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 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 3.926768 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DHCR24	disease_causing_automatic	0.999999999926684	simple_aae		affected	0	Y471S	single base exchange	rs28939092		show file
DHCR24	disease_causing_automatic	0.999999999926684	simple_aae		affected	0	Y430S	single base exchange	rs28939092		show file
DHCR24	disease_causing_automatic	0.999999999926684	simple_aae		affected	0	Y255S	single base exchange	rs28939092		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999926684 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014567)
known disease mutation: rs4367 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:55318045T>GN/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.1412A>C
cDNA.1511A>C
g.34847A>C

AA changes

Y471S Score: 144 explain score(s)

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

471

frameshift

known variant

Reference ID: rs28939092
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4367 (pathogenic for Desmosterolosis) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.422	0.923
	5.007	1
(flanking)	5.007	1

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 increased	34838	wt: 0.71 / mu: 0.82	wt: TCTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCT mu: TCTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCT	tcca\|GATG
Acc increased	34839	wt: 0.70 / mu: 0.77	wt: CTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCTA mu: CTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCTA	ccag\|ATGC
Acc marginally increased	34848	wt: 0.6335 / mu: 0.6721 (marginal change - not scored)	wt: TGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACCG mu: TGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCG	gtat\|GCCG
Acc gained	34852	0.43	mu: GCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCGGGAG	gccg\|ACTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

471

mutated

not conserved

471

Ptroglodytes

all identical

ENSPTRG00000000779

471

Mmulatta

all identical

ENSMMUG00000021577

471

Fcatus

all identical

ENSFCAG00000003989

394

Mmusculus

all identical

ENSMUSG00000034926

471

Ggallus

all identical

ENSGALG00000010798

471

Trubripes

all identical

ENSTRUG00000016297

474

Drerio

all identical

ENSDARG00000013236

471

Dmelanogaster

no homologue

Celegans

all identical

F52H2.6

480

Xtropicalis

all identical

ENSXETG00000020010

471

protein features

start (aa)	end (aa)	feature	details
53	516	TOPO_DOM	Cytoplasmic (Potential).	lost

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

1412

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

1511

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

34847

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

55318045

original gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

original cDNA sequence snippet

GCATGGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered cDNA sequence snippet

GCATGGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

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 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 SADCYMNREE
FWEMFDGSLY HKLREKLGCQ DAFPEVYDKI CKAARH*

speed

1.26 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: 0.999999999926684 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014567)
known disease mutation: rs4367 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:55318045T>GN/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.1289A>C
cDNA.1372A>C
g.34847A>C

AA changes

Y430S Score: 144 explain score(s)

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

430

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.422	0.923
	5.007	1
(flanking)	5.007	1

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 increased	34838	wt: 0.71 / mu: 0.82	wt: TCTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCT mu: TCTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCT	tcca\|GATG
Acc increased	34839	wt: 0.70 / mu: 0.77	wt: CTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCTA mu: CTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCTA	ccag\|ATGC
Acc marginally increased	34848	wt: 0.6335 / mu: 0.6721 (marginal change - not scored)	wt: TGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACCG mu: TGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCG	gtat\|GCCG
Acc gained	34852	0.43	mu: GCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCGGGAG	gccg\|ACTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

430

mutated

not conserved

430

Ptroglodytes

all identical

ENSPTRG00000000779

471

Mmulatta

all identical

ENSMMUG00000021577

471

Fcatus

all identical

ENSFCAG00000003989

394

Mmusculus

all identical

ENSMUSG00000034926

471

Ggallus

all identical

ENSGALG00000010798

471

Trubripes

all identical

ENSTRUG00000016297

474

Drerio

all identical

ENSDARG00000013236

471

Dmelanogaster

no homologue

Celegans

all identical

F52H2.6

480

Xtropicalis

all identical

ENSXETG00000020010

471

protein features

start (aa)	end (aa)	feature	details
53	516	TOPO_DOM	Cytoplasmic (Potential).	lost

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

1289

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

1372

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

34847

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

55318045

original gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

original cDNA sequence snippet

GCATGGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered cDNA sequence snippet

GCATGGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

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 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
RSVHGFQMLS ADCYMNREEF WEMFDGSLYH KLREKLGCQD AFPEVYDKIC KAARH*

speed

1.40 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999926684 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014567)
known disease mutation: rs4367 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:55318045T>GN/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.764A>C
cDNA.829A>C
g.34847A>C

AA changes

Y255S Score: 144 explain score(s)

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

255

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.422	0.923
	5.007	1
(flanking)	5.007	1

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 increased	34838	wt: 0.71 / mu: 0.82	wt: TCTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCT mu: TCTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCT	tcca\|GATG
Acc increased	34839	wt: 0.70 / mu: 0.77	wt: CTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCTA mu: CTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCTA	ccag\|ATGC
Acc marginally increased	34848	wt: 0.6335 / mu: 0.6721 (marginal change - not scored)	wt: TGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACCG mu: TGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCG	gtat\|GCCG
Acc gained	34852	0.43	mu: GCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCGGGAG	gccg\|ACTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

255

mutated

not conserved

255

Ptroglodytes

all identical

ENSPTRG00000000779

471

Mmulatta

all identical

ENSMMUG00000021577

471

Fcatus

all identical

ENSFCAG00000003989

394

Mmusculus

all identical

ENSMUSG00000034926

471

Ggallus

all identical

ENSGALG00000010798

471

Trubripes

all identical

ENSTRUG00000016297

474

Drerio

all identical

ENSDARG00000013236

471

Dmelanogaster

no homologue

Celegans

all identical

F52H2.6

480

Xtropicalis

all identical

ENSXETG00000020010

471

protein features

start (aa)	end (aa)	feature	details
53	516	TOPO_DOM	Cytoplasmic (Potential).	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

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

764

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

829

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

34847

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

55318045

original gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

original cDNA sequence snippet

GCATGGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered cDNA sequence snippet

GCATGGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

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

speed

0.50 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