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: ENST00000407721
Querying Taster for transcript #2: ENST00000355527
MT speed 0 s - this script 3.683403 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DHCR7	disease_causing_automatic	0.296077466533412	simple_aae		affected	0	T289I	single base exchange	rs121909765		show file
DHCR7	disease_causing_automatic	0.296077466533412	simple_aae		affected	0	T289I	single base exchange	rs121909765		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.296077466533412 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000684)
known disease mutation: rs6789 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:71148955G>AN/A show variant in all transcripts IGV

HGNC symbol

DHCR7

Ensembl transcript ID

ENST00000407721

Genbank transcript ID

N/A

UniProt peptide

Q9UBM7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.866C>T
cDNA.1078C>T
g.14960C>T

AA changes

T289I Score: 89 explain score(s)

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

289

frameshift

known variant

Reference ID: rs121909765

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs6789 (pathogenic for Smith-Lemli-Opitz syndrome|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000684)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000684)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000684)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.262	0.976
	3.5	1
(flanking)	0.376	0.999

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	14951	wt: 0.7702 / mu: 0.7819 (marginal change - not scored)	wt: CTACGTGATTGACTTCTTCTGGAACGAAACCTGGTACCTGA mu: CTACGTGATTGACTTCTTCTGGAACGAAATCTGGTACCTGA	tctg\|GAAC
Acc increased	14950	wt: 0.54 / mu: 0.61	wt: TCTACGTGATTGACTTCTTCTGGAACGAAACCTGGTACCTG mu: TCTACGTGATTGACTTCTTCTGGAACGAAATCTGGTACCTG	ttct\|GGAA
Donor gained	14953	0.94	mu: TCTGGAACGAAATCT	TGGA\|acga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

289

mutated

not conserved

289

Ptroglodytes

all identical

ENSPTRG00000004013

289

Mmulatta

all identical

ENSMMUG00000011976

289

Fcatus

not conserved

ENSFCAG00000004115

289

Mmusculus

all identical

ENSMUSG00000058454

285

Ggallus

not conserved

ENSGALG00000004106

289

Trubripes

not conserved

ENSTRUG00000003928

289

Drerio

not conserved

ENSDARG00000015564

292

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000008945

287

protein features

start (aa)	end (aa)	feature	details
266	286	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
306	326	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	351	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
420	440	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

1428 / 1428

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

476 / 476

position of stopcodon in wt / mu cDNA

1640 / 1640

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

213 / 213

chromosome

strand

-1

last intron/exon boundary

1176

theoretical NMD boundary in CDS

913

length of CDS

1428

coding sequence (CDS) position

866

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

1078

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

14960

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

71148955

original gDNA sequence snippet

TGACTTCTTCTGGAACGAAACCTGGTACCTGAAGACCATTG

altered gDNA sequence snippet

TGACTTCTTCTGGAACGAAATCTGGTACCTGAAGACCATTG

original cDNA sequence snippet

TGACTTCTTCTGGAACGAAACCTGGTACCTGAAGACCATTG

altered cDNA sequence snippet

TGACTTCTTCTGGAACGAAATCTGGTACCTGAAGACCATTG

wildtype AA sequence

MAAKSQPNIP KAKSLDGVTN DRTASQGQWG RAWEVDWFSL ASVIFLLLFA PFIVYYFIMA
CDQYSCALTG PVVDIVTGHA RLSDIWAKTP PITRKAAQLY TLWVTFQVLL YTSLPDFCHK
FLPGYVGGIQ EGAVTPAGVV NKYQINGLQA WLLTHLLWFA NAHLLSWFSP TIIFDNWIPL
LWCANILGYA VSTFAMVKGY FFPTSARDCK FTGNFFYNYM MGIEFNPRIG KWFDFKLFFN
GRPGIVAWTL INLSFAAKQR ELHSHVTNAM VLVNVLQAIY VIDFFWNETW YLKTIDICHD
HFGWYLGWGD CVWLPYLYTL QGLYLVYHPV QLSTPHAVGV LLLGLVGYYI FRVANHQKDL
FRRTDGRCLI WGRKPKVIEC SYTSADGQRH HSKLLVSGFW GVARHFNYVG DLMGSLAYCL
ACGGGHLLPY FYIIYMAILL THRCLRDEHR CASKYGRDWE RYTAAVPYRL LPGIF*

mutated AA sequence

MAAKSQPNIP KAKSLDGVTN DRTASQGQWG RAWEVDWFSL ASVIFLLLFA PFIVYYFIMA
CDQYSCALTG PVVDIVTGHA RLSDIWAKTP PITRKAAQLY TLWVTFQVLL YTSLPDFCHK
FLPGYVGGIQ EGAVTPAGVV NKYQINGLQA WLLTHLLWFA NAHLLSWFSP TIIFDNWIPL
LWCANILGYA VSTFAMVKGY FFPTSARDCK FTGNFFYNYM MGIEFNPRIG KWFDFKLFFN
GRPGIVAWTL INLSFAAKQR ELHSHVTNAM VLVNVLQAIY VIDFFWNEIW YLKTIDICHD
HFGWYLGWGD CVWLPYLYTL QGLYLVYHPV QLSTPHAVGV LLLGLVGYYI FRVANHQKDL
FRRTDGRCLI WGRKPKVIEC SYTSADGQRH HSKLLVSGFW GVARHFNYVG DLMGSLAYCL
ACGGGHLLPY FYIIYMAILL THRCLRDEHR CASKYGRDWE RYTAAVPYRL LPGIF*

speed

1.37 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

disease causing

Model: simple_aae, prob: 0.296077466533412 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000684)
known disease mutation: rs6789 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:71148955G>AN/A show variant in all transcripts IGV

HGNC symbol

DHCR7

Ensembl transcript ID

ENST00000355527

Genbank transcript ID

NM_001163817

UniProt peptide

Q9UBM7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.866C>T
cDNA.1143C>T
g.14960C>T

AA changes

T289I Score: 89 explain score(s)

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

289

frameshift

known variant

Reference ID: rs121909765

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.262	0.976
	3.5	1
(flanking)	0.376	0.999

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	14951	wt: 0.7702 / mu: 0.7819 (marginal change - not scored)	wt: CTACGTGATTGACTTCTTCTGGAACGAAACCTGGTACCTGA mu: CTACGTGATTGACTTCTTCTGGAACGAAATCTGGTACCTGA	tctg\|GAAC
Acc increased	14950	wt: 0.54 / mu: 0.61	wt: TCTACGTGATTGACTTCTTCTGGAACGAAACCTGGTACCTG mu: TCTACGTGATTGACTTCTTCTGGAACGAAATCTGGTACCTG	ttct\|GGAA
Donor gained	14953	0.94	mu: TCTGGAACGAAATCT	TGGA\|acga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

289

mutated

not conserved

289

Ptroglodytes

all identical

ENSPTRG00000004013

289

Mmulatta

all identical

ENSMMUG00000011976

289

Fcatus

not conserved

ENSFCAG00000004115

289

Mmusculus

all identical

ENSMUSG00000058454

285

Ggallus

not conserved

ENSGALG00000004106

289

Trubripes

not conserved

ENSTRUG00000003928

289

Drerio

not conserved

ENSDARG00000015564

292

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000008945

287

protein features

start (aa)	end (aa)	feature	details
266	286	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
306	326	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	351	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
420	440	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

1428 / 1428

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

476 / 476

position of stopcodon in wt / mu cDNA

1705 / 1705

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

278 / 278

chromosome

strand

-1

last intron/exon boundary

1241

theoretical NMD boundary in CDS

913

length of CDS

1428

coding sequence (CDS) position

866

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

1143

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

14960

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

71148955

original gDNA sequence snippet

TGACTTCTTCTGGAACGAAACCTGGTACCTGAAGACCATTG

altered gDNA sequence snippet

TGACTTCTTCTGGAACGAAATCTGGTACCTGAAGACCATTG

original cDNA sequence snippet

TGACTTCTTCTGGAACGAAACCTGGTACCTGAAGACCATTG

altered cDNA sequence snippet

TGACTTCTTCTGGAACGAAATCTGGTACCTGAAGACCATTG

wildtype AA sequence

mutated AA sequence

MAAKSQPNIP KAKSLDGVTN DRTASQGQWG RAWEVDWFSL ASVIFLLLFA PFIVYYFIMA
CDQYSCALTG PVVDIVTGHA RLSDIWAKTP PITRKAAQLY TLWVTFQVLL YTSLPDFCHK
FLPGYVGGIQ EGAVTPAGVV NKYQINGLQA WLLTHLLWFA NAHLLSWFSP TIIFDNWIPL
LWCANILGYA VSTFAMVKGY FFPTSARDCK FTGNFFYNYM MGIEFNPRIG KWFDFKLFFN
GRPGIVAWTL INLSFAAKQR ELHSHVTNAM VLVNVLQAIY VIDFFWNEIW YLKTIDICHD
HFGWYLGWGD CVWLPYLYTL QGLYLVYHPV QLSTPHAVGV LLLGLVGYYI FRVANHQKDL
FRRTDGRCLI WGRKPKVIEC SYTSADGQRH HSKLLVSGFW GVARHFNYVG DLMGSLAYCL
ACGGGHLLPY FYIIYMAILL THRCLRDEHR CASKYGRDWE RYTAAVPYRL LPGIF*

speed

1.43 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems