MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000380027
Querying Taster for transcript #2: ENST00000317037
MT speed 0 s - this script 2.140796 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR52N2	polymorphism_automatic	0.912524868579406	simple_aae		affected		H264R	single base exchange	rs8181512		show file
TRIM5	polymorphism_automatic	1	without_aae		affected			single base exchange	rs8181512		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0874751314205942 (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)

chr11:5842356A>GN/A show variant in all transcripts IGV

HGNC symbol

OR52N2

Ensembl transcript ID

ENST00000317037

Genbank transcript ID

NM_001005174

UniProt peptide

Q8NGI0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.791A>G
cDNA.813A>G
g.813A>G

AA changes

H264R Score: 29 explain score(s)

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

264

frameshift

known variant

Reference ID: rs8181512

database	homozygous (G/G)	heterozygous	allele carriers
1000G	546	1183	1729
ExAC	16212	343	16555

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.972	0.986
	4.669	0.986
(flanking)	-0.764	0.321

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	824	wt: 0.8844 / mu: 0.8905 (marginal change - not scored)	wt: TTTTCACTCATCGTTTTGTAGGACACAATATCCCAAACCAC mu: TTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAACCAC	gtag\|GACA
Acc increased	821	wt: 0.34 / mu: 0.44	wt: CTTTTTTCACTCATCGTTTTGTAGGACACAATATCCCAAAC mu: CTTTTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAAC	tttg\|TAGG
Acc marginally increased	814	wt: 0.9030 / mu: 0.9043 (marginal change - not scored)	wt: TTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAATAT mu: TTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAATAT	tcat\|CGTT
Acc marginally increased	803	wt: 0.9874 / mu: 0.9883 (marginal change - not scored)	wt: ATGTTGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTA mu: ATGTTGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTA	actt\|TTTT
Acc marginally increased	807	wt: 0.9830 / mu: 0.9841 (marginal change - not scored)	wt: TGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGAC mu: TGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGAC	tttt\|CACT
Acc marginally increased	810	wt: 0.9836 / mu: 0.9854 (marginal change - not scored)	wt: TGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACA mu: TGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACA	tcac\|TCAT
Acc marginally increased	812	wt: 0.9963 / mu: 0.9979 (marginal change - not scored)	wt: CTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAAT mu: CTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAAT	actc\|ATCG
Acc increased	811	wt: 0.21 / mu: 0.34	wt: GCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAA mu: GCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAA	cact\|CATC
Acc marginally increased	806	wt: 0.9604 / mu: 0.9773 (marginal change - not scored)	wt: TTGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGA mu: TTGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGA	tttt\|TCAC
Acc marginally increased	805	wt: 0.7587 / mu: 0.8037 (marginal change - not scored)	wt: GTTGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGG mu: GTTGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGG	tttt\|TTCA
Acc marginally increased	822	wt: 0.8641 / mu: 0.8913 (marginal change - not scored)	wt: TTTTTTCACTCATCGTTTTGTAGGACACAATATCCCAAACC mu: TTTTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAACC	ttgt\|AGGA
Acc marginally increased	809	wt: 0.9894 / mu: 0.9934 (marginal change - not scored)	wt: CTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACAC mu: CTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACAC	ttca\|CTCA
Acc increased	820	wt: 0.74 / mu: 0.90	wt: ACTTTTTTCACTCATCGTTTTGTAGGACACAATATCCCAAA mu: ACTTTTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAA	tttt\|GTAG

distance from splice site

223

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

264

mutated

not conserved

264

Ptroglodytes

all identical

ENSPTRG00000003265

264

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000007096

264

Mmusculus

no homologue

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
261	276	TOPO_DOM	Extracellular (Potential).	lost
277	297	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
298	321	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

966 / 966

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

322 / 322

position of stopcodon in wt / mu cDNA

988 / 988

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

23 / 23

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

966

coding sequence (CDS) position

791

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

813

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

813

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

5842356

original gDNA sequence snippet

TTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAATA

altered gDNA sequence snippet

TTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAATA

original cDNA sequence snippet

TTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAATA

altered cDNA sequence snippet

TTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAATA

wildtype AA sequence

MSGDNSSSLT PGFFILNGVP GLEATHIWIS LPFCFMYIIA VVGNCGLICL ISHEEALHRP
MYYFLALLSF TDVTLCTTMV PNMLCIFWFN LKEIDFNACL AQMFFVHMLT GMESGVLMLM
ALDRYVAICY PLRYATILTN PVIAKAGLAT FLRNVMLIIP FTLLTKRLPY CRGNFIPHTY
CDHMSVAKVS CGNFKVNAIY GLMVALLIGV FDICCISVSY TMILQAVMSL SSADARHKAF
STCTSHMCSI VITYVAAFFT FFTHRFVGHN IPNHIHIIVA NLYLLLPPTM NPIVYGVKTK
QIQEGVIKFL LGDKVSFTYD K*

mutated AA sequence

MSGDNSSSLT PGFFILNGVP GLEATHIWIS LPFCFMYIIA VVGNCGLICL ISHEEALHRP
MYYFLALLSF TDVTLCTTMV PNMLCIFWFN LKEIDFNACL AQMFFVHMLT GMESGVLMLM
ALDRYVAICY PLRYATILTN PVIAKAGLAT FLRNVMLIIP FTLLTKRLPY CRGNFIPHTY
CDHMSVAKVS CGNFKVNAIY GLMVALLIGV FDICCISVSY TMILQAVMSL SSADARHKAF
STCTSHMCSI VITYVAAFFT FFTRRFVGHN IPNHIHIIVA NLYLLLPPTM NPIVYGVKTK
QIQEGVIKFL LGDKVSFTYD K*

speed

0.10 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

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.63605388744436e-46 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr11:5842356A>GN/A show variant in all transcripts IGV

HGNC symbol

TRIM5

Ensembl transcript ID

ENST00000380027

Genbank transcript ID

N/A

UniProt peptide

Q9C035

alteration type

single base exchange

alteration region

intron

DNA changes

g.117494T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs8181512

database	homozygous (G/G)	heterozygous	allele carriers
1000G	546	1183	1729
ExAC	16212	343	16555

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.972	0.986
	4.669	0.986
(flanking)	-0.764	0.321

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -146) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	117488	wt: 0.8607 / mu: 0.8796 (marginal change - not scored)	wt: TTGGGATATTGTGTCCTACAAAACGATGAGTGAAAAAAGTG mu: TTGGGATATTGTGTCCTACAAAACGACGAGTGAAAAAAGTG	acaa\|AACG
Donor increased	117486	wt: 0.31 / mu: 0.52	wt: TCCTACAAAACGATG mu: TCCTACAAAACGACG	CTAC\|aaaa
Donor marginally increased	117496	wt: 0.9953 / mu: 0.9969 (marginal change - not scored)	wt: CGATGAGTGAAAAAA mu: CGACGAGTGAAAAAA	ATGA\|gtga
Donor increased	117489	wt: 0.63 / mu: 0.87	wt: TACAAAACGATGAGT mu: TACAAAACGACGAGT	CAAA\|acga
Acc gained	117486	0.32	mu: GTTTGGGATATTGTGTCCTACAAAACGACGAGTGAAAAAAG	ctac\|AAAA
Donor gained	117485	0.32	mu: GTCCTACAAAACGAC	CCTA\|caaa

distance from splice site

34626

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
15	15	MUTAGEN	C->A: Abolishes E3 ligase activity.	might get lost (downstream of altered splice site)
15	59	ZN_FING	RING-type.	might get lost (downstream of altered splice site)
16	18	TURN		might get lost (downstream of altered splice site)
29	31	STRAND		might get lost (downstream of altered splice site)
38	45	HELIX		might get lost (downstream of altered splice site)
46	50	TURN		might get lost (downstream of altered splice site)
56	58	TURN		might get lost (downstream of altered splice site)
64	66	STRAND		might get lost (downstream of altered splice site)
76	76	CONFLICT	I -> L (in Ref. 2; BAB55218).	might get lost (downstream of altered splice site)
86	86	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
90	132	ZN_FING	B box-type.	might get lost (downstream of altered splice site)
92	94	STRAND		might get lost (downstream of altered splice site)
96	98	TURN		might get lost (downstream of altered splice site)
104	106	STRAND		might get lost (downstream of altered splice site)
107	109	TURN		might get lost (downstream of altered splice site)
111	113	STRAND		might get lost (downstream of altered splice site)
115	118	HELIX		might get lost (downstream of altered splice site)
121	125	TURN		might get lost (downstream of altered splice site)
130	130	CONFLICT	L -> P (in Ref. 2; BAB55218).	might get lost (downstream of altered splice site)
130	241	COILED	Potential.	might get lost (downstream of altered splice site)
281	493	DOMAIN	B30.2/SPRY.	might get lost (downstream of altered splice site)
332	332	MUTAGEN	R->K: No effect on HIV-1 and SIVmac infection.	might get lost (downstream of altered splice site)
332	332	MUTAGEN	R->D,E,L: Increases strongly cell restriction against HIV-1 infection.	might get lost (downstream of altered splice site)
332	332	MUTAGEN	R->A,G,H,P,Q,S: Increases strongly cell restriction against HIV-1 and SIVmac infection.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

785 / 785

chromosome

strand

-1

last intron/exon boundary

1680

theoretical NMD boundary in CDS

845

length of CDS

981

coding sequence (CDS) position

N/A

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

N/A

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

117494

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

5842356

original gDNA sequence snippet

TATTGTGTCCTACAAAACGATGAGTGAAAAAAGTGAAAAAA

altered gDNA sequence snippet

TATTGTGTCCTACAAAACGACGAGTGAAAAAAGTGAAAAAA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MASGILVNVK EEVTCPICLE LLTQPLSLDC GHSFCQACLT ANHKKSMLDK GESSCPVCRI
SYQPENIRPN RHVANIVEKL REVKLSPEGQ KVDHCARHGE KLLLFCQEDG KVICWLCERS
QEHRGHHTFL TEEVAREYQV KLQAALEMLR QKQQEAEELE ADIREEKASW KTQIQYDKTN
VLADFEQLRD ILDWEESNEL QNLEKEEEDI LKSLTNSETE MVQQTQSLRE LISDLEHRLQ
GSVMELLQGV DGVIKRTENV TLKKPETFPK NQRRVFRAPD LKGMLEVFRE LTDVRRYWGW
SAMARSRFTA TSTSQIQAIL LPQPPK*

mutated AA sequence

N/A

speed

0.09 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems