MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000374566
MT speed 0 s - this script 2.188336 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPB41L4B	polymorphism_automatic	0.137670022928046	simple_aae		affected		N816T	single base exchange	rs3750450		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.862329977071954 (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)

chr9:111945049T>GN/A show variant in all transcripts IGV

HGNC symbol

EPB41L4B

Ensembl transcript ID

ENST00000374566

Genbank transcript ID

NM_019114

UniProt peptide

Q9H329

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2447A>C
cDNA.2965A>C
g.138196A>C

AA changes

N816T Score: 65 explain score(s)

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

816

frameshift

known variant

Reference ID: rs3750450

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1327	971	2298
ExAC	32110	-31453	657

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.236	0.993
	0.422	0.994
(flanking)	1.96	0.998

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 increased	138207	wt: 0.22 / mu: 0.40	wt: ATACAATGAACCCGTTTCCTGATACTTTCACCACAGGGCCA mu: ATACAATGACCCCGTTTCCTGATACTTTCACCACAGGGCCA	cctg\|ATAC
Acc gained	138206	0.43	mu: GATACAATGACCCCGTTTCCTGATACTTTCACCACAGGGCC	tcct\|GATA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

816

mutated

not conserved

816

Ptroglodytes

all identical

ENSPTRG00000021239

714

Mmulatta

all identical

ENSMMUG00000017515

714

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028434

814

Ggallus

all identical

ENSGALG00000013145

732

Trubripes

not conserved

ENSTRUG00000009133

516

Drerio

no alignment

ENSDARG00000061398

n/a

Dmelanogaster

no alignment

FBgn0004049

n/a

Celegans

no alignment

T04C9.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
899	899	CONFLICT	E -> R (in Ref. 1; AAG43366).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2703 / 2703

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

901 / 901

position of stopcodon in wt / mu cDNA

3221 / 3221

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

519 / 519

chromosome

strand

-1

last intron/exon boundary

3152

theoretical NMD boundary in CDS

2583

length of CDS

2703

coding sequence (CDS) position

2447

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

2965

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

138196

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

111945049

original gDNA sequence snippet

ATTCCCGGTTGATACAATGAACCCGTTTCCTGATACTTTCA

altered gDNA sequence snippet

ATTCCCGGTTGATACAATGACCCCGTTTCCTGATACTTTCA

original cDNA sequence snippet

ATTCCCGGTTGATACAATGAACCCGTTTCCTGATACTTTCA

altered cDNA sequence snippet

ATTCCCGGTTGATACAATGACCCCGTTTCCTGATACTTTCA

wildtype AA sequence

MLRFLRRTFG RRSMQRYARG AAGRGAAGLG DERDGGPRGG PAAAASSSAL PAAPGGSVFP
AGGGPLLTGG AAVHISAAGA AKATLYCRVF LLDGTEVSVD LPKHAKGQDL FDQIVYHLDL
VETDYFGLQF LDSAQVAHWL DHAKPIKKQM KIGPAYALHF RVKYYSSEPN NLREEFTRYL
FVLQLRHDIL SGKLKCPYET AVELAALCLQ AELGECELPE HTPELVSEFR FIPNQTEAME
FDIFQRWKEC RGKSPAQAEL SYLNKAKWLE MYGVDMHVVR GRDGCEYSLG LTPTGILIFE
GANKIGLFFW PKITKMDFKK SKLTLVVVED DDQGREQEHT FVFRLDSART CKHLWKCAVE
HHAFFRLRTP GNSKSNRSDF IRLGSRFRFS GRTEYQATHG SRLRRTSTFE RKPSKRYPSR
RHSTFKASNP VIAAQLCSKT NPEVHNYQPQ YHPNIHPSQP RWHPHSPNVS YPLPSPVLSS
SDRLPFGIEE NGGTPFLTAA SGRHHHQHQH QHQHQHHSNY SLSLTLENKE GPLRSPNSSS
KSLTKLSPGT PALFSEAAAH LKKLELETVK AAGPWPPLHI NINKAEEKKV SEKTLQTPLL
PSPVADHVKC NILKAQLENA SRVNIQGGKE ESPFVNINKK SSLQDASVRS PIPIRVETAQ
PAVEKPEIKP PRVRKLTRQY SFDEDDLPPD LAEAVGVTTS TTTNTTTAAT QVSVPLPSPK
VQNVSSPHKS EGKGLLSPGA KSPSDRGGAF TLEPGDLLMD FTEATPLAEP ASNPHCAHSR
CSPPLSLPMK EETTGVCMYP PIKTRLIKTF PVDTMNPFPD TFTTGPQFTA DFRDSKLQCC
PGPTSPLIPA ATLRPLTETV STVQTIYTTR KPVSLAASAE TLRQELEREK MMKRLLMTEL
*

mutated AA sequence

MLRFLRRTFG RRSMQRYARG AAGRGAAGLG DERDGGPRGG PAAAASSSAL PAAPGGSVFP
AGGGPLLTGG AAVHISAAGA AKATLYCRVF LLDGTEVSVD LPKHAKGQDL FDQIVYHLDL
VETDYFGLQF LDSAQVAHWL DHAKPIKKQM KIGPAYALHF RVKYYSSEPN NLREEFTRYL
FVLQLRHDIL SGKLKCPYET AVELAALCLQ AELGECELPE HTPELVSEFR FIPNQTEAME
FDIFQRWKEC RGKSPAQAEL SYLNKAKWLE MYGVDMHVVR GRDGCEYSLG LTPTGILIFE
GANKIGLFFW PKITKMDFKK SKLTLVVVED DDQGREQEHT FVFRLDSART CKHLWKCAVE
HHAFFRLRTP GNSKSNRSDF IRLGSRFRFS GRTEYQATHG SRLRRTSTFE RKPSKRYPSR
RHSTFKASNP VIAAQLCSKT NPEVHNYQPQ YHPNIHPSQP RWHPHSPNVS YPLPSPVLSS
SDRLPFGIEE NGGTPFLTAA SGRHHHQHQH QHQHQHHSNY SLSLTLENKE GPLRSPNSSS
KSLTKLSPGT PALFSEAAAH LKKLELETVK AAGPWPPLHI NINKAEEKKV SEKTLQTPLL
PSPVADHVKC NILKAQLENA SRVNIQGGKE ESPFVNINKK SSLQDASVRS PIPIRVETAQ
PAVEKPEIKP PRVRKLTRQY SFDEDDLPPD LAEAVGVTTS TTTNTTTAAT QVSVPLPSPK
VQNVSSPHKS EGKGLLSPGA KSPSDRGGAF TLEPGDLLMD FTEATPLAEP ASNPHCAHSR
CSPPLSLPMK EETTGVCMYP PIKTRLIKTF PVDTMTPFPD TFTTGPQFTA DFRDSKLQCC
PGPTSPLIPA ATLRPLTETV STVQTIYTTR KPVSLAASAE TLRQELEREK MMKRLLMTEL
*

speed

0.13 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems