MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000371269
Querying Taster for transcript #2: ENST00000535035
Querying Taster for transcript #3: ENST00000537443
MT speed 0 s - this script 3.154358 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DHCR24	disease_causing	0.999999999994288	simple_aae		affected		E23K	single base exchange	rs119475041		show file
DHCR24	disease_causing	0.99999999999656	simple_aae		affected		E191K	single base exchange	rs119475041		show file
DHCR24	disease_causing	0.99999999999656	simple_aae		affected		E150K	single base exchange	rs119475041		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999994288 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs4369 (probable pathogenic)
known disease mutation at this position (HGMD CM014564)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:55340807C>TN/A show variant in all transcripts IGV

HGNC symbol

DHCR24

Ensembl transcript ID

ENST00000537443

Genbank transcript ID

N/A

UniProt peptide

Q15392

alteration type

single base exchange

alteration region

CDS

DNA changes

c.67G>A
cDNA.132G>A
g.12085G>A

AA changes

E23K Score: 56 explain score(s)

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

frameshift

known variant

Reference ID: rs119475041

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known as potential disease variant: rs4369 (probable pathogenic for Desmosterolosis) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014564)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014564)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014564)

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)	5.123	1
	6.205	1
(flanking)	-0.866	0.462

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	12081	0.93	mu: ACTGCTTACAAGCTG	TGCT\|taca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000000779

191

Mmulatta

all identical

ENSMMUG00000021577

191

Fcatus

all identical

ENSFCAG00000003989

114

Mmusculus

all identical

ENSMUSG00000034926

191

Ggallus

all identical

ENSGALG00000010798

191

Trubripes

all identical

ENSTRUG00000016297

194

Drerio

all identical

ENSDARG00000013236

191

Dmelanogaster

no homologue

Celegans

all identical

F52H2.6

187

Xtropicalis

all identical

ENSXETG00000020010

191

protein features

start (aa)	end (aa)	feature	details
1	22	SIGNAL	Potential.	might get lost (downstream of altered splice site)
23	31	TOPO_DOM	Lumenal (Potential).	lost
32	52	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
53	516	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
58	234	DOMAIN	FAD-binding PCMH-type.	might get lost (downstream of altered splice site)
110	110	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
122	123	SITE	Cleavage; by caspase (Potential).	might get lost (downstream of altered splice site)
163	175	NP_BIND	FAD (Potential).	might get lost (downstream of altered splice site)
383	384	SITE	Cleavage; by caspase (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

903 / 903

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

301 / 301

position of stopcodon in wt / mu cDNA

968 / 968

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

66 / 66

chromosome

strand

-1

last intron/exon boundary

815

theoretical NMD boundary in CDS

699

length of CDS

903

coding sequence (CDS) position

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

132

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

12085

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

55340807

original gDNA sequence snippet

AACACATCTGCACTGCTTACGAGCTGGTCCTGGCTGATGGC

altered gDNA sequence snippet

AACACATCTGCACTGCTTACAAGCTGGTCCTGGCTGATGGC

original cDNA sequence snippet

AACACATCTGCACTGCTTACGAGCTGGTCCTGGCTGATGGC

altered cDNA sequence snippet

AACACATCTGCACTGCTTACAAGCTGGTCCTGGCTGATGGC

wildtype AA sequence

MGTGIESSSH KYGLFQHICT AYELVLADGS FVRCTPSENS DLFYAVPWSC GTLGFLVAAE
IRIIPAKKYV KLRFEPVRGL EAICAKFTHE SQRQENHFVE GLLYSLDEAV IMTGVMTDEA
EPSKDIIPFG NNPIFRYLFG WMVPPKISLL KLTQGETLRK LYEQHHVVQD MLVPMKCLQQ
ALHTFQNDIH VYPIWLCPFI LPSQPGLVHP KGNEAELYID IGAYGEPRVK HFEARSCMRQ
LEKFVRSVHG FQMLYADCYM NREEFWEMFD GSLYHKLREK LGCQDAFPEV YDKICKAARH
*

mutated AA sequence

MGTGIESSSH KYGLFQHICT AYKLVLADGS FVRCTPSENS DLFYAVPWSC GTLGFLVAAE
IRIIPAKKYV KLRFEPVRGL EAICAKFTHE SQRQENHFVE GLLYSLDEAV IMTGVMTDEA
EPSKDIIPFG NNPIFRYLFG WMVPPKISLL KLTQGETLRK LYEQHHVVQD MLVPMKCLQQ
ALHTFQNDIH VYPIWLCPFI LPSQPGLVHP KGNEAELYID IGAYGEPRVK HFEARSCMRQ
LEKFVRSVHG FQMLYADCYM NREEFWEMFD GSLYHKLREK LGCQDAFPEV YDKICKAARH
*

speed

0.56 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: 0.99999999999656 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs4369 (probable pathogenic)
known disease mutation at this position (HGMD CM014564)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:55340807C>TN/A show variant in all transcripts IGV

HGNC symbol

DHCR24

Ensembl transcript ID

ENST00000371269

Genbank transcript ID

NM_014762

UniProt peptide

Q15392

alteration type

single base exchange

alteration region

CDS

DNA changes

c.571G>A
cDNA.670G>A
g.12085G>A

AA changes

E191K Score: 56 explain score(s)

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

191

frameshift

known variant

Reference ID: rs119475041

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

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)	5.123	1
	6.205	1
(flanking)	-0.866	0.462

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	12081	0.93	mu: ACTGCTTACAAGCTG	TGCT\|taca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

191

mutated

all conserved

191

Ptroglodytes

all identical

ENSPTRG00000000779

191

Mmulatta

all identical

ENSMMUG00000021577

191

Fcatus

all identical

ENSFCAG00000003989

114

Mmusculus

all identical

ENSMUSG00000034926

191

Ggallus

all identical

ENSGALG00000010798

191

Trubripes

all identical

ENSTRUG00000016297

194

Drerio

all identical

ENSDARG00000013236

191

Dmelanogaster

no homologue

Celegans

all identical

F52H2.6

187

Xtropicalis

all identical

ENSXETG00000020010

191

protein features

start (aa)	end (aa)	feature	details
53	516	TOPO_DOM	Cytoplasmic (Potential).	lost
58	234	DOMAIN	FAD-binding PCMH-type.	lost
383	384	SITE	Cleavage; by caspase (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1551 / 1551

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

517 / 517

position of stopcodon in wt / mu cDNA

1650 / 1650

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

100 / 100

chromosome

strand

-1

last intron/exon boundary

1497

theoretical NMD boundary in CDS

1347

length of CDS

1551

coding sequence (CDS) position

571

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

670

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

12085

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

55340807

original gDNA sequence snippet

AACACATCTGCACTGCTTACGAGCTGGTCCTGGCTGATGGC

altered gDNA sequence snippet

AACACATCTGCACTGCTTACAAGCTGGTCCTGGCTGATGGC

original cDNA sequence snippet

AACACATCTGCACTGCTTACGAGCTGGTCCTGGCTGATGGC

altered cDNA sequence snippet

AACACATCTGCACTGCTTACAAGCTGGTCCTGGCTGATGGC

wildtype AA sequence

MEPAVSLAVC ALLFLLWVRL KGLEFVLIHQ RWVFVCLFLL PLSLIFDIYY YVRAWVVFKL
SSAPRLHEQR VRDIQKQVRE WKEQGSKTFM CTGRPGWLTV SLRVGKYKKT HKNIMINLMD
ILEVDTKKQI VRVEPLVTMG QVTALLTSIG WTLPVLPELD DLTVGGLIMG TGIESSSHKY
GLFQHICTAY ELVLADGSFV RCTPSENSDL FYAVPWSCGT LGFLVAAEIR IIPAKKYVKL
RFEPVRGLEA ICAKFTHESQ RQENHFVEGL LYSLDEAVIM TGVMTDEAEP SKLNSIGNYY
KPWFFKHVEN YLKTNREGLE YIPLRHYYHR HTRSIFWELQ DIIPFGNNPI FRYLFGWMVP
PKISLLKLTQ GETLRKLYEQ HHVVQDMLVP MKCLQQALHT FQNDIHVYPI WLCPFILPSQ
PGLVHPKGNE AELYIDIGAY GEPRVKHFEA RSCMRQLEKF VRSVHGFQML YADCYMNREE
FWEMFDGSLY HKLREKLGCQ DAFPEVYDKI CKAARH*

mutated AA sequence

MEPAVSLAVC ALLFLLWVRL KGLEFVLIHQ RWVFVCLFLL PLSLIFDIYY YVRAWVVFKL
SSAPRLHEQR VRDIQKQVRE WKEQGSKTFM CTGRPGWLTV SLRVGKYKKT HKNIMINLMD
ILEVDTKKQI VRVEPLVTMG QVTALLTSIG WTLPVLPELD DLTVGGLIMG TGIESSSHKY
GLFQHICTAY KLVLADGSFV RCTPSENSDL FYAVPWSCGT LGFLVAAEIR IIPAKKYVKL
RFEPVRGLEA ICAKFTHESQ RQENHFVEGL LYSLDEAVIM TGVMTDEAEP SKLNSIGNYY
KPWFFKHVEN YLKTNREGLE YIPLRHYYHR HTRSIFWELQ DIIPFGNNPI FRYLFGWMVP
PKISLLKLTQ GETLRKLYEQ HHVVQDMLVP MKCLQQALHT FQNDIHVYPI WLCPFILPSQ
PGLVHPKGNE AELYIDIGAY GEPRVKHFEA RSCMRQLEKF VRSVHGFQML YADCYMNREE
FWEMFDGSLY HKLREKLGCQ DAFPEVYDKI CKAARH*

speed

0.58 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999999656 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs4369 (probable pathogenic)
known disease mutation at this position (HGMD CM014564)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:55340807C>TN/A show variant in all transcripts IGV

HGNC symbol

DHCR24

Ensembl transcript ID

ENST00000535035

Genbank transcript ID

N/A

UniProt peptide

Q15392

alteration type

single base exchange

alteration region

CDS

DNA changes

c.448G>A
cDNA.531G>A
g.12085G>A

AA changes

E150K Score: 56 explain score(s)

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

150

frameshift

known variant

Reference ID: rs119475041

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

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)	5.123	1
	6.205	1
(flanking)	-0.866	0.462

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	12081	0.93	mu: ACTGCTTACAAGCTG	TGCT\|taca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

150

mutated

all conserved

150

Ptroglodytes

all identical

ENSPTRG00000000779

191

Mmulatta

all identical

ENSMMUG00000021577

191

Fcatus

all identical

ENSFCAG00000003989

114

Mmusculus

all identical

ENSMUSG00000034926

191

Ggallus

all identical

ENSGALG00000010798

191

Trubripes

all identical

ENSTRUG00000016297

194

Drerio

all identical

ENSDARG00000013236

191

Dmelanogaster

no homologue

Celegans

all identical

F52H2.6

187

Xtropicalis

all identical

ENSXETG00000020010

191

protein features

start (aa)	end (aa)	feature	details
53	516	TOPO_DOM	Cytoplasmic (Potential).	lost
58	234	DOMAIN	FAD-binding PCMH-type.	lost
163	175	NP_BIND	FAD (Potential).	might get lost (downstream of altered splice site)
383	384	SITE	Cleavage; by caspase (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

1511 / 1511

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

84 / 84

chromosome

strand

-1

last intron/exon boundary

1358

theoretical NMD boundary in CDS

1224

length of CDS

1428

coding sequence (CDS) position

448

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

531

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

12085

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

55340807

original gDNA sequence snippet

AACACATCTGCACTGCTTACGAGCTGGTCCTGGCTGATGGC

altered gDNA sequence snippet

AACACATCTGCACTGCTTACAAGCTGGTCCTGGCTGATGGC

original cDNA sequence snippet

AACACATCTGCACTGCTTACGAGCTGGTCCTGGCTGATGGC

altered cDNA sequence snippet

AACACATCTGCACTGCTTACAAGCTGGTCCTGGCTGATGGC

wildtype AA sequence

MGAGEQNRQS AHCVQGICGY LEGDEEGEEG EVRSTQVREW KEQGSKTFMC TGRPGWLTVS
LRVGKYKKTH KNIMINLMDI LEVDTKKQIV RVEPLVTMGQ VTALLTSIGW TLPVLPELDD
LTVGGLIMGT GIESSSHKYG LFQHICTAYE LVLADGSFVR CTPSENSDLF YAVPWSCGTL
GFLVAAEIRI IPAKKYVKLR FEPVRGLEAI CAKFTHESQR QENHFVEGLL YSLDEAVIMT
GVMTDEAEPS KLNSIGNYYK PWFFKHVENY LKTNREGLEY IPLRHYYHRH TRSIFWELQD
IIPFGNNPIF RYLFGWMVPP KISLLKLTQG ETLRKLYEQH HVVQDMLVPM KCLQQALHTF
QNDIHVYPIW LCPFILPSQP GLVHPKGNEA ELYIDIGAYG EPRVKHFEAR SCMRQLEKFV
RSVHGFQMLY ADCYMNREEF WEMFDGSLYH KLREKLGCQD AFPEVYDKIC KAARH*

mutated AA sequence

MGAGEQNRQS AHCVQGICGY LEGDEEGEEG EVRSTQVREW KEQGSKTFMC TGRPGWLTVS
LRVGKYKKTH KNIMINLMDI LEVDTKKQIV RVEPLVTMGQ VTALLTSIGW TLPVLPELDD
LTVGGLIMGT GIESSSHKYG LFQHICTAYK LVLADGSFVR CTPSENSDLF YAVPWSCGTL
GFLVAAEIRI IPAKKYVKLR FEPVRGLEAI CAKFTHESQR QENHFVEGLL YSLDEAVIMT
GVMTDEAEPS KLNSIGNYYK PWFFKHVENY LKTNREGLEY IPLRHYYHRH TRSIFWELQD
IIPFGNNPIF RYLFGWMVPP KISLLKLTQG ETLRKLYEQH HVVQDMLVPM KCLQQALHTF
QNDIHVYPIW LCPFILPSQP GLVHPKGNEA ELYIDIGAYG EPRVKHFEAR SCMRQLEKFV
RSVHGFQMLY ADCYMNREEF WEMFDGSLYH KLREKLGCQD AFPEVYDKIC KAARH*

speed

0.62 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems