gDNA sequence snippet

CTGTGACCACACCTGCGGACACTGTCATTGGCCACTACTCG

original cDNA sequence snippet

CTGTGACCACACCTGCGGACGCTGTCATTGGCCACTACTCG

altered cDNA sequence snippet

CTGTGACCACACCTGCGGACACTGTCATTGGCCACTACTCG

wildtype AA sequence

MGQGEPSQRS TGLAGLYAAP AASPVFIKGS GMDALGIKSC DFQAARNNEE HHTKALSSRR
LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKWW
SAVVEERDAQ SWTISVTTPA DAVIGHYSLL LQVSGRKQLL LGQFTLLFNP WNREDAVFLK
NEAQRMEYLL NQNGLIYLGT ADCIQAESWD FGQFEGDVID LSLRLLSKDK QVEKWSQPVH
VARVLGALLH FLKEQRVLPT PQTQATQEGA LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV
LAAVACTVLR CLGIPARVVT TFASAQGTGG RLLIDEYYNE EGLQNGEGQR GRIWIFQTST
ECWMTRPALP QGYDGWQILH PSAPNGGGVL GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN
ASCVVWKCCE DGTLELTDSN TKYVGNNIST KGVGSDRCED ITQNYKYPEG SLQEKEVLER
VEKEKMEREK DNGIRPPSLE TASPLYLLLK APSSLPLRGD AQISVTLVNH SEQEKAVQLA
IGVQAVHYNG VLAAKLWRKK LHLTLSANLE KIITIGLFFS NFERNPPENT FLRLTAMATH
SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ YQPLTASVSL QNSLDAPMED CVISILGRGL
IHRERSYRFR SVWPENTMCA KFQFTPTHVG LQRLTVEVDC NMFQNLTNYK SVTVVAPELS
A*

mutated AA sequence

MGQGEPSQRS TGLAGLYAAP AASPVFIKGS GMDALGIKSC DFQAARNNEE HHTKALSSRR
LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKWW
SAVVEERDAQ SWTISVTTPA DTVIGHYSLL LQVSGRKQLL LGQFTLLFNP WNREDAVFLK
NEAQRMEYLL NQNGLIYLGT ADCIQAESWD FGQFEGDVID LSLRLLSKDK QVEKWSQPVH
VARVLGALLH FLKEQRVLPT PQTQATQEGA LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV
LAAVACTVLR CLGIPARVVT TFASAQGTGG RLLIDEYYNE EGLQNGEGQR GRIWIFQTST
ECWMTRPALP QGYDGWQILH PSAPNGGGVL GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN
ASCVVWKCCE DGTLELTDSN TKYVGNNIST KGVGSDRCED ITQNYKYPEG SLQEKEVLER
VEKEKMEREK DNGIRPPSLE TASPLYLLLK APSSLPLRGD AQISVTLVNH SEQEKAVQLA
IGVQAVHYNG VLAAKLWRKK LHLTLSANLE KIITIGLFFS NFERNPPENT FLRLTAMATH
SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ YQPLTASVSL QNSLDAPMED CVISILGRGL
IHRERSYRFR SVWPENTMCA KFQFTPTHVG LQRLTVEVDC NMFQNLTNYK SVTVVAPELS
A*

speed

0.68 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

disease causing

Model: simple_aae, prob: 0.99984978881091 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM920241)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:43507389C>TN/A show variant in all transcripts IGV

HGNC symbol

EPB42

Ensembl transcript ID

ENST00000441366

Genbank transcript ID

NM_001114134

UniProt peptide

P16452

alteration type

single base exchange

alteration region

CDS

DNA changes

c.334G>A
cDNA.560G>A
g.6093G>A

AA changes

A112T Score: 58 explain score(s)

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

112

frameshift

known variant

Reference ID: rs104894487

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	9	9

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.209	0.996
	4.209	0.993
(flanking)	-1.244	0.113

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	6086	wt: 0.2089 / mu: 0.2396 (marginal change - not scored)	wt: ACACCTGCGGACGCT mu: ACACCTGCGGACACT	ACCT\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

112

mutated

not conserved

112

Ptroglodytes

all identical

ENSPTRG00000006988

112

Mmulatta

all identical

ENSMMUG00000022255

142

Fcatus

all identical

ENSFCAG00000013219

139

Mmusculus

all identical

ENSMUSG00000023216

112

Ggallus

all identical

ENSGALG00000021230

112

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2076 / 2076

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

692 / 692

position of stopcodon in wt / mu cDNA

2302 / 2302

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

227 / 227

chromosome

strand

-1

last intron/exon boundary

2140

theoretical NMD boundary in CDS

1863

length of CDS

2076

coding sequence (CDS) position

334

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

560

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

6093

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

43507389

original gDNA sequence snippet

CTGTGACCACACCTGCGGACGCTGTCATTGGCCACTACTCG

altered gDNA sequence snippet

CTGTGACCACACCTGCGGACACTGTCATTGGCCACTACTCG

original cDNA sequence snippet

CTGTGACCACACCTGCGGACGCTGTCATTGGCCACTACTCG

altered cDNA sequence snippet

CTGTGACCACACCTGCGGACACTGTCATTGGCCACTACTCG

wildtype AA sequence

MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA
LTAQTGEQPS KINRTQATFP ISSLGDRKWW SAVVEERDAQ SWTISVTTPA DAVIGHYSLL
LQVSGRKQLL LGQFTLLFNP WNREDAVFLK NEAQRMEYLL NQNGLIYLGT ADCIQAESWD
FGQFEGDVID LSLRLLSKDK QVEKWSQPVH VARVLGALLH FLKEQRVLPT PQTQATQEGA
LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV LAAVACTVLR CLGIPARVVT TFASAQGTGG
RLLIDEYYNE EGLQNGEGQR GRIWIFQTST ECWMTRPALP QGYDGWQILH PSAPNGGGVL
GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN ASCVVWKCCE DGTLELTDSN TKYVGNNIST
KGVGSDRCED ITQNYKYPEG SLQEKEVLER VEKEKMEREK DNGIRPPSLE TASPLYLLLK
APSSLPLRGD AQISVTLVNH SEQEKAVQLA IGVQAVHYNG VLAAKLWRKK LHLTLSANLE
KIITIGLFFS NFERNPPENT FLRLTAMATH SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ
YQPLTASVSL QNSLDAPMED CVISILGRGL IHRERSYRFR SVWPENTMCA KFQFTPTHVG
LQRLTVEVDC NMFQNLTNYK SVTVVAPELS A*

mutated AA sequence

MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA
LTAQTGEQPS KINRTQATFP ISSLGDRKWW SAVVEERDAQ SWTISVTTPA DTVIGHYSLL
LQVSGRKQLL LGQFTLLFNP WNREDAVFLK NEAQRMEYLL NQNGLIYLGT ADCIQAESWD
FGQFEGDVID LSLRLLSKDK QVEKWSQPVH VARVLGALLH FLKEQRVLPT PQTQATQEGA
LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV LAAVACTVLR CLGIPARVVT TFASAQGTGG
RLLIDEYYNE EGLQNGEGQR GRIWIFQTST ECWMTRPALP QGYDGWQILH PSAPNGGGVL
GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN ASCVVWKCCE DGTLELTDSN TKYVGNNIST
KGVGSDRCED ITQNYKYPEG SLQEKEVLER VEKEKMEREK DNGIRPPSLE TASPLYLLLK
APSSLPLRGD AQISVTLVNH SEQEKAVQLA IGVQAVHYNG VLAAKLWRKK LHLTLSANLE
KIITIGLFFS NFERNPPENT FLRLTAMATH SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ
YQPLTASVSL QNSLDAPMED CVISILGRGL IHRERSYRFR SVWPENTMCA KFQFTPTHVG
LQRLTVEVDC NMFQNLTNYK SVTVVAPELS A*

speed

0.96 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known disease mutation at this position (HGMD CM920241)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:43507389C>TN/A show variant in all transcripts IGV

HGNC symbol

EPB42

Ensembl transcript ID

ENST00000540029

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.6093G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs104894487

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	9	9

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.209	0.996
	4.209	0.993
(flanking)	-1.244	0.113

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	6086	wt: 0.2089 / mu: 0.2396 (marginal change - not scored)	wt: ACACCTGCGGACGCT mu: ACACCTGCGGACACT	ACCT\|gcgg

distance from splice site

1077

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

-1

last intron/exon boundary

1864

theoretical NMD boundary in CDS

1629

length of CDS

1842

coding sequence (CDS) position

N/A

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

N/A

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

6093

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

43507389

original gDNA sequence snippet

CTGTGACCACACCTGCGGACGCTGTCATTGGCCACTACTCG

altered gDNA sequence snippet

CTGTGACCACACCTGCGGACACTGTCATTGGCCACTACTCG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA
LTAQTEDAVF LKNEAQRMEY LLNQNGLIYL GTADCIQAES WDFGQFEGDV IDLSLRLLSK
DKQVEKWSQP VHVARVLGAL LHFLKEQRVL PTPQTQATQE GALLNKRRGS VPILRQWLTG
RGRPVYDGQA WVLAAVACTV LRCLGIPARV VTTFASAQGT GGRLLIDEYY NEEGLQNGEG
QRGRIWIFQT STECWMTRPA LPQGYDGWQI LHPSAPNGGG VLGSCDLVPV RAVKEGTLGL
TPAVSDLFAA INASCVVWKC CEDGTLELTD SNTKYVGNNI STKGVGSDRC EDITQNYKYP
EGSLQEKEVL ERVEKEKMER EKDNGIRPPS LETASPLYLL LKAPSSLPLR GDAQISVTLV
NHSEQEKAVQ LAIGVQAVHY NGVLAAKLWR KKLHLTLSAN LEKIITIGLF FSNFERNPPE
NTFLRLTAMA THSESNLSCF AQEDIAICRP HLAIKMPEKA EQYQPLTASV SLQNSLDAPM
EDCVISILGR GLIHRERSYR FRSVWPENTM CAKFQFTPTH VGLQRLTVEV DCNMFQNLTN
YKSVTVVAPE LSA*

mutated AA sequence

N/A

speed

0.80 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems