MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000260630
Querying Taster for transcript #2: ENST00000407341
MT speed 0 s - this script 3.249573 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CYP1B1	polymorphism_automatic	7.5049966241636e-12	simple_aae		affected		V432L	single base exchange	rs1056836		show file
CYP1B1	polymorphism_automatic	7.5049966241636e-12	simple_aae		affected		V432L	single base exchange	rs1056836		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999992495 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM004465)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:38298203C>GN/A show variant in all transcripts IGV

HGNC symbol

CYP1B1

Ensembl transcript ID

ENST00000260630

Genbank transcript ID

NM_000104

UniProt peptide

Q16678

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1294G>C
cDNA.1696G>C
g.38842G>C

AA changes

V432L Score: 32 explain score(s)

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

432

frameshift

known variant

Reference ID: rs1056836

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1147	785	1932
ExAC	25066	-17365	7701

known disease mutation at this position, please check HGMD for details (HGMD ID CM004465)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.16	0
	1.133	0.001
(flanking)	-1.249	0.001

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 increased	38843	wt: 0.40 / mu: 0.78	wt: CCCAGTGAAGTGGCC mu: CCCACTGAAGTGGCC	CAGT\|gaag
Donor marginally increased	38846	wt: 0.7081 / mu: 0.7319 (marginal change - not scored)	wt: AGTGAAGTGGCCTAA mu: ACTGAAGTGGCCTAA	TGAA\|gtgg

distance from splice site

251

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

432

mutated

all conserved

432

Ptroglodytes

all identical

ENSPTRG00000011843

432

Mmulatta

all identical

ENSMMUG00000013945

432

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000024087

432

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000068934

413

Dmelanogaster

not conserved

FBgn0086917

422

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
431	433	TURN		lost
435	439	STRAND		might get lost (downstream of altered splice site)
442	445	HELIX		might get lost (downstream of altered splice site)
454	457	HELIX		might get lost (downstream of altered splice site)
470	470	METAL	Iron (heme axial ligand) (By similarity).	might get lost (downstream of altered splice site)
473	490	HELIX		might get lost (downstream of altered splice site)
491	495	STRAND		might get lost (downstream of altered splice site)
505	513	STRAND		might get lost (downstream of altered splice site)
518	524	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1632 / 1632

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

544 / 544

position of stopcodon in wt / mu cDNA

2034 / 2034

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

403 / 403

chromosome

strand

-1

last intron/exon boundary

1446

theoretical NMD boundary in CDS

993

length of CDS

1632

coding sequence (CDS) position

1294

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

1696

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

38842

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

38298203

original gDNA sequence snippet

GGTCTGTGAATCATGACCCAGTGAAGTGGCCTAACCCGGAG

altered gDNA sequence snippet

GGTCTGTGAATCATGACCCACTGAAGTGGCCTAACCCGGAG

original cDNA sequence snippet

GGTCTGTGAATCATGACCCAGTGAAGTGGCCTAACCCGGAG

altered cDNA sequence snippet

GGTCTGTGAATCATGACCCACTGAAGTGGCCTAACCCGGAG

wildtype AA sequence

MGTSLSPNDP WPLNPLSIQQ TTLLLLLSVL ATVHVGQRLL RQRRRQLRSA PPGPFAWPLI
GNAAAVGQAA HLSFARLARR YGDVFQIRLG SCPIVVLNGE RAIHQALVQQ GSAFADRPAF
ASFRVVSGGR SMAFGHYSEH WKVQRRAAHS MMRNFFTRQP RSRQVLEGHV LSEARELVAL
LVRGSADGAF LDPRPLTVVA VANVMSAVCF GCRYSHDDPE FRELLSHNEE FGRTVGAGSL
VDVMPWLQYF PNPVRTVFRE FEQLNRNFSN FILDKFLRHC ESLRPGAAPR DMMDAFILSA
EKKAAGDSHG GGARLDLENV PATITDIFGA SQDTLSTALQ WLLLLFTRYP DVQTRVQAEL
DQVVGRDRLP CMGDQPNLPY VLAFLYEAMR FSSFVPVTIP HATTANTSVL GYHIPKDTVV
FVNQWSVNHD PVKWPNPENF DPARFLDKDG LINKDLTSRV MIFSVGKRRC IGEELSKMQL
FLFISILAHQ CDFRANPNEP AKMNFSYGLT IKPKSFKVNV TLRESMELLD SAVQNLQAKE
TCQ*

mutated AA sequence

MGTSLSPNDP WPLNPLSIQQ TTLLLLLSVL ATVHVGQRLL RQRRRQLRSA PPGPFAWPLI
GNAAAVGQAA HLSFARLARR YGDVFQIRLG SCPIVVLNGE RAIHQALVQQ GSAFADRPAF
ASFRVVSGGR SMAFGHYSEH WKVQRRAAHS MMRNFFTRQP RSRQVLEGHV LSEARELVAL
LVRGSADGAF LDPRPLTVVA VANVMSAVCF GCRYSHDDPE FRELLSHNEE FGRTVGAGSL
VDVMPWLQYF PNPVRTVFRE FEQLNRNFSN FILDKFLRHC ESLRPGAAPR DMMDAFILSA
EKKAAGDSHG GGARLDLENV PATITDIFGA SQDTLSTALQ WLLLLFTRYP DVQTRVQAEL
DQVVGRDRLP CMGDQPNLPY VLAFLYEAMR FSSFVPVTIP HATTANTSVL GYHIPKDTVV
FVNQWSVNHD PLKWPNPENF DPARFLDKDG LINKDLTSRV MIFSVGKRRC IGEELSKMQL
FLFISILAHQ CDFRANPNEP AKMNFSYGLT IKPKSFKVNV TLRESMELLD SAVQNLQAKE
TCQ*

speed

0.78 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: simple_aae, prob: 0.999999999992495 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM004465)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:38298203C>GN/A show variant in all transcripts IGV

HGNC symbol

CYP1B1

Ensembl transcript ID

ENST00000407341

Genbank transcript ID

N/A

UniProt peptide

Q16678

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1294G>C
cDNA.1595G>C
g.38842G>C

AA changes

V432L Score: 32 explain score(s)

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

432

frameshift

known variant

Reference ID: rs1056836

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1147	785	1932
ExAC	25066	-17365	7701

known disease mutation at this position, please check HGMD for details (HGMD ID CM004465)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.16	0
	1.133	0.001
(flanking)	-1.249	0.001

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 increased	38843	wt: 0.40 / mu: 0.78	wt: CCCAGTGAAGTGGCC mu: CCCACTGAAGTGGCC	CAGT\|gaag
Donor marginally increased	38846	wt: 0.7081 / mu: 0.7319 (marginal change - not scored)	wt: AGTGAAGTGGCCTAA mu: ACTGAAGTGGCCTAA	TGAA\|gtgg

distance from splice site

251

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

432

mutated

all conserved

432

Ptroglodytes

all identical

ENSPTRG00000011843

432

Mmulatta

all identical

ENSMMUG00000013945

432

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000024087

432

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000068934

413

Dmelanogaster

not conserved

FBgn0086917

422

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
431	433	TURN		lost
435	439	STRAND		might get lost (downstream of altered splice site)
442	445	HELIX		might get lost (downstream of altered splice site)
454	457	HELIX		might get lost (downstream of altered splice site)
470	470	METAL	Iron (heme axial ligand) (By similarity).	might get lost (downstream of altered splice site)
473	490	HELIX		might get lost (downstream of altered splice site)
491	495	STRAND		might get lost (downstream of altered splice site)
505	513	STRAND		might get lost (downstream of altered splice site)
518	524	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1632 / 1632

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

544 / 544

position of stopcodon in wt / mu cDNA

1933 / 1933

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

302 / 302

chromosome

strand

-1

last intron/exon boundary

1345

theoretical NMD boundary in CDS

993

length of CDS

1632

coding sequence (CDS) position

1294

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

1595

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

38842

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

38298203

original gDNA sequence snippet

GGTCTGTGAATCATGACCCAGTGAAGTGGCCTAACCCGGAG

altered gDNA sequence snippet

GGTCTGTGAATCATGACCCACTGAAGTGGCCTAACCCGGAG

original cDNA sequence snippet

GGTCTGTGAATCATGACCCAGTGAAGTGGCCTAACCCGGAG

altered cDNA sequence snippet

GGTCTGTGAATCATGACCCACTGAAGTGGCCTAACCCGGAG

wildtype AA sequence

mutated AA sequence

MGTSLSPNDP WPLNPLSIQQ TTLLLLLSVL ATVHVGQRLL RQRRRQLRSA PPGPFAWPLI
GNAAAVGQAA HLSFARLARR YGDVFQIRLG SCPIVVLNGE RAIHQALVQQ GSAFADRPAF
ASFRVVSGGR SMAFGHYSEH WKVQRRAAHS MMRNFFTRQP RSRQVLEGHV LSEARELVAL
LVRGSADGAF LDPRPLTVVA VANVMSAVCF GCRYSHDDPE FRELLSHNEE FGRTVGAGSL
VDVMPWLQYF PNPVRTVFRE FEQLNRNFSN FILDKFLRHC ESLRPGAAPR DMMDAFILSA
EKKAAGDSHG GGARLDLENV PATITDIFGA SQDTLSTALQ WLLLLFTRYP DVQTRVQAEL
DQVVGRDRLP CMGDQPNLPY VLAFLYEAMR FSSFVPVTIP HATTANTSVL GYHIPKDTVV
FVNQWSVNHD PLKWPNPENF DPARFLDKDG LINKDLTSRV MIFSVGKRRC IGEELSKMQL
FLFISILAHQ CDFRANPNEP AKMNFSYGLT IKPKSFKVNV TLRESMELLD SAVQNLQAKE
TCQ*

speed

0.49 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems