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: ENST00000449592
MT speed 0 s - this script 2.340117 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TMEM120B	polymorphism_automatic	0.999883180422402	simple_aae		affected		D92N	single base exchange	rs28655666		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00011681957759829 (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)

chr12:122186317G>AN/A show variant in all transcripts IGV

HGNC symbol

TMEM120B

Ensembl transcript ID

ENST00000449592

Genbank transcript ID

NM_001080825

UniProt peptide

A0PK00

alteration type

single base exchange

alteration region

CDS

DNA changes

c.274G>A
cDNA.375G>A
g.35660G>A

AA changes

D92N Score: 23 explain score(s)

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

frameshift

known variant

Reference ID: rs28655666

database	homozygous (A/A)	heterozygous	allele carriers
1000G	497	1139	1636
ExAC	15268	2231	17499

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.308	0.951
	2.256	0.999
(flanking)	3.993	1

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	35660	wt: 0.2781 / mu: 0.3167 (marginal change - not scored)	wt: AGCGGCAGGACGTCTTCTTCGACATGGAGGCCTACCTGCCC mu: AGCGGCAGGACGTCTTCTTCAACATGGAGGCCTACCTGCCC	ttcg\|ACAT
Acc marginally increased	35664	wt: 0.5337 / mu: 0.5396 (marginal change - not scored)	wt: GCAGGACGTCTTCTTCGACATGGAGGCCTACCTGCCCAAGA mu: GCAGGACGTCTTCTTCAACATGGAGGCCTACCTGCCCAAGA	acat\|GGAG
Donor increased	35662	wt: 0.25 / mu: 0.55	wt: TTCGACATGGAGGCC mu: TTCAACATGGAGGCC	CGAC\|atgg
Donor increased	35663	wt: 0.35 / mu: 0.51	wt: TCGACATGGAGGCCT mu: TCAACATGGAGGCCT	GACA\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000005564

Mmulatta

not conserved

ENSMMUG00000031504

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000054434

Ggallus

all identical

ENSGALG00000004254

121

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042929

Dmelanogaster

all conserved

FBgn0040384

Celegans

all identical

M01G5.3

VANLR

Xtropicalis

all identical

ENSXETG00000003756

protein features

start (aa)	end (aa)	feature	details
92	92	CONFLICT	D -> N (in Ref. 2; AAI27770).	lost
102	124	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
132	152	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
159	179	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
187	207	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
270	290	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
302	322	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1020 / 1020

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

340 / 340

position of stopcodon in wt / mu cDNA

1121 / 1121

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

102 / 102

chromosome

strand

last intron/exon boundary

1008

theoretical NMD boundary in CDS

856

length of CDS

1020

coding sequence (CDS) position

274

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

375

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

35660

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

122186317

original gDNA sequence snippet

AGCGGCAGGACGTCTTCTTCGACATGGAGGCCTACCTGCCC

altered gDNA sequence snippet

AGCGGCAGGACGTCTTCTTCAACATGGAGGCCTACCTGCCC

original cDNA sequence snippet

AGCGGCAGGACGTCTTCTTCGACATGGAGGCCTACCTGCCC

altered cDNA sequence snippet

AGCGGCAGGACGTCTTCTTCAACATGGAGGCCTACCTGCCC

wildtype AA sequence

MSGQLERCER EWHELEGEFQ ELQETHRIYK QKLEELAALQ TLCSSSISKQ KKHLKDLKLT
LQRCKRHASR EEAELVQQMA ANIKERQDVF FDMEAYLPKK NGLYLNLVLG NVNVTLLSNQ
AKFAYKDEYE KFKLYLTIIL LLGAVACRFV LHYRVTDEVF NFLLVWYYCT LTIRESILIS
NGSRIKGWWV SHHYVSTFLS GVMLTWPNGP IYQKFRNQFL AFSIFQSCVQ FLQYYYQRGC
LYRLRALGER NHLDLTVEGF QSWMWRGLTF LLPFLFCGHF WQLYNAVTLF ELSSHEECRE
WQVFVLAFTF LILFLGNFLT TLKVVHAKLQ KNRGKTKQP*

mutated AA sequence

MSGQLERCER EWHELEGEFQ ELQETHRIYK QKLEELAALQ TLCSSSISKQ KKHLKDLKLT
LQRCKRHASR EEAELVQQMA ANIKERQDVF FNMEAYLPKK NGLYLNLVLG NVNVTLLSNQ
AKFAYKDEYE KFKLYLTIIL LLGAVACRFV LHYRVTDEVF NFLLVWYYCT LTIRESILIS
NGSRIKGWWV SHHYVSTFLS GVMLTWPNGP IYQKFRNQFL AFSIFQSCVQ FLQYYYQRGC
LYRLRALGER NHLDLTVEGF QSWMWRGLTF LLPFLFCGHF WQLYNAVTLF ELSSHEECRE
WQVFVLAFTF LILFLGNFLT TLKVVHAKLQ KNRGKTKQP*

speed

0.32 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