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: ENST00000331493
Querying Taster for transcript #2: ENST00000517484
MT speed 0 s - this script 3.695512 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EFCAB13	polymorphism_automatic	3.99680288865056e-15	simple_aae				V312I	single base exchange	rs4968318		show file
EFCAB13	polymorphism_automatic	3.99680288865056e-15	simple_aae				V216I	single base exchange	rs4968318		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999996 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:45451894G>AN/A show variant in all transcripts IGV

HGNC symbol

EFCAB13

Ensembl transcript ID

ENST00000331493

Genbank transcript ID

NM_152347

UniProt peptide

Q8IY85

alteration type

single base exchange

alteration region

CDS

DNA changes

c.934G>A
cDNA.1345G>A
g.51239G>A

AA changes

V312I Score: 29 explain score(s)

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

312

frameshift

known variant

Reference ID: rs4968318

database	homozygous (A/A)	heterozygous	allele carriers
1000G	985	1144	2129
ExAC	21450	-10133	11317

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.192	0
	-3.471	0
(flanking)	0.399	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

312

mutated

all conserved

312

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000010588

312

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000040838

526

KSLD

Ggallus

no homologue

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

2922 / 2922

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

974 / 974

position of stopcodon in wt / mu cDNA

3333 / 3333

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

412 / 412

chromosome

strand

last intron/exon boundary

3050

theoretical NMD boundary in CDS

2588

length of CDS

2922

coding sequence (CDS) position

934

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

1345

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

51239

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

45451894

original gDNA sequence snippet

CAGACAGAAAGTTATCAAGTGTAGCAGGATGCTATCTAAAA

altered gDNA sequence snippet

CAGACAGAAAGTTATCAAGTATAGCAGGATGCTATCTAAAA

original cDNA sequence snippet

CAGACAGAAAGTTATCAAGTGTAGCAGGATGCTATCTAAAA

altered cDNA sequence snippet

CAGACAGAAAGTTATCAAGTATAGCAGGATGCTATCTAAAA

wildtype AA sequence

METKVHLFCQ AEENIDLLDD GSNSFATDLS SGTINHKKYI KFSKTIEKEI SPEIRSLSPE
YKKIFETSII FCGEEKSSDF SGEKKVGRKS LQVQQHSKRT EIIPPFLKLS KEKVTRKENS
LCKLPNQYSV HKTSSPLCTS SAITREKEML SNLYMTLYDE VTHGYLHSKE LSALHKACKI
FSKIRSGKIY VNDLPVILCI LRISISDLEM RQALKTVDID AFQDALKIFC RIKGGRVSTD
DVFAVLDSMG IPINREILEE VTKHTYIDSN HMVDIGDIIF TLNELQEQYE DVSITEGSPL
NEITSDRKLS SVAGCYLKYK KKNSLSSKLP EPSISKKLNK KSNQYYSKIM ENDDLESKRP
KNTWQIRKFL GGVGSSNVGV QEPYSKNGIN FKKHSEKGEI HDSKSKPQSL KSSTSLSKSL
DKSDISSIPK LQKPAVRKHS SLQKQVSSTE KTAISTLENF CEAISKLQEN YIAAEELQSI
LPSTGINLLD EEFQKIVTDT SRNENGMVEL DDFVNALAKE RSFPECNALP GVIKAIDKIK
DKNVDYEDLN TCLQNFGIYL SKPEFKKITE LTEAGETKKV NFKEFIDTMM SNTECFSEKL
VLPDAIETLD DLRKETMSVS DLWNTLSSLN SNLKKDEFLA ALELVTVDEG DKVQFEEFAK
VVRNMRDAAR LEELQEVVLA ADLLEGDMIA GKNLEDFLRN VGIKSPKEEV EKILQSDFVS
EDNMVNIKDC MRALRDTQKF SNYIDFRKEA SNLKLPKVNE IKEAANILSH VDNGKIGIPD
LEHALKCLNV NLTEEDFNEA LNCCNVSDNM EVDLKDFLMK MKESPHFQKS KATQILLATT
QILQNDLVDV SDLKTLLMDK DLHTANAILT VMLRHVPEHE SGKVSIQEFM TKLSDILTIP
KAAGKFYLIC TYCPDLERQA VVYMLKTIQD SIVKAQVSKK QYNMNIKQHK ISLHNFCLNS
KANIAKLNPN SKF*

mutated AA sequence

METKVHLFCQ AEENIDLLDD GSNSFATDLS SGTINHKKYI KFSKTIEKEI SPEIRSLSPE
YKKIFETSII FCGEEKSSDF SGEKKVGRKS LQVQQHSKRT EIIPPFLKLS KEKVTRKENS
LCKLPNQYSV HKTSSPLCTS SAITREKEML SNLYMTLYDE VTHGYLHSKE LSALHKACKI
FSKIRSGKIY VNDLPVILCI LRISISDLEM RQALKTVDID AFQDALKIFC RIKGGRVSTD
DVFAVLDSMG IPINREILEE VTKHTYIDSN HMVDIGDIIF TLNELQEQYE DVSITEGSPL
NEITSDRKLS SIAGCYLKYK KKNSLSSKLP EPSISKKLNK KSNQYYSKIM ENDDLESKRP
KNTWQIRKFL GGVGSSNVGV QEPYSKNGIN FKKHSEKGEI HDSKSKPQSL KSSTSLSKSL
DKSDISSIPK LQKPAVRKHS SLQKQVSSTE KTAISTLENF CEAISKLQEN YIAAEELQSI
LPSTGINLLD EEFQKIVTDT SRNENGMVEL DDFVNALAKE RSFPECNALP GVIKAIDKIK
DKNVDYEDLN TCLQNFGIYL SKPEFKKITE LTEAGETKKV NFKEFIDTMM SNTECFSEKL
VLPDAIETLD DLRKETMSVS DLWNTLSSLN SNLKKDEFLA ALELVTVDEG DKVQFEEFAK
VVRNMRDAAR LEELQEVVLA ADLLEGDMIA GKNLEDFLRN VGIKSPKEEV EKILQSDFVS
EDNMVNIKDC MRALRDTQKF SNYIDFRKEA SNLKLPKVNE IKEAANILSH VDNGKIGIPD
LEHALKCLNV NLTEEDFNEA LNCCNVSDNM EVDLKDFLMK MKESPHFQKS KATQILLATT
QILQNDLVDV SDLKTLLMDK DLHTANAILT VMLRHVPEHE SGKVSIQEFM TKLSDILTIP
KAAGKFYLIC TYCPDLERQA VVYMLKTIQD SIVKAQVSKK QYNMNIKQHK ISLHNFCLNS
KANIAKLNPN SKF*

speed

1.29 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: 0.999999999999996 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:45451894G>AN/A show variant in all transcripts IGV

HGNC symbol

EFCAB13

Ensembl transcript ID

ENST00000517484

Genbank transcript ID

NM_001195192

UniProt peptide

Q8IY85

alteration type

single base exchange

alteration region

CDS

DNA changes

c.646G>A
cDNA.1013G>A
g.51239G>A

AA changes

V216I Score: 29 explain score(s)

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

216

frameshift

known variant

Reference ID: rs4968318

database	homozygous (A/A)	heterozygous	allele carriers
1000G	985	1144	2129
ExAC	21450	-10133	11317

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.192	0
	-3.471	0
(flanking)	0.399	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

216

mutated

all conserved

216

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000010588

312

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000040838

526

KSLD

Ggallus

no homologue

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

2355 / 2355

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

785 / 785

position of stopcodon in wt / mu cDNA

2722 / 2722

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

368 / 368

chromosome

strand

last intron/exon boundary

2574

theoretical NMD boundary in CDS

2156

length of CDS

2355

coding sequence (CDS) position

646

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

1013

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

51239

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

45451894

original gDNA sequence snippet

CAGACAGAAAGTTATCAAGTGTAGCAGGATGCTATCTAAAA

altered gDNA sequence snippet

CAGACAGAAAGTTATCAAGTATAGCAGGATGCTATCTAAAA

original cDNA sequence snippet

CAGACAGAAAGTTATCAAGTGTAGCAGGATGCTATCTAAAA

altered cDNA sequence snippet

CAGACAGAAAGTTATCAAGTATAGCAGGATGCTATCTAAAA

wildtype AA sequence

METKVHLFCQ AEENIDLLDD GSNSFATDLS SGTINHKKYI KFSKTIEKEI SPEIRSLSPE
YKKIFETSII FCGEEKSSDF SGEKKVGRKS LQVQQHSKRT EIIPPFLKLS KEKVTRKENS
LCKLPNQYSV HKTSSPLCTS SAITREKEML SNLYMTLYDE VTHGYLHSKE LSGNHMVDIG
DIIFTLNELQ EQYEDVSITE GSPLNEITSD RKLSSVAGCY LKYKKKNSLS SKLPEPSISK
KLNKKSNQYY SKIMENDDLE SKRPKNTWQI RKFLGGVGSS NVGVQEPYSK NGINFKKHSE
KGEIHDSKSK PQSLKSSTSL SKSLDKSDIS SIPKLQKPAV RKHSSLQKQV SSTEKTAIST
LENFCEAISK LQENYIAAEE LQSILPSTGI NLLDEEFQKI VTDTSRNENG MVELDDFVNA
LAKERSFPEC NALPGVIKAI DKIKDKNVDY EDLNTCLQNF GIYLSKPEFK KITELTEAGE
TKKVNFKEFI DTMMSNTECF SEKLVLPDAI ETLDDLRKET MSVSDLWNTL SSLNSNLKKD
EFLAALELVT VDEGDKVQFE EFAKVVRNMR DAARLEELQE VVLAADLLEG DMIAGKNLED
FLRNVGIKSP KEEVEKILQS DFVSEDNMVN IKDCMRALRD TQKFSNYIDF RKEASNLKLP
KVNEIKEAAN ILSHVDNGKI GIPDLEHALK CLNVNLTEED FNEALNCCNV SDNMEVDLKD
FLMKMKESPH FQKSKATQIL LATTQILQND LVDVSDLKTL LMDKDLHTAN AILTVMLRHV
PEHG*

mutated AA sequence

METKVHLFCQ AEENIDLLDD GSNSFATDLS SGTINHKKYI KFSKTIEKEI SPEIRSLSPE
YKKIFETSII FCGEEKSSDF SGEKKVGRKS LQVQQHSKRT EIIPPFLKLS KEKVTRKENS
LCKLPNQYSV HKTSSPLCTS SAITREKEML SNLYMTLYDE VTHGYLHSKE LSGNHMVDIG
DIIFTLNELQ EQYEDVSITE GSPLNEITSD RKLSSIAGCY LKYKKKNSLS SKLPEPSISK
KLNKKSNQYY SKIMENDDLE SKRPKNTWQI RKFLGGVGSS NVGVQEPYSK NGINFKKHSE
KGEIHDSKSK PQSLKSSTSL SKSLDKSDIS SIPKLQKPAV RKHSSLQKQV SSTEKTAIST
LENFCEAISK LQENYIAAEE LQSILPSTGI NLLDEEFQKI VTDTSRNENG MVELDDFVNA
LAKERSFPEC NALPGVIKAI DKIKDKNVDY EDLNTCLQNF GIYLSKPEFK KITELTEAGE
TKKVNFKEFI DTMMSNTECF SEKLVLPDAI ETLDDLRKET MSVSDLWNTL SSLNSNLKKD
EFLAALELVT VDEGDKVQFE EFAKVVRNMR DAARLEELQE VVLAADLLEG DMIAGKNLED
FLRNVGIKSP KEEVEKILQS DFVSEDNMVN IKDCMRALRD TQKFSNYIDF RKEASNLKLP
KVNEIKEAAN ILSHVDNGKI GIPDLEHALK CLNVNLTEED FNEALNCCNV SDNMEVDLKD
FLMKMKESPH FQKSKATQIL LATTQILQND LVDVSDLKTL LMDKDLHTAN AILTVMLRHV
PEHG*

speed

0.46 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems