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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000590230
Querying Taster for transcript #2: ENST00000263621
MT speed 1.75 s - this script 3.787427 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ELANE	disease_causing_automatic	0.999999998990038	simple_aae		affected	0	C71R	single base exchange	rs28931611		show file
ELANE	disease_causing_automatic	0.999999998990038	simple_aae		affected	0	C71R	single base exchange	rs28931611		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998990038 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002593)
known disease mutation at this position (HGMD CM021582)
known disease mutation: rs16746 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:853019T>CN/A show variant in all transcripts IGV

HGNC symbol

ELANE

Ensembl transcript ID

ENST00000590230

Genbank transcript ID

NM_001972

UniProt peptide

P08246

alteration type

single base exchange

alteration region

CDS

DNA changes

c.211T>C
cDNA.352T>C
g.2006T>C

AA changes

C71R Score: 180 explain score(s)

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

frameshift

known variant

Reference ID: rs28931611
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16746 (pathogenic for Neutropenia, severe congenital 1, autosomal dominant) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002593)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002593)
known disease mutation at this position, please check HGMD for details (HGMD ID CM021582)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002593)
known disease mutation at this position, please check HGMD for details (HGMD ID CM021582)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002593)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002593)
known disease mutation at this position, please check HGMD for details (HGMD ID CM021582)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002593)
known disease mutation at this position, please check HGMD for details (HGMD ID CM021582)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.291	1
	2.72	1
(flanking)	3.291	0.984

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	2001	wt: 0.41 / mu: 0.54	wt: CAACTTCGTCATGTCGGCCGCGCACTGCGTGGCGAATGTGT mu: CAACTTCGTCATGTCGGCCGCGCACCGCGTGGCGAATGTGT	ccgc\|GCAC
Donor increased	2008	wt: 0.83 / mu: 0.93	wt: CACTGCGTGGCGAAT mu: CACCGCGTGGCGAAT	CTGC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000023440

Mmulatta

all identical

ENSMMUG00000009674

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020125

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000021647

protein features

start (aa)	end (aa)	feature	details
30	247	DOMAIN	Peptidase S1.	lost
69	72	HELIX		lost
70	70	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
71	71	DISULFID		lost
77	79	HELIX		might get lost (downstream of altered splice site)
81	85	STRAND		might get lost (downstream of altered splice site)
88	88	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
97	107	STRAND		might get lost (downstream of altered splice site)
111	114	TURN		might get lost (downstream of altered splice site)
117	117	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
119	125	STRAND		might get lost (downstream of altered splice site)
124	124	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
130	132	STRAND		might get lost (downstream of altered splice site)
150	158	STRAND		might get lost (downstream of altered splice site)
151	151	DISULFID		might get lost (downstream of altered splice site)
160	162	STRAND		might get lost (downstream of altered splice site)
170	177	STRAND		might get lost (downstream of altered splice site)
173	173	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
181	181	DISULFID		might get lost (downstream of altered splice site)
185	189	STRAND		might get lost (downstream of altered splice site)
187	187	DISULFID		might get lost (downstream of altered splice site)
191	193	STRAND		might get lost (downstream of altered splice site)
198	198	DISULFID		might get lost (downstream of altered splice site)
202	202	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
205	208	STRAND		might get lost (downstream of altered splice site)
208	208	DISULFID		might get lost (downstream of altered splice site)
211	222	STRAND		might get lost (downstream of altered splice site)
223	223	DISULFID		might get lost (downstream of altered splice site)
226	228	STRAND		might get lost (downstream of altered splice site)
230	234	STRAND		might get lost (downstream of altered splice site)
235	238	HELIX		might get lost (downstream of altered splice site)
239	246	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

position of stopcodon in wt / mu cDNA

945 / 945

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

142 / 142

chromosome

strand

last intron/exon boundary

739

theoretical NMD boundary in CDS

547

length of CDS

804

coding sequence (CDS) position

211

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

352

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

2006

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

853019

original gDNA sequence snippet

TCGTCATGTCGGCCGCGCACTGCGTGGCGAATGTGTGAGTA

altered gDNA sequence snippet

TCGTCATGTCGGCCGCGCACCGCGTGGCGAATGTGTGAGTA

original cDNA sequence snippet

TCGTCATGTCGGCCGCGCACTGCGTGGCGAATGTAAACGTC

altered cDNA sequence snippet

TCGTCATGTCGGCCGCGCACCGCGTGGCGAATGTAAACGTC

wildtype AA sequence

MTLGRRLACL FLACVLPALL LGGTALASEI VGGRRARPHA WPFMVSLQLR GGHFCGATLI
APNFVMSAAH CVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*

mutated AA sequence

MTLGRRLACL FLACVLPALL LGGTALASEI VGGRRARPHA WPFMVSLQLR GGHFCGATLI
APNFVMSAAH RVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*

speed

0.98 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: 0.999999998990038 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002593)
known disease mutation at this position (HGMD CM021582)
known disease mutation: rs16746 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:853019T>CN/A show variant in all transcripts IGV

HGNC symbol

ELANE

Ensembl transcript ID

ENST00000263621

Genbank transcript ID

NM_001972

UniProt peptide

P08246

alteration type

single base exchange

alteration region

CDS

DNA changes

c.211T>C
cDNA.249T>C
g.2006T>C

AA changes

C71R Score: 180 explain score(s)

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

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.291	1
	2.72	1
(flanking)	3.291	0.984

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	2001	wt: 0.41 / mu: 0.54	wt: CAACTTCGTCATGTCGGCCGCGCACTGCGTGGCGAATGTGT mu: CAACTTCGTCATGTCGGCCGCGCACCGCGTGGCGAATGTGT	ccgc\|GCAC
Donor increased	2008	wt: 0.83 / mu: 0.93	wt: CACTGCGTGGCGAAT mu: CACCGCGTGGCGAAT	CTGC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000023440

Mmulatta

all identical

ENSMMUG00000009674

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020125

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000021647

protein features

start (aa)	end (aa)	feature	details
30	247	DOMAIN	Peptidase S1.	lost
69	72	HELIX		lost
70	70	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
71	71	DISULFID		lost
77	79	HELIX		might get lost (downstream of altered splice site)
81	85	STRAND		might get lost (downstream of altered splice site)
88	88	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
97	107	STRAND		might get lost (downstream of altered splice site)
111	114	TURN		might get lost (downstream of altered splice site)
117	117	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
119	125	STRAND		might get lost (downstream of altered splice site)
124	124	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
130	132	STRAND		might get lost (downstream of altered splice site)
150	158	STRAND		might get lost (downstream of altered splice site)
151	151	DISULFID		might get lost (downstream of altered splice site)
160	162	STRAND		might get lost (downstream of altered splice site)
170	177	STRAND		might get lost (downstream of altered splice site)
173	173	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
181	181	DISULFID		might get lost (downstream of altered splice site)
185	189	STRAND		might get lost (downstream of altered splice site)
187	187	DISULFID		might get lost (downstream of altered splice site)
191	193	STRAND		might get lost (downstream of altered splice site)
198	198	DISULFID		might get lost (downstream of altered splice site)
202	202	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
205	208	STRAND		might get lost (downstream of altered splice site)
208	208	DISULFID		might get lost (downstream of altered splice site)
211	222	STRAND		might get lost (downstream of altered splice site)
223	223	DISULFID		might get lost (downstream of altered splice site)
226	228	STRAND		might get lost (downstream of altered splice site)
230	234	STRAND		might get lost (downstream of altered splice site)
235	238	HELIX		might get lost (downstream of altered splice site)
239	246	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

position of stopcodon in wt / mu cDNA

842 / 842

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

39 / 39

chromosome

strand

last intron/exon boundary

636

theoretical NMD boundary in CDS

547

length of CDS

804

coding sequence (CDS) position

211

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

249

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

2006

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

853019

original gDNA sequence snippet

TCGTCATGTCGGCCGCGCACTGCGTGGCGAATGTGTGAGTA

altered gDNA sequence snippet

TCGTCATGTCGGCCGCGCACCGCGTGGCGAATGTGTGAGTA

original cDNA sequence snippet

TCGTCATGTCGGCCGCGCACTGCGTGGCGAATGTAAACGTC

altered cDNA sequence snippet

TCGTCATGTCGGCCGCGCACCGCGTGGCGAATGTAAACGTC

wildtype AA sequence

mutated AA sequence

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems