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: ENST00000284268
Querying Taster for transcript #2: ENST00000535119
MT speed 0.18 s - this script 2.214641 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ANKH	disease_causing_automatic	0.999999998075194	simple_aae		affected	0	G389R	single base exchange	rs28939080		show file
ANKH	disease_causing_automatic	0.999999998906802	simple_aae		affected	0	G191R	single base exchange	rs28939080		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998075194 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM011274)
known disease mutation: rs5192 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:14713753C>TN/A show variant in all transcripts IGV

HGNC symbol

ANKH

Ensembl transcript ID

ENST00000284268

Genbank transcript ID

NM_054027

UniProt peptide

Q9HCJ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1165G>A
cDNA.1496G>A
g.158135G>A

AA changes

G389R Score: 125 explain score(s)

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

389

frameshift

known variant

Reference ID: rs28939080
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5192 (pathogenic for Familial calcium pyrophosphate deposition|Craniometaphyseal dysplasia, autosomal dominant) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011274)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011274)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011274)

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.125	0.998
	5.839	0.998
(flanking)	-1.935	0.018

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	158135	wt: 0.44 / mu: 0.50	wt: CAGTGAGGGCGCATCTCACCGGGTGGCTGATGACACTGAAG mu: CAGTGAGGGCGCATCTCACCAGGTGGCTGATGACACTGAAG	accg\|GGTG
Donor gained	158131	0.76	mu: CATCTCACCAGGTGG	TCTC\|acca

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

all identical

ENSPTRG00000016739

389

Mmulatta

all identical

ENSMMUG00000021942

389

Fcatus

all identical

ENSFCAG00000012251

357

Mmusculus

all identical

ENSMUSG00000022265

389

Ggallus

all identical

ENSGALG00000012964

389

Trubripes

not conserved

ENSTRUG00000008542

388

Drerio

all identical

ENSDARG00000014969

389

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001724

362

protein features

start (aa)	end (aa)	feature	details
372	403	TOPO_DOM	Cytoplasmic (Potential).	lost
404	426	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
427	429	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
430	452	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
453	492	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1479 / 1479

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

493 / 493

position of stopcodon in wt / mu cDNA

1810 / 1810

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

332 / 332

chromosome

strand

-1

last intron/exon boundary

1697

theoretical NMD boundary in CDS

1315

length of CDS

1479

coding sequence (CDS) position

1165

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

1496

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

158135

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

14713753

original gDNA sequence snippet

CAGTGAGGGCGCATCTCACCGGGTGGCTGATGACACTGAAG

altered gDNA sequence snippet

CAGTGAGGGCGCATCTCACCAGGTGGCTGATGACACTGAAG

original cDNA sequence snippet

CAGTGAGGGCGCATCTCACCGGGTGGCTGATGACACTGAAG

altered cDNA sequence snippet

CAGTGAGGGCGCATCTCACCAGGTGGCTGATGACACTGAAG

wildtype AA sequence

MVKFPALTHY WPLIRFLVPL GITNIAIDFG EQALNRGIAA VKEDAVEMLA SYGLAYSLMK
FFTGPMSDFK NVGLVFVNSK RDRTKAVLCM VVAGAIAAVF HTLIAYSDLG YYIINKLHHV
DESVGSKTRR AFLYLAAFPF MDAMAWTHAG ILLKHKYSFL VGCASISDVI AQVVFVAILL
HSHLECREPL LIPILSLYMG ALVRCTTLCL GYYKNIHDII PDRSGPELGG DATIRKMLSF
WWPLALILAT QRISRPIVNL FVSRDLGGSS AATEAVAILT ATYPVGHMPY GWLTEIRAVY
PAFDKNNPSN KLVSTSNTVT AAHIKKFTFV CMALSLTLCF VMFWTPNVSE KILIDIIGVD
FAFAELCVVP LRIFSFFPVP VTVRAHLTGW LMTLKKTFVL APSSVLRIIV LIASLVVLPY
LGVHGATLGV GSLLAGFVGE STMVAIAACY VYRKQKKKME NESATEGEDS AMTDMPPTEE
VTDIVEMREE NE*

mutated AA sequence

MVKFPALTHY WPLIRFLVPL GITNIAIDFG EQALNRGIAA VKEDAVEMLA SYGLAYSLMK
FFTGPMSDFK NVGLVFVNSK RDRTKAVLCM VVAGAIAAVF HTLIAYSDLG YYIINKLHHV
DESVGSKTRR AFLYLAAFPF MDAMAWTHAG ILLKHKYSFL VGCASISDVI AQVVFVAILL
HSHLECREPL LIPILSLYMG ALVRCTTLCL GYYKNIHDII PDRSGPELGG DATIRKMLSF
WWPLALILAT QRISRPIVNL FVSRDLGGSS AATEAVAILT ATYPVGHMPY GWLTEIRAVY
PAFDKNNPSN KLVSTSNTVT AAHIKKFTFV CMALSLTLCF VMFWTPNVSE KILIDIIGVD
FAFAELCVVP LRIFSFFPVP VTVRAHLTRW LMTLKKTFVL APSSVLRIIV LIASLVVLPY
LGVHGATLGV GSLLAGFVGE STMVAIAACY VYRKQKKKME NESATEGEDS AMTDMPPTEE
VTDIVEMREE NE*

speed

0.08 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: 0.999999998906802 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM011274)
known disease mutation: rs5192 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:14713753C>TN/A show variant in all transcripts IGV

HGNC symbol

ANKH

Ensembl transcript ID

ENST00000535119

Genbank transcript ID

N/A

UniProt peptide

Q9HCJ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.571G>A
cDNA.621G>A
g.158135G>A

AA changes

G191R Score: 125 explain score(s)

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

191

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.125	0.998
	5.839	0.998
(flanking)	-1.935	0.018

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	158135	wt: 0.44 / mu: 0.50	wt: CAGTGAGGGCGCATCTCACCGGGTGGCTGATGACACTGAAG mu: CAGTGAGGGCGCATCTCACCAGGTGGCTGATGACACTGAAG	accg\|GGTG
Donor gained	158131	0.76	mu: CATCTCACCAGGTGG	TCTC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

191

mutated

not conserved

191

Ptroglodytes

all identical

ENSPTRG00000016739

389

Mmulatta

all identical

ENSMMUG00000021942

389

Fcatus

all identical

ENSFCAG00000012251

357

Mmusculus

all identical

ENSMUSG00000022265

389

Ggallus

all identical

ENSGALG00000012964

389

Trubripes

not conserved

ENSTRUG00000008542

388

Drerio

all identical

ENSDARG00000014969

389

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001724

362

protein features

start (aa)	end (aa)	feature	details
190	210	TRANSMEM	Helical; (Potential).	lost
211	326	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
327	347	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
348	350	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
351	371	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
372	403	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
404	426	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
427	429	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
430	452	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
453	492	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

885 / 885

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

295 / 295

position of stopcodon in wt / mu cDNA

935 / 935

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

51 / 51

chromosome

strand

-1

last intron/exon boundary

1102

theoretical NMD boundary in CDS

1001

length of CDS

885

coding sequence (CDS) position

571

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

621

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

158135

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

14713753

original gDNA sequence snippet

CAGTGAGGGCGCATCTCACCGGGTGGCTGATGACACTGAAG

altered gDNA sequence snippet

CAGTGAGGGCGCATCTCACCAGGTGGCTGATGACACTGAAG

original cDNA sequence snippet

CAGTGAGGGCGCATCTCACCGGGTGGCTGATGACACTGAAG

altered cDNA sequence snippet

CAGTGAGGGCGCATCTCACCAGGTGGCTGATGACACTGAAG

wildtype AA sequence

MGALVRCTTL CLGYYKNIHD IIPDRSGPEL GGDATIRKML SFWWPLALIL ATQRISRPIV
NLFVSRDLGG SSAATEAVAI LTATYPVGHM PYGWLTEIRA VYPAFDKNNP SNKLVSTSNT
VTAAHIKKFT FVCMALSLTL CFVMFWTPNV SEKILIDIIG VDFAFAELCV VPLRIFSFFP
VPVTVRAHLT GWLMTLKKTF VLAPSSVLRI IVLIASLVVL PYLGVHGATL GVGSLLAGFV
GESTMVAIAA CYVYRKQKKK MENESATEGE DSAMTDMPPT EEVTDIVEMR EENE*

mutated AA sequence

MGALVRCTTL CLGYYKNIHD IIPDRSGPEL GGDATIRKML SFWWPLALIL ATQRISRPIV
NLFVSRDLGG SSAATEAVAI LTATYPVGHM PYGWLTEIRA VYPAFDKNNP SNKLVSTSNT
VTAAHIKKFT FVCMALSLTL CFVMFWTPNV SEKILIDIIG VDFAFAELCV VPLRIFSFFP
VPVTVRAHLT RWLMTLKKTF VLAPSSVLRI IVLIASLVVL PYLGVHGATL GVGSLLAGFV
GESTMVAIAA CYVYRKQKKK MENESATEGE DSAMTDMPPT EEVTDIVEMR EENE*

speed

0.10 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems