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: ENST00000265295
MT speed 0 s - this script 3.361283 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPDL1	polymorphism_automatic	0	simple_aae		affected		Y508H	single base exchange	rs3797713		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr5:169028481T>CN/A show variant in all transcripts IGV

HGNC symbol

SPDL1

Ensembl transcript ID

ENST00000265295

Genbank transcript ID

NM_017785

UniProt peptide

Q96EA4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1522T>C
cDNA.1801T>C
g.17844T>C

AA changes

Y508H Score: 83 explain score(s)

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

508

frameshift

known variant

Reference ID: rs3797713

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1086	1117	2203
ExAC	26825	-20883	5942

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.011	0
	-1.474	0
(flanking)	0.321	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
Donor gained	17845	0.35	mu: TATACACACACCAGT	TACA\|caca

distance from splice site

149

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

508

mutated

all conserved

508

Ptroglodytes

all conserved

ENSPTRG00000017512

508

Mmulatta

all conserved

ENSMMUG00000009365

506

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000069910

511

Ggallus

not conserved

ENSGALG00000001942

511

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078054

501

Dmelanogaster

no alignment

FBgn0031549

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000019919

507

protein features

start (aa)	end (aa)	feature	details
515	515	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
555	555	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1818 / 1818

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

606 / 606

position of stopcodon in wt / mu cDNA

2097 / 2097

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

280 / 280

chromosome

strand

last intron/exon boundary

1950

theoretical NMD boundary in CDS

1620

length of CDS

1818

coding sequence (CDS) position

1522

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

1801

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

17844

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

169028481

original gDNA sequence snippet

TAGAAAAATCAGTTTCTATATACACACCAGTAGTCAGTCTC

altered gDNA sequence snippet

TAGAAAAATCAGTTTCTATACACACACCAGTAGTCAGTCTC

original cDNA sequence snippet

TAGAAAAATCAGTTTCTATATACACACCAGTAGTCAGTCTC

altered cDNA sequence snippet

TAGAAAAATCAGTTTCTATACACACACCAGTAGTCAGTCTC

wildtype AA sequence

MEADIITNLR CRLKEAEEER LKAAQYGLQL VESQNELQNQ LDKCRNEMMT MTESYEQEKY
TLQREVELKS RMLESLSCEC EAIKQQQKMH LEKLEEQLSR SHGQEVNELK TKIEKLKVEL
DEARLSEKQL KHQVDHQKEL LSCKSEELRV MSERVQESMS SEMLALQIEL TEMESMKTTL
KEEVNELQYR QEQLELLITN LMRQVDRLKE EKEEREKEAV SYYNALEKAR VANQDLQVQL
DQALQQALDP NSKGNSLFAE VEDRRAAMER QLISMKVKYQ SLKKQNVFNR EQMQRMKLQI
ATLLQMKGSQ TEFEQQERLL AMLEQKNGEI KHLLGEIRNL EKFKNLYDSM ESKPSVDSGT
LEDNTYYTDL LQMKLDNLNK EIESTKGELS IQRMKALFES QRALDIERKL FANERCLQLS
ESENMKLRAK LDELKLKYEP EETVEVPVLK KRREVLPVDI TTAKDACVNN SALGGEVYRL
PPQKEETQSC PNSLEDNNLQ LEKSVSIYTP VVSLSPHKNL PVDMQLKKEK KCVKLIGVPA
DAEALSERSG NTPNSPRLAA ESKLQTEVKE GKETSSKLEK ETCKKLHPIL YVSSKSTPET
QCPQQ*

mutated AA sequence

MEADIITNLR CRLKEAEEER LKAAQYGLQL VESQNELQNQ LDKCRNEMMT MTESYEQEKY
TLQREVELKS RMLESLSCEC EAIKQQQKMH LEKLEEQLSR SHGQEVNELK TKIEKLKVEL
DEARLSEKQL KHQVDHQKEL LSCKSEELRV MSERVQESMS SEMLALQIEL TEMESMKTTL
KEEVNELQYR QEQLELLITN LMRQVDRLKE EKEEREKEAV SYYNALEKAR VANQDLQVQL
DQALQQALDP NSKGNSLFAE VEDRRAAMER QLISMKVKYQ SLKKQNVFNR EQMQRMKLQI
ATLLQMKGSQ TEFEQQERLL AMLEQKNGEI KHLLGEIRNL EKFKNLYDSM ESKPSVDSGT
LEDNTYYTDL LQMKLDNLNK EIESTKGELS IQRMKALFES QRALDIERKL FANERCLQLS
ESENMKLRAK LDELKLKYEP EETVEVPVLK KRREVLPVDI TTAKDACVNN SALGGEVYRL
PPQKEETQSC PNSLEDNNLQ LEKSVSIHTP VVSLSPHKNL PVDMQLKKEK KCVKLIGVPA
DAEALSERSG NTPNSPRLAA ESKLQTEVKE GKETSSKLEK ETCKKLHPIL YVSSKSTPET
QCPQQ*

speed

1.30 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