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 3.445521 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DHCR7	disease_causing	0.999999999365634	simple_aae		affected		Q107H	single base exchange	rs104886040		show file
DHCR7	disease_causing	0.999999999365634	simple_aae		affected		Q107H	single base exchange	rs104886040		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999365634 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs813426 (probable pathogenic)
known disease mutation at this position (HGMD CM003135)
known disease mutation at this position (HGMD CS002445)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:71155039C>GN/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.321G>C
cDNA.533G>C
g.8876G>C

AA changes

Q107H Score: 24 explain score(s)

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

107

frameshift

known variant

Reference ID: rs104886040

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

known as potential disease variant: rs813426 (probable pathogenic for Smith-Lemli-Opitz syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CS002445)

known disease mutation at this position, please check HGMD for details (HGMD ID CS002445)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003135)

known disease mutation at this position, please check HGMD for details (HGMD ID CS002445)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003135)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003135)

known disease mutation at this position, please check HGMD for details (HGMD ID CS002445)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003135)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003135)
known disease mutation at this position, please check HGMD for details (HGMD ID CS002445)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.997	1
	3.997	1
(flanking)	3.321	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	8876	sequence motif lost	-	wt: CCAG\|gtca mu: CCAC.gtca
Acc increased	8874	wt: 0.23 / mu: 0.29	wt: ATACCTTGTGGGTCACCTTCCAGGTCAGCAGCCCCTGCCCT mu: ATACCTTGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCT	ttcc\|AGGT
Acc increased	8880	wt: 0.58 / mu: 0.94	wt: TGTGGGTCACCTTCCAGGTCAGCAGCCCCTGCCCTGGGGTT mu: TGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCTGGGGTT	gtca\|GCAG
Donor increased	8871	wt: 0.62 / mu: 0.85	wt: TCACCTTCCAGGTCA mu: TCACCTTCCACGTCA	ACCT\|tcca
Donor decreased	8876	wt: 0.32 / mu: 0.25	wt: TTCCAGGTCAGCAGC mu: TTCCACGTCAGCAGC	CCAG\|gtca
Acc gained	8878	0.58	mu: CTTGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCTGGGG	acgt\|CAGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

all identical

ENSPTRG00000004013

107

Mmulatta

all identical

ENSMMUG00000011976

107

Fcatus

all identical

ENSFCAG00000004115

107

Mmusculus

all identical

ENSMUSG00000058454

103

Ggallus

all identical

ENSGALG00000004106

107

Trubripes

all identical

ENSTRUG00000003928

107

Drerio

all identical

ENSDARG00000015564

110

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000008945

105

protein features

start (aa)	end (aa)	feature	details
154	174	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
177	197	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
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

321

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

533

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

8876

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

71155039

original gDNA sequence snippet

ACCTTGTGGGTCACCTTCCAGGTCAGCAGCCCCTGCCCTGG

altered gDNA sequence snippet

ACCTTGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCTGG

original cDNA sequence snippet

ACCTTGTGGGTCACCTTCCAGGTGCTTCTGTACACGTCTCT

altered cDNA sequence snippet

ACCTTGTGGGTCACCTTCCACGTGCTTCTGTACACGTCTCT

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 TLWVTFHVLL 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*

speed

0.44 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: 0.999999999365634 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs813426 (probable pathogenic)
known disease mutation at this position (HGMD CM003135)
known disease mutation at this position (HGMD CS002445)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:71155039C>GN/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.321G>C
cDNA.598G>C
g.8876G>C

AA changes

Q107H Score: 24 explain score(s)

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

107

frameshift

known variant

Reference ID: rs104886040

database	homozygous (G/G)	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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.997	1
	3.997	1
(flanking)	3.321	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	8876	sequence motif lost	-	wt: CCAG\|gtca mu: CCAC.gtca
Acc increased	8874	wt: 0.23 / mu: 0.29	wt: ATACCTTGTGGGTCACCTTCCAGGTCAGCAGCCCCTGCCCT mu: ATACCTTGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCT	ttcc\|AGGT
Acc increased	8880	wt: 0.58 / mu: 0.94	wt: TGTGGGTCACCTTCCAGGTCAGCAGCCCCTGCCCTGGGGTT mu: TGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCTGGGGTT	gtca\|GCAG
Donor increased	8871	wt: 0.62 / mu: 0.85	wt: TCACCTTCCAGGTCA mu: TCACCTTCCACGTCA	ACCT\|tcca
Donor decreased	8876	wt: 0.32 / mu: 0.25	wt: TTCCAGGTCAGCAGC mu: TTCCACGTCAGCAGC	CCAG\|gtca
Acc gained	8878	0.58	mu: CTTGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCTGGGG	acgt\|CAGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

all identical

ENSPTRG00000004013

107

Mmulatta

all identical

ENSMMUG00000011976

107

Fcatus

all identical

ENSFCAG00000004115

107

Mmusculus

all identical

ENSMUSG00000058454

103

Ggallus

all identical

ENSGALG00000004106

107

Trubripes

all identical

ENSTRUG00000003928

107

Drerio

all identical

ENSDARG00000015564

110

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000008945

105

protein features

start (aa)	end (aa)	feature	details
154	174	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
177	197	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
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

321

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

598

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

8876

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

71155039

original gDNA sequence snippet

ACCTTGTGGGTCACCTTCCAGGTCAGCAGCCCCTGCCCTGG

altered gDNA sequence snippet

ACCTTGTGGGTCACCTTCCACGTCAGCAGCCCCTGCCCTGG

original cDNA sequence snippet

ACCTTGTGGGTCACCTTCCAGGTGCTTCTGTACACGTCTCT

altered cDNA sequence snippet

ACCTTGTGGGTCACCTTCCACGTGCTTCTGTACACGTCTCT

wildtype AA sequence

mutated AA sequence

speed

0.95 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems