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: ENST00000291707
MT speed 1.25 s - this script 3.844231 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SIGLEC12	polymorphism_automatic	6.03752603467456e-09	simple_aae		affected		H398Y	single base exchange	rs11668530		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999993962474 (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)

chr19:52001485G>AN/A show variant in all transcripts IGV

HGNC symbol

SIGLEC12

Ensembl transcript ID

ENST00000291707

Genbank transcript ID

NM_033329

UniProt peptide

Q96PQ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1192C>T
cDNA.1248C>T
g.3559C>T

AA changes

H398Y Score: 83 explain score(s)

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

398

frameshift

known variant

Reference ID: rs11668530

database	homozygous (A/A)	heterozygous	allele carriers
1000G	429	912	1341
ExAC	14915	2937	17852

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.824	0.058
	1.093	0.219
(flanking)	1.093	0.275

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 marginally increased	3570	wt: 0.9067 / mu: 0.9327 (marginal change - not scored)	wt: CAGTCCCTGCACCTTGTCTGTGCTGTCGACAGCAATCCCCC mu: CAGTCCCTGTACCTTGTCTGTGCTGTCGACAGCAATCCCCC	ctgt\|GCTG
Acc increased	3564	wt: 0.53 / mu: 0.67	wt: GAGGGCCAGTCCCTGCACCTTGTCTGTGCTGTCGACAGCAA mu: GAGGGCCAGTCCCTGTACCTTGTCTGTGCTGTCGACAGCAA	cctt\|GTCT
Acc marginally increased	3568	wt: 0.7517 / mu: 0.8212 (marginal change - not scored)	wt: GCCAGTCCCTGCACCTTGTCTGTGCTGTCGACAGCAATCCC mu: GCCAGTCCCTGTACCTTGTCTGTGCTGTCGACAGCAATCCC	gtct\|GTGC
Acc increased	3569	wt: 0.48 / mu: 0.60	wt: CCAGTCCCTGCACCTTGTCTGTGCTGTCGACAGCAATCCCC mu: CCAGTCCCTGTACCTTGTCTGTGCTGTCGACAGCAATCCCC	tctg\|TGCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

398

mutated

all conserved

398

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000030474

275

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
19	481	TOPO_DOM	Extracellular (Potential).	lost
365	462	DOMAIN	Ig-like C2-type 2.	lost
401	401	DISULFID	By similarity.	might get lost (downstream of altered splice site)
446	446	DISULFID	By similarity.	might get lost (downstream of altered splice site)
482	502	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
503	595	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
528	528	CONFLICT	R -> W (in Ref. 3; AAQ88507).	might get lost (downstream of altered splice site)
563	568	MOTIF	ITIM motif.	might get lost (downstream of altered splice site)
586	591	MOTIF	SLAM-like motif.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1788 / 1788

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

596 / 596

position of stopcodon in wt / mu cDNA

1844 / 1844

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

57 / 57

chromosome

strand

-1

last intron/exon boundary

1656

theoretical NMD boundary in CDS

1549

length of CDS

1788

coding sequence (CDS) position

1192

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

1248

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

3559

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

52001485

original gDNA sequence snippet

TCCTGGAGGGCCAGTCCCTGCACCTTGTCTGTGCTGTCGAC

altered gDNA sequence snippet

TCCTGGAGGGCCAGTCCCTGTACCTTGTCTGTGCTGTCGAC

original cDNA sequence snippet

TCCTGGAGGGCCAGTCCCTGCACCTTGTCTGTGCTGTCGAC

altered cDNA sequence snippet

TCCTGGAGGGCCAGTCCCTGTACCTTGTCTGTGCTGTCGAC

wildtype AA sequence

MLLLLLLLPP LLCGRVGAKE QKDYLLTMQK SVTVQEGLCV SVLCSFSYPQ NGWTASDPVH
GYWFRAGDHV SRNIPVATNN PARAVQEETR DRFHLLGDPQ NKDCTLSIRD TRESDAGTYV
FCVERGNMKW NYKYDQLSVN VTASQDLLSR YRLEVPESVT VQEGLCVSVP CSVLYPHYNW
TASSPVYGSW FKEGADIPWD IPVATNTPSG KVQEDTHGRF LLLGDPQTNN CSLSIRDARK
GDSGKYYFQV ERGSRKWNYI YDKLSVHVTA LTHMPTFSIP GTLESGHPRN LTCSVPWACE
QGTPPTITWM GASVSSLDPT ITRSSMLSLI PQPQDHGTSL TCQVTLPGAG VTMTRAVRLN
ISYPPQNLTM TVFQGDGTAS TTLRNGSALS VLEGQSLHLV CAVDSNPPAR LSWTWGSLTL
SPSQSSNLGV LELPRVHVKD EGEFTCRAQN PLGSQHISLS LSLQNEYTGK MRPISGVTLG
AFGGAGATAL VFLYFCIIFV VVRSCRKKSA RPAVGVGDTG MEDANAVRGS ASQGPLIESP
ADDSPPHHAP PALATPSPEE GEIQYASLSF HKARPQYPQE QEAIGYEYSE INIPK*

mutated AA sequence

MLLLLLLLPP LLCGRVGAKE QKDYLLTMQK SVTVQEGLCV SVLCSFSYPQ NGWTASDPVH
GYWFRAGDHV SRNIPVATNN PARAVQEETR DRFHLLGDPQ NKDCTLSIRD TRESDAGTYV
FCVERGNMKW NYKYDQLSVN VTASQDLLSR YRLEVPESVT VQEGLCVSVP CSVLYPHYNW
TASSPVYGSW FKEGADIPWD IPVATNTPSG KVQEDTHGRF LLLGDPQTNN CSLSIRDARK
GDSGKYYFQV ERGSRKWNYI YDKLSVHVTA LTHMPTFSIP GTLESGHPRN LTCSVPWACE
QGTPPTITWM GASVSSLDPT ITRSSMLSLI PQPQDHGTSL TCQVTLPGAG VTMTRAVRLN
ISYPPQNLTM TVFQGDGTAS TTLRNGSALS VLEGQSLYLV CAVDSNPPAR LSWTWGSLTL
SPSQSSNLGV LELPRVHVKD EGEFTCRAQN PLGSQHISLS LSLQNEYTGK MRPISGVTLG
AFGGAGATAL VFLYFCIIFV VVRSCRKKSA RPAVGVGDTG MEDANAVRGS ASQGPLIESP
ADDSPPHHAP PALATPSPEE GEIQYASLSF HKARPQYPQE QEAIGYEYSE INIPK*

speed

1.25 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