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: ENST00000231173
MT speed 0 s - this script 2.856788 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PCDHB15	polymorphism_automatic	1.99840144432528e-15	simple_aae		affected		R494Q	single base exchange	rs618096		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (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)

chr5:140626627G>AN/A show variant in all transcripts IGV

HGNC symbol

PCDHB15

Ensembl transcript ID

ENST00000231173

Genbank transcript ID

NM_018935

UniProt peptide

Q9Y5E8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1481G>A
cDNA.1481G>A
g.1481G>A

AA changes

R494Q Score: 43 explain score(s)

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

494

frameshift

known variant

Reference ID: rs618096

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1066	1121	2187
ExAC	21955	-11143	10812

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.161	0
	-1.2	0
(flanking)	-1.535	0

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	1481	wt: 0.54 / mu: 0.62	wt: CTACTCGCTGCTGCCGCCCCGGGACCCGCACCTGCCCCTCA mu: CTACTCGCTGCTGCCGCCCCAGGACCCGCACCTGCCCCTCA	cccg\|GGAC

distance from splice site

1173

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

494

mutated

all conserved

494

Ptroglodytes

all conserved

ENSPTRG00000017343

494

Mmulatta

all conserved

ENSMMUG00000021941

494

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000073591

492

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
27	690	TOPO_DOM	Extracellular (Potential).	lost
456	561	DOMAIN	Cadherin 5.	lost
567	567	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
568	671	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
691	711	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
712	787	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2364 / 2364

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

788 / 788

position of stopcodon in wt / mu cDNA

2364 / 2364

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

1 / 1

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

2364

coding sequence (CDS) position

1481

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

1481

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

1481

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

140626627

original gDNA sequence snippet

CTACTCGCTGCTGCCGCCCCGGGACCCGCACCTGCCCCTCA

altered gDNA sequence snippet

CTACTCGCTGCTGCCGCCCCAGGACCCGCACCTGCCCCTCA

original cDNA sequence snippet

CTACTCGCTGCTGCCGCCCCGGGACCCGCACCTGCCCCTCA

altered cDNA sequence snippet

CTACTCGCTGCTGCCGCCCCAGGACCCGCACCTGCCCCTCA

wildtype AA sequence

MEPAGERFPE QRQVLILLLL LEVTLAGWEP RRYSVMEETE RGSFVANLAN DLGLGVGELA
ERGARVVSED NEQGLQLDLQ TGQLILNEKL DREKLCGPTE PCIMHFQVLL KKPLEVFRAE
LLVTDINDHS PEFPEREMTL KIPETSSLGT VFPLKKARDL DVGSNNVQNY NISPNSHFHV
STRTRGDGRK YPELVLDTEL DREEQAELRL TLTAVDGGSP PRSGTVQILI LVLDANDNAP
EFVQALYEVQ VPENSPVGSL VVKVSARDLD TGTNGEISYS LYYSSQEIDK PFELSSLSGE
IRLIKKLDFE TMSSYDLDIE ASDGGGLSGK CSVSVKVLDV NDNFPELSIS SLTSPIPENS
PETEVALFRI RDRDSGENGK MICSIQDDVP FKLKPSVENF YRLVTEGALD RETRAEYNIT
ITITDLGTPR LKTEQSITVL VSDVNDNAPA FTQTSYTLFV RENNSPALHI GSVSATDRDS
GTNAQVTYSL LPPRDPHLPL TSLVSINTDN GHLFALQSLD YEALQAFEFR VGATDRGFPA
LSSEALVRVL VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDVAKHRL VVLVKDNGEP PRSATATLQV
LLVDGFSQPY LPLPEAAPAQ AQADSLTVYL VVALASVSSL FLFSVFLFVA VRLCRRSRAA
SVGRCSVPEG PFPGHLVDVS GTGTLSQSYQ YEVCLTGGSE SNDFKFLKPI FPNIVSQDSR
RKSEFLE*

mutated AA sequence

MEPAGERFPE QRQVLILLLL LEVTLAGWEP RRYSVMEETE RGSFVANLAN DLGLGVGELA
ERGARVVSED NEQGLQLDLQ TGQLILNEKL DREKLCGPTE PCIMHFQVLL KKPLEVFRAE
LLVTDINDHS PEFPEREMTL KIPETSSLGT VFPLKKARDL DVGSNNVQNY NISPNSHFHV
STRTRGDGRK YPELVLDTEL DREEQAELRL TLTAVDGGSP PRSGTVQILI LVLDANDNAP
EFVQALYEVQ VPENSPVGSL VVKVSARDLD TGTNGEISYS LYYSSQEIDK PFELSSLSGE
IRLIKKLDFE TMSSYDLDIE ASDGGGLSGK CSVSVKVLDV NDNFPELSIS SLTSPIPENS
PETEVALFRI RDRDSGENGK MICSIQDDVP FKLKPSVENF YRLVTEGALD RETRAEYNIT
ITITDLGTPR LKTEQSITVL VSDVNDNAPA FTQTSYTLFV RENNSPALHI GSVSATDRDS
GTNAQVTYSL LPPQDPHLPL TSLVSINTDN GHLFALQSLD YEALQAFEFR VGATDRGFPA
LSSEALVRVL VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDVAKHRL VVLVKDNGEP PRSATATLQV
LLVDGFSQPY LPLPEAAPAQ AQADSLTVYL VVALASVSSL FLFSVFLFVA VRLCRRSRAA
SVGRCSVPEG PFPGHLVDVS GTGTLSQSYQ YEVCLTGGSE SNDFKFLKPI FPNIVSQDSR
RKSEFLE*

speed

0.79 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