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: ENST00000260645
Querying Taster for transcript #2: ENST00000405322
Querying Taster for transcript #3: ENST00000543989
MT speed 0 s - this script 3.020818 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ABCG5	disease_causing_automatic	0.999999950784102	simple_aae			0	R218H	single base exchange	rs119480069		show file
ABCG5	disease_causing_automatic	0.99999997204771	simple_aae			0	R389H	single base exchange	rs119480069		show file
ABCG5	disease_causing_automatic	1	without_aae			0		single base exchange	rs119480069		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999950784102 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010002)
known disease mutation: rs4980 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:44051210C>TN/A show variant in all transcripts IGV

HGNC symbol

ABCG5

Ensembl transcript ID

ENST00000405322

Genbank transcript ID

N/A

UniProt peptide

Q9H222

alteration type

single base exchange

alteration region

CDS

DNA changes

c.653G>A
cDNA.1550G>A
g.14795G>A

AA changes

R218H Score: 29 explain score(s)

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

218

frameshift

known variant

Reference ID: rs119480069

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	18	18

known disease mutation: rs4980 (pathogenic for Sitosterolemia|Sitosterolemia 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010002)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.047	0.988
	5.775	1
(flanking)	5.775	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 marginally increased	14806	wt: 0.8011 / mu: 0.8141 (marginal change - not scored)	wt: TGATTACGCGTCTCCTTCAGAATCTGATCATGGGTTTGTTC mu: TGATTACGCATCTCCTTCAGAATCTGATCATGGGTTTGTTC	caga\|ATCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

218

mutated

not conserved

218

Ptroglodytes

not conserved

ENSPTRG00000011878

248

Mmulatta

all identical

ENSMMUG00000008080

389

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040505

390

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009436

387

Drerio

all identical

ENSDARG00000063078

393

Dmelanogaster

all conserved

FBgn0051121

622

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000009290

391

protein features

start (aa)	end (aa)	feature	details
1	383	TOPO_DOM	Cytoplasmic (Potential).	lost
52	293	DOMAIN	ABC transporter.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1443 / 1443

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

481 / 481

position of stopcodon in wt / mu cDNA

2340 / 2340

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

898 / 898

chromosome

strand

-1

last intron/exon boundary

2147

theoretical NMD boundary in CDS

1199

length of CDS

1443

coding sequence (CDS) position

653

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

1550

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

14795

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

44051210

original gDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered gDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

original cDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered cDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

wildtype AA sequence

MCILGSSGSG KTTLLDAMSG RLGRAGTFLG EVYVNGRALR REQFQDCFSY VLQSDTLLSS
LTVRETLHYT ALLAIRRGNP GSFQKKVEAV MAELSLSHVA DRLIGNYSLG GISTGERRRV
SIAAQLLQDP MDLTSVDTQS KEREIETSKR VQMIESAYKK SAICHKTLKN IERMKHLKTL
PMVPFKTKDS PGVFSKLGVL LRRVTRNLVR NKLAVITRLL QNLIMGLFLL FFVLRVRSNV
LKGAIQDRVG LLYQFVGATP YTGMLNAVNL FPVLRAVSDQ ESQDGLYQKW QMMLAYALHV
LPFSVVATMI FSSVCYWTLG LHPEVARFGY FSAALLAPHL IGEFLTLVLL GIVQNPNIVN
SVVALLSIAG VLVGSGFLRN IQEMPIPFKI ISYFTFQKYC SEILVVNEFY GLNFTCGSSN
VSVTTNPMCA FTQGIQFIEK TCPGATSRFT MNFLILYSFI PALVILGIVV FKIRDHLISR
*

mutated AA sequence

MCILGSSGSG KTTLLDAMSG RLGRAGTFLG EVYVNGRALR REQFQDCFSY VLQSDTLLSS
LTVRETLHYT ALLAIRRGNP GSFQKKVEAV MAELSLSHVA DRLIGNYSLG GISTGERRRV
SIAAQLLQDP MDLTSVDTQS KEREIETSKR VQMIESAYKK SAICHKTLKN IERMKHLKTL
PMVPFKTKDS PGVFSKLGVL LRRVTRNLVR NKLAVITHLL QNLIMGLFLL FFVLRVRSNV
LKGAIQDRVG LLYQFVGATP YTGMLNAVNL FPVLRAVSDQ ESQDGLYQKW QMMLAYALHV
LPFSVVATMI FSSVCYWTLG LHPEVARFGY FSAALLAPHL IGEFLTLVLL GIVQNPNIVN
SVVALLSIAG VLVGSGFLRN IQEMPIPFKI ISYFTFQKYC SEILVVNEFY GLNFTCGSSN
VSVTTNPMCA FTQGIQFIEK TCPGATSRFT MNFLILYSFI PALVILGIVV FKIRDHLISR
*

speed

0.38 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: 0.99999997204771 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010002)
known disease mutation: rs4980 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:44051210C>TN/A show variant in all transcripts IGV

HGNC symbol

ABCG5

Ensembl transcript ID

ENST00000260645

Genbank transcript ID

NM_022436

UniProt peptide

Q9H222

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1166G>A
cDNA.1306G>A
g.14795G>A

AA changes

R389H Score: 29 explain score(s)

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

389

frameshift

known variant

Reference ID: rs119480069

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	18	18

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.047	0.988
	5.775	1
(flanking)	5.775	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 marginally increased	14806	wt: 0.8011 / mu: 0.8141 (marginal change - not scored)	wt: TGATTACGCGTCTCCTTCAGAATCTGATCATGGGTTTGTTC mu: TGATTACGCATCTCCTTCAGAATCTGATCATGGGTTTGTTC	caga\|ATCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

389

mutated

not conserved

389

Ptroglodytes

not conserved

ENSPTRG00000011878

389

Mmulatta

all identical

ENSMMUG00000008080

389

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040505

390

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009436

387

Drerio

all identical

ENSDARG00000063078

393

Dmelanogaster

all conserved

FBgn0051121

622

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000009290

391

protein features

start (aa)	end (aa)	feature	details
384	404	TRANSMEM	Helical; Name=1; (Potential).	lost
388	645	DOMAIN	ABC transmembrane type-2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1956 / 1956

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

652 / 652

position of stopcodon in wt / mu cDNA

2096 / 2096

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

141 / 141

chromosome

strand

-1

last intron/exon boundary

1903

theoretical NMD boundary in CDS

1712

length of CDS

1956

coding sequence (CDS) position

1166

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

1306

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

14795

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

44051210

original gDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered gDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

original cDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered cDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

wildtype AA sequence

MGDLSSLTPG GSMGLQVNRG SQSSLEGAPA TAPEPHSLGI LHASYSVSHR VRPWWDITSC
RQQWTRQILK DVSLYVESGQ IMCILGSSGS GKTTLLDAMS GRLGRAGTFL GEVYVNGRAL
RREQFQDCFS YVLQSDTLLS SLTVRETLHY TALLAIRRGN PGSFQKKVEA VMAELSLSHV
ADRLIGNYSL GGISTGERRR VSIAAQLLQD PKVMLFDEPT TGLDCMTANQ IVVLLVELAR
RNRIVVLTIH QPRSELFQLF DKIAILSFGE LIFCGTPAEM LDFFNDCGYP CPEHSNPFDF
YMDLTSVDTQ SKEREIETSK RVQMIESAYK KSAICHKTLK NIERMKHLKT LPMVPFKTKD
SPGVFSKLGV LLRRVTRNLV RNKLAVITRL LQNLIMGLFL LFFVLRVRSN VLKGAIQDRV
GLLYQFVGAT PYTGMLNAVN LFPVLRAVSD QESQDGLYQK WQMMLAYALH VLPFSVVATM
IFSSVCYWTL GLHPEVARFG YFSAALLAPH LIGEFLTLVL LGIVQNPNIV NSVVALLSIA
GVLVGSGFLR NIQEMPIPFK IISYFTFQKY CSEILVVNEF YGLNFTCGSS NVSVTTNPMC
AFTQGIQFIE KTCPGATSRF TMNFLILYSF IPALVILGIV VFKIRDHLIS R*

mutated AA sequence

MGDLSSLTPG GSMGLQVNRG SQSSLEGAPA TAPEPHSLGI LHASYSVSHR VRPWWDITSC
RQQWTRQILK DVSLYVESGQ IMCILGSSGS GKTTLLDAMS GRLGRAGTFL GEVYVNGRAL
RREQFQDCFS YVLQSDTLLS SLTVRETLHY TALLAIRRGN PGSFQKKVEA VMAELSLSHV
ADRLIGNYSL GGISTGERRR VSIAAQLLQD PKVMLFDEPT TGLDCMTANQ IVVLLVELAR
RNRIVVLTIH QPRSELFQLF DKIAILSFGE LIFCGTPAEM LDFFNDCGYP CPEHSNPFDF
YMDLTSVDTQ SKEREIETSK RVQMIESAYK KSAICHKTLK NIERMKHLKT LPMVPFKTKD
SPGVFSKLGV LLRRVTRNLV RNKLAVITHL LQNLIMGLFL LFFVLRVRSN VLKGAIQDRV
GLLYQFVGAT PYTGMLNAVN LFPVLRAVSD QESQDGLYQK WQMMLAYALH VLPFSVVATM
IFSSVCYWTL GLHPEVARFG YFSAALLAPH LIGEFLTLVL LGIVQNPNIV NSVVALLSIA
GVLVGSGFLR NIQEMPIPFK IISYFTFQKY CSEILVVNEF YGLNFTCGSS NVSVTTNPMC
AFTQGIQFIE KTCPGATSRF TMNFLILYSF IPALVILGIV VFKIRDHLIS R*

speed

0.39 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM010002)
known disease mutation: rs4980 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:44051210C>TN/A show variant in all transcripts IGV

HGNC symbol

ABCG5

Ensembl transcript ID

ENST00000543989

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.1687G>A
g.14795G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs119480069

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	18	18

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.047	0.988
	5.775	1
(flanking)	5.775	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 marginally increased	14806	wt: 0.8011 / mu: 0.8141 (marginal change - not scored)	wt: TGATTACGCGTCTCCTTCAGAATCTGATCATGGGTTTGTTC mu: TGATTACGCATCTCCTTCAGAATCTGATCATGGGTTTGTTC	caga\|ATCT

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

1707 / 1707

chromosome

strand

-1

last intron/exon boundary

2284

theoretical NMD boundary in CDS

527

length of CDS

771

coding sequence (CDS) position

N/A

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

1687

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

14795

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

44051210

original gDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered gDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

original cDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered cDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

wildtype AA sequence

MGLFLLFFVL RVRSNVLKGA IQDRVGLLYQ FVGATPYTGM LNAVNLFPVL RAVSDQESQD
GLYQKWQMML AYALHVLPFS VVATMIFSSV CYWTLGLHPE VARFGYFSAA LLAPHLIGEF
LTLVLLGIVQ NPNIVNSVVA LLSIAGVLVG SGFLRNIQEM PIPFKIISYF TFQKYCSEIL
VVNEFYGLNF TCGSSNVSVT TNPMCAFTQG IQFIEKTCPG ATSRFTMNFL ILYSFIPALV
ILGIVVFKIR DHLISR*

mutated AA sequence

N/A

speed

0.64 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