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: ENST00000374580
Querying Taster for transcript #2: ENST00000374574
MT speed 0 s - this script 4.67055 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BMPR2	disease_causing_automatic	0.999999999852356	simple_aae		affected	0	C118W	single base exchange	rs137852743		show file
BMPR2	disease_causing_automatic	0.999999999852356	simple_aae		affected	0	C118W	single base exchange	rs137852743		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999852356 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002237)
known disease mutation: rs8799 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:203332348T>GN/A show variant in all transcripts IGV

HGNC symbol

BMPR2

Ensembl transcript ID

ENST00000374580

Genbank transcript ID

NM_001204

UniProt peptide

Q13873

alteration type

single base exchange

alteration region

CDS

DNA changes

c.354T>G
cDNA.893T>G
g.90690T>G

AA changes

C118W Score: 215 explain score(s)

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

118

frameshift

known variant

Reference ID: rs137852743
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8799 (pathogenic for Pulmonary Hypertension, Primary, 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002237)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002237)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002237)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.257	1
	0.277	0.999
(flanking)	2.672	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 gained	90689	0.74	mu: AACATACCGTTTCTGCTGTTGGAGCACAGATTTATGTAATG	gttg\|GAGC
Donor gained	90691	0.41	mu: GTTGGAGCACAGATT	TGGA\|gcac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

118

mutated

not conserved

118

Ptroglodytes

all identical

ENSPTRG00000029076

118

Mmulatta

all identical

ENSMMUG00000009009

118

Fcatus

no alignment

ENSFCAG00000014094

n/a

Mmusculus

all identical

ENSMUSG00000067336

118

Ggallus

all identical

ENSGALG00000008459

108

Trubripes

no homologue

Drerio

all identical

ENSDARG00000020057

124

Dmelanogaster

all identical

FBgn0024179

129

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022074

119

protein features

start (aa)	end (aa)	feature	details
27	150	TOPO_DOM	Extracellular (Potential).	lost
113	118	STRAND		lost
117	117	DISULFID	By similarity.	might get lost (downstream of altered splice site)
123	125	HELIX		might get lost (downstream of altered splice site)
126	126	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
151	171	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
172	1038	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
202	211	STRAND		might get lost (downstream of altered splice site)
203	504	DOMAIN	Protein kinase.	might get lost (downstream of altered splice site)
209	217	NP_BIND	ATP.	might get lost (downstream of altered splice site)
213	222	STRAND		might get lost (downstream of altered splice site)
225	233	STRAND		might get lost (downstream of altered splice site)
230	230	BINDING	ATP.	might get lost (downstream of altered splice site)
234	236	HELIX		might get lost (downstream of altered splice site)
237	247	HELIX		might get lost (downstream of altered splice site)
260	267	STRAND		might get lost (downstream of altered splice site)
273	279	STRAND		might get lost (downstream of altered splice site)
280	282	NP_BIND	ATP.	might get lost (downstream of altered splice site)
287	293	HELIX		might get lost (downstream of altered splice site)
298	316	HELIX		might get lost (downstream of altered splice site)
322	324	HELIX		might get lost (downstream of altered splice site)
333	333	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
337	338	NP_BIND	ATP.	might get lost (downstream of altered splice site)
338	341	STRAND		might get lost (downstream of altered splice site)
347	349	STRAND		might get lost (downstream of altered splice site)
351	351	BINDING	ATP.	might get lost (downstream of altered splice site)
359	362	STRAND		might get lost (downstream of altered splice site)
375	375	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
379	379	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
380	382	HELIX		might get lost (downstream of altered splice site)
385	388	HELIX		might get lost (downstream of altered splice site)
394	396	HELIX		might get lost (downstream of altered splice site)
397	417	HELIX		might get lost (downstream of altered splice site)
421	423	HELIX		might get lost (downstream of altered splice site)
437	440	HELIX		might get lost (downstream of altered splice site)
446	453	HELIX		might get lost (downstream of altered splice site)
471	483	HELIX		might get lost (downstream of altered splice site)
488	490	HELIX		might get lost (downstream of altered splice site)
494	506	HELIX		might get lost (downstream of altered splice site)
513	513	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
515	515	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
547	550	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)
586	586	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
610	618	COMPBIAS	Poly-Thr.	might get lost (downstream of altered splice site)
680	680	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
681	681	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
757	757	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
828	828	CONFLICT	G -> R (in Ref. 1; CAA88759).	might get lost (downstream of altered splice site)
862	862	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
863	863	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
901	908	COMPBIAS	Poly-Asn.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3117 / 3117

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

1039 / 1039

position of stopcodon in wt / mu cDNA

3656 / 3656

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

540 / 540

chromosome

strand

last intron/exon boundary

3406

theoretical NMD boundary in CDS

2816

length of CDS

3117

coding sequence (CDS) position

354

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

893

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

90690

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

203332348

original gDNA sequence snippet

ACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGT

altered gDNA sequence snippet

ACATACCGTTTCTGCTGTTGGAGCACAGATTTATGTAATGT

original cDNA sequence snippet

ACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGT

altered cDNA sequence snippet

ACATACCGTTTCTGCTGTTGGAGCACAGATTTATGTAATGT

wildtype AA sequence

MTSSLQRPWR VPWLPWTILL VSTAAASQNQ ERLCAFKDPY QQDLGIGESR ISHENGTILC
SKGSTCYGLW EKSKGDINLV KQGCWSHIGD PQECHYEECV VTTTPPSIQN GTYRFCCCST
DLCNVNFTEN FPPPDTTPLS PPHSFNRDET IIIALASVSV LAVLIVALCF GYRMLTGDRK
QGLHSMNMME AAASEPSLDL DNLKLLELIG RGRYGAVYKG SLDERPVAVK VFSFANRQNF
INEKNIYRVP LMEHDNIARF IVGDERVTAD GRMEYLLVME YYPNGSLCKY LSLHTSDWVS
SCRLAHSVTR GLAYLHTELP RGDHYKPAIS HRDLNSRNVL VKNDGTCVIS DFGLSMRLTG
NRLVRPGEED NAAISEVGTI RYMAPEVLEG AVNLRDCESA LKQVDMYALG LIYWEIFMRC
TDLFPGESVP EYQMAFQTEV GNHPTFEDMQ VLVSREKQRP KFPEAWKENS LAVRSLKETI
EDCWDQDAEA RLTAQCAEER MAELMMIWER NKSVSPTVNP MSTAMQNERN LSHNRRVPKI
GPYPDYSSSS YIEDSIHHTD SIVKNISSEH SMSSTPLTIG EKNRNSINYE RQQAQARIPS
PETSVTSLST NTTTTNTTGL TPSTGMTTIS EMPYPDETNL HTTNVAQSIG PTPVCLQLTE
EDLETNKLDP KEVDKNLKES SDENLMEHSL KQFSGPDPLS STSSSLLYPL IKLAVEATGQ
QDFTQTANGQ ACLIPDVLPT QIYPLPKQQN LPKRPTSLPL NTKNSTKEPR LKFGSKHKSN
LKQVETGVAK MNTINAAEPH VVTVTMNGVA GRNHSVNSHA ATTQYANGTV LSGQTTNIVT
HRAQEMLQNQ FIGEDTRLNI NSSPDEHEPL LRREQQAGHD EGVLDRLVDR RERPLEGGRT
NSNNNNSNPC SEQDVLAQGV PSTAADPGPS KPRRAQRPNS LDLSATNVLD GSSIQIGEST
QDGKSGSGEK IKKRVKTPYS LKRWRPSTWV ISTESLDCEV NNNGSNRAVH SKSSTAVYLA
EGGTATTMVS KDIGMNCL*

mutated AA sequence

MTSSLQRPWR VPWLPWTILL VSTAAASQNQ ERLCAFKDPY QQDLGIGESR ISHENGTILC
SKGSTCYGLW EKSKGDINLV KQGCWSHIGD PQECHYEECV VTTTPPSIQN GTYRFCCWST
DLCNVNFTEN FPPPDTTPLS PPHSFNRDET IIIALASVSV LAVLIVALCF GYRMLTGDRK
QGLHSMNMME AAASEPSLDL DNLKLLELIG RGRYGAVYKG SLDERPVAVK VFSFANRQNF
INEKNIYRVP LMEHDNIARF IVGDERVTAD GRMEYLLVME YYPNGSLCKY LSLHTSDWVS
SCRLAHSVTR GLAYLHTELP RGDHYKPAIS HRDLNSRNVL VKNDGTCVIS DFGLSMRLTG
NRLVRPGEED NAAISEVGTI RYMAPEVLEG AVNLRDCESA LKQVDMYALG LIYWEIFMRC
TDLFPGESVP EYQMAFQTEV GNHPTFEDMQ VLVSREKQRP KFPEAWKENS LAVRSLKETI
EDCWDQDAEA RLTAQCAEER MAELMMIWER NKSVSPTVNP MSTAMQNERN LSHNRRVPKI
GPYPDYSSSS YIEDSIHHTD SIVKNISSEH SMSSTPLTIG EKNRNSINYE RQQAQARIPS
PETSVTSLST NTTTTNTTGL TPSTGMTTIS EMPYPDETNL HTTNVAQSIG PTPVCLQLTE
EDLETNKLDP KEVDKNLKES SDENLMEHSL KQFSGPDPLS STSSSLLYPL IKLAVEATGQ
QDFTQTANGQ ACLIPDVLPT QIYPLPKQQN LPKRPTSLPL NTKNSTKEPR LKFGSKHKSN
LKQVETGVAK MNTINAAEPH VVTVTMNGVA GRNHSVNSHA ATTQYANGTV LSGQTTNIVT
HRAQEMLQNQ FIGEDTRLNI NSSPDEHEPL LRREQQAGHD EGVLDRLVDR RERPLEGGRT
NSNNNNSNPC SEQDVLAQGV PSTAADPGPS KPRRAQRPNS LDLSATNVLD GSSIQIGEST
QDGKSGSGEK IKKRVKTPYS LKRWRPSTWV ISTESLDCEV NNNGSNRAVH SKSSTAVYLA
EGGTATTMVS KDIGMNCL*

speed

1.33 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: 0.999999999852356 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002237)
known disease mutation: rs8799 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:203332348T>GN/A show variant in all transcripts IGV

HGNC symbol

BMPR2

Ensembl transcript ID

ENST00000374574

Genbank transcript ID

N/A

UniProt peptide

Q13873

alteration type

single base exchange

alteration region

CDS

DNA changes

c.354T>G
cDNA.395T>G
g.90690T>G

AA changes

C118W Score: 215 explain score(s)

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

118

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.257	1
	0.277	0.999
(flanking)	2.672	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 gained	90689	0.74	mu: AACATACCGTTTCTGCTGTTGGAGCACAGATTTATGTAATG	gttg\|GAGC
Donor gained	90691	0.41	mu: GTTGGAGCACAGATT	TGGA\|gcac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

118

mutated

not conserved

118

Ptroglodytes

all identical

ENSPTRG00000029076

118

Mmulatta

all identical

ENSMMUG00000009009

118

Fcatus

no alignment

ENSFCAG00000014094

n/a

Mmusculus

all identical

ENSMUSG00000067336

118

Ggallus

all identical

ENSGALG00000008459

108

Trubripes

no homologue

Drerio

all identical

ENSDARG00000020057

124

Dmelanogaster

all identical

FBgn0024179

129

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022074

119

protein features

start (aa)	end (aa)	feature	details
27	150	TOPO_DOM	Extracellular (Potential).	lost
113	118	STRAND		lost
117	117	DISULFID	By similarity.	might get lost (downstream of altered splice site)
123	125	HELIX		might get lost (downstream of altered splice site)
126	126	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
151	171	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
172	1038	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
202	211	STRAND		might get lost (downstream of altered splice site)
203	504	DOMAIN	Protein kinase.	might get lost (downstream of altered splice site)
209	217	NP_BIND	ATP.	might get lost (downstream of altered splice site)
213	222	STRAND		might get lost (downstream of altered splice site)
225	233	STRAND		might get lost (downstream of altered splice site)
230	230	BINDING	ATP.	might get lost (downstream of altered splice site)
234	236	HELIX		might get lost (downstream of altered splice site)
237	247	HELIX		might get lost (downstream of altered splice site)
260	267	STRAND		might get lost (downstream of altered splice site)
273	279	STRAND		might get lost (downstream of altered splice site)
280	282	NP_BIND	ATP.	might get lost (downstream of altered splice site)
287	293	HELIX		might get lost (downstream of altered splice site)
298	316	HELIX		might get lost (downstream of altered splice site)
322	324	HELIX		might get lost (downstream of altered splice site)
333	333	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
337	338	NP_BIND	ATP.	might get lost (downstream of altered splice site)
338	341	STRAND		might get lost (downstream of altered splice site)
347	349	STRAND		might get lost (downstream of altered splice site)
351	351	BINDING	ATP.	might get lost (downstream of altered splice site)
359	362	STRAND		might get lost (downstream of altered splice site)
375	375	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
379	379	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
380	382	HELIX		might get lost (downstream of altered splice site)
385	388	HELIX		might get lost (downstream of altered splice site)
394	396	HELIX		might get lost (downstream of altered splice site)
397	417	HELIX		might get lost (downstream of altered splice site)
421	423	HELIX		might get lost (downstream of altered splice site)
437	440	HELIX		might get lost (downstream of altered splice site)
446	453	HELIX		might get lost (downstream of altered splice site)
471	483	HELIX		might get lost (downstream of altered splice site)
488	490	HELIX		might get lost (downstream of altered splice site)
494	506	HELIX		might get lost (downstream of altered splice site)
513	513	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
515	515	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
547	550	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)
586	586	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
610	618	COMPBIAS	Poly-Thr.	might get lost (downstream of altered splice site)
680	680	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
681	681	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
757	757	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
828	828	CONFLICT	G -> R (in Ref. 1; CAA88759).	might get lost (downstream of altered splice site)
862	862	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
863	863	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
901	908	COMPBIAS	Poly-Asn.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1593 / 1593

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

531 / 531

position of stopcodon in wt / mu cDNA

1634 / 1634

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

42 / 42

chromosome

strand

last intron/exon boundary

1628

theoretical NMD boundary in CDS

1536

length of CDS

1593

coding sequence (CDS) position

354

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

395

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

90690

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

203332348

original gDNA sequence snippet

ACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGT

altered gDNA sequence snippet

ACATACCGTTTCTGCTGTTGGAGCACAGATTTATGTAATGT

original cDNA sequence snippet

ACATACCGTTTCTGCTGTTGTAGCACAGATTTATGTAATGT

altered cDNA sequence snippet

ACATACCGTTTCTGCTGTTGGAGCACAGATTTATGTAATGT

wildtype AA sequence

mutated AA sequence

speed

1.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems