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: ENST00000255078
Querying Taster for transcript #2: ENST00000539224
MT speed 0 s - this script 3.509203 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
IGHMBP2	polymorphism_automatic	0	simple_aae		affected		L201S	single base exchange	rs560096		show file
IGHMBP2	polymorphism_automatic	7.3696392988154e-08	without_aae		affected			single base exchange	rs560096		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)

chr11:68678962T>CN/A show variant in all transcripts IGV

HGNC symbol

IGHMBP2

Ensembl transcript ID

ENST00000255078

Genbank transcript ID

NM_002180

UniProt peptide

P38935

alteration type

single base exchange

alteration region

CDS

DNA changes

c.602T>C
cDNA.713T>C
g.7653T>C

AA changes

L201S Score: 145 explain score(s)

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

201

frameshift

known variant

Reference ID: rs560096

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1234	940	2174
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.234	0.001
	-0.372	0
(flanking)	-2.075	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	7645	0.51	mu: AAAGAAGCGGTTTCA	AGAA\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

201

mutated

not conserved

201

Ptroglodytes

not conserved

ENSPTRG00000003989

201

Mmulatta

not conserved

ENSMMUG00000010128

201

Fcatus

not conserved

ENSFCAG00000010879

112

Mmusculus

not conserved

ENSMUSG00000024831

200

Ggallus

not conserved

ENSGALG00000004328

197

Trubripes

not conserved

ENSTRUG00000003491

200

Drerio

not conserved

ENSDARG00000069274

199

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
214	221	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)
251	426	COMPBIAS	Leu-rich.	might get lost (downstream of altered splice site)
292	292	CONFLICT	I -> N (in Ref. 1; AAA53082).	might get lost (downstream of altered splice site)
461	461	CONFLICT	L -> V (in Ref. 1; AAA53082).	might get lost (downstream of altered splice site)
491	494	CONFLICT	VDTA -> GGRV (in Ref. 6; AAA58611).	might get lost (downstream of altered splice site)
638	785	REGION	SS DNA-binding (By similarity).	might get lost (downstream of altered splice site)
656	656	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
723	786	DOMAIN	R3H.	might get lost (downstream of altered splice site)
727	739	HELIX		might get lost (downstream of altered splice site)
742	746	STRAND		might get lost (downstream of altered splice site)
753	764	HELIX		might get lost (downstream of altered splice site)
767	772	STRAND		might get lost (downstream of altered splice site)
774	776	STRAND		might get lost (downstream of altered splice site)
779	784	STRAND		might get lost (downstream of altered splice site)
795	859	COMPBIAS	Gln/Pro-rich.	might get lost (downstream of altered splice site)
863	863	CONFLICT	E -> K (in Ref. 6; AAA58611).	might get lost (downstream of altered splice site)
864	868	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)
864	870	COMPBIAS	Poly-Lys.	might get lost (downstream of altered splice site)
866	866	CONFLICT	K -> T (in Ref. 6; AAA58611).	might get lost (downstream of altered splice site)
894	940	ZN_FING	AN1-type.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2982 / 2982

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

994 / 994

position of stopcodon in wt / mu cDNA

3093 / 3093

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

112 / 112

chromosome

strand

last intron/exon boundary

2896

theoretical NMD boundary in CDS

2734

length of CDS

2982

coding sequence (CDS) position

602

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

713

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

7653

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

68678962

original gDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTTATTTGCGCTGTCTCAGAAAG

altered gDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTCATTTGCGCTGTCTCAGAAAG

original cDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTTATTTGCGCTGTCTCAGAAAG

altered cDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTCATTTGCGCTGTCTCAGAAAG

wildtype AA sequence

MASAAVESFV TKQLDLLELE RDAEVEERRS WQENISLKEL QSRGVCLLKL QVSSQRTGLY
GRLLVTFEPR RYGSAAALPS NSFTSGDIVG LYDAANEGSQ LATGILTRVT QKSVTVAFDE
SHDFQLSLDR ENSYRLLKLA NDVTYRRLKK ALIALKKYHS GPASSLIEVL FGRSAPSPAS
EIHPLTFFNT CLDTSQKEAV LFALSQKELA IIHGPPGTGK TTTVVEIILQ AVKQGLKVLC
CAPSNIAVDN LVERLALCKQ RILRLGHPAR LLESIQQHSL DAVLARSDSA QIVADIRKDI
DQVFVKNKKT QDKREKSNFR NEIKLLRKEL KEREEAAMLE SLTSANVVLA TNTGASADGP
LKLLPESYFD VVVIDECAQA LEASCWIPLL KARKCILAGD HKQLPPTTVS HKAALAGLSL
SLMERLAEEY GARVVRTLTV QYRMHQAIMR WASDTMYLGQ LTAHSSVARH LLRDLPGVAA
TEETGVPLLL VDTAGCGLFE LEEEDEQSKG NPGEVRLVSL HIQALVDAGV PARDIAVVSP
YNLQVDLLRQ SLVHRHPELE IKSVDGFQGR EKEAVILSFV RSNRKGEVGF LAEDRRINVA
VTRARRHVAV ICDSRTVNNH AFLKTLVEYF TQHGEVRTAF EYLDDIVPEN YSHENSQGSS
HAATKPQGPA TSTRTGSQRQ EGGQEAAAPA RQGRKKPAGK SLASEAPSQP SLNGGSPEGV
ESQDGVDHFR AMIVEFMASK KMQLEFPPSL NSHDRLRVHQ IAEEHGLRHD SSGEGKRRFI
TVSKRAPRPR AALGPPAGTG GPAPLQPVPP TPAQTEQPPR EQRGPDQPDL RTLHLERLQR
VRSAQGQPAS KEQQASGQQK LPEKKKKKAK GHPATDLPTE EDFEALVSAA VKADNTCGFA
KCTAGVTTLG QFCQLCSRRY CLSHHLPEIH GCGERARAHA RQRISREGVL YAGSGTKNGS
LDPAKRAQLQ RRLDKKLSEL SNQRTSRRKE RGT*

mutated AA sequence

MASAAVESFV TKQLDLLELE RDAEVEERRS WQENISLKEL QSRGVCLLKL QVSSQRTGLY
GRLLVTFEPR RYGSAAALPS NSFTSGDIVG LYDAANEGSQ LATGILTRVT QKSVTVAFDE
SHDFQLSLDR ENSYRLLKLA NDVTYRRLKK ALIALKKYHS GPASSLIEVL FGRSAPSPAS
EIHPLTFFNT CLDTSQKEAV SFALSQKELA IIHGPPGTGK TTTVVEIILQ AVKQGLKVLC
CAPSNIAVDN LVERLALCKQ RILRLGHPAR LLESIQQHSL DAVLARSDSA QIVADIRKDI
DQVFVKNKKT QDKREKSNFR NEIKLLRKEL KEREEAAMLE SLTSANVVLA TNTGASADGP
LKLLPESYFD VVVIDECAQA LEASCWIPLL KARKCILAGD HKQLPPTTVS HKAALAGLSL
SLMERLAEEY GARVVRTLTV QYRMHQAIMR WASDTMYLGQ LTAHSSVARH LLRDLPGVAA
TEETGVPLLL VDTAGCGLFE LEEEDEQSKG NPGEVRLVSL HIQALVDAGV PARDIAVVSP
YNLQVDLLRQ SLVHRHPELE IKSVDGFQGR EKEAVILSFV RSNRKGEVGF LAEDRRINVA
VTRARRHVAV ICDSRTVNNH AFLKTLVEYF TQHGEVRTAF EYLDDIVPEN YSHENSQGSS
HAATKPQGPA TSTRTGSQRQ EGGQEAAAPA RQGRKKPAGK SLASEAPSQP SLNGGSPEGV
ESQDGVDHFR AMIVEFMASK KMQLEFPPSL NSHDRLRVHQ IAEEHGLRHD SSGEGKRRFI
TVSKRAPRPR AALGPPAGTG GPAPLQPVPP TPAQTEQPPR EQRGPDQPDL RTLHLERLQR
VRSAQGQPAS KEQQASGQQK LPEKKKKKAK GHPATDLPTE EDFEALVSAA VKADNTCGFA
KCTAGVTTLG QFCQLCSRRY CLSHHLPEIH GCGERARAHA RQRISREGVL YAGSGTKNGS
LDPAKRAQLQ RRLDKKLSEL SNQRTSRRKE RGT*

speed

0.87 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: 0.999999926303607 (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)

chr11:68678962T>CN/A show variant in all transcripts IGV

HGNC symbol

IGHMBP2

Ensembl transcript ID

ENST00000539224

Genbank transcript ID

N/A

UniProt peptide

P38935

alteration type

single base exchange

alteration region

CDS

DNA changes

c.504T>C
cDNA.560T>C
g.7653T>C

AA changes

no AA changes

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

N/A

frameshift

known variant

Reference ID: rs560096

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1234	940	2174
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.234	0.001
	-0.372	0
(flanking)	-2.075	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	7645	0.51	mu: AAAGAAGCGGTTTCA	AGAA\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
214	221	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)
251	426	COMPBIAS	Leu-rich.	might get lost (downstream of altered splice site)
292	292	CONFLICT	I -> N (in Ref. 1; AAA53082).	might get lost (downstream of altered splice site)
461	461	CONFLICT	L -> V (in Ref. 1; AAA53082).	might get lost (downstream of altered splice site)
491	494	CONFLICT	VDTA -> GGRV (in Ref. 6; AAA58611).	might get lost (downstream of altered splice site)
638	785	REGION	SS DNA-binding (By similarity).	might get lost (downstream of altered splice site)
656	656	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
723	786	DOMAIN	R3H.	might get lost (downstream of altered splice site)
727	739	HELIX		might get lost (downstream of altered splice site)
742	746	STRAND		might get lost (downstream of altered splice site)
753	764	HELIX		might get lost (downstream of altered splice site)
767	772	STRAND		might get lost (downstream of altered splice site)
774	776	STRAND		might get lost (downstream of altered splice site)
779	784	STRAND		might get lost (downstream of altered splice site)
795	859	COMPBIAS	Gln/Pro-rich.	might get lost (downstream of altered splice site)
863	863	CONFLICT	E -> K (in Ref. 6; AAA58611).	might get lost (downstream of altered splice site)
864	868	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)
864	870	COMPBIAS	Poly-Lys.	might get lost (downstream of altered splice site)
866	866	CONFLICT	K -> T (in Ref. 6; AAA58611).	might get lost (downstream of altered splice site)
894	940	ZN_FING	AN1-type.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

position of stopcodon in wt / mu CDS

579 / 579

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

193 / 193

position of stopcodon in wt / mu cDNA

635 / 635

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

last intron/exon boundary

670

theoretical NMD boundary in CDS

563

length of CDS

579

coding sequence (CDS) position

504

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

560

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

7653

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

68678962

original gDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTTATTTGCGCTGTCTCAGAAAG

altered gDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTCATTTGCGCTGTCTCAGAAAG

original cDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTTATTTGCGCTGTCTCAGAAAG

altered cDNA sequence snippet

CTCCCAGAAAGAAGCGGTTTCATTTGCGCTGTCTCAGAAAG

wildtype AA sequence

mutated AA sequence

speed

0.64 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems