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: ENST00000372037
Querying Taster for transcript #2: ENST00000224764
MT speed 0 s - this script 3.383558 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BMPR1A	disease_causing_automatic	0.999999999983472	simple_aae		affected	0	C376Y	single base exchange	rs199476088		show file
BMPR1A	disease_causing_automatic	0.999999999983472	simple_aae		affected	0	C376Y	single base exchange	rs199476088		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999983472 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014519)
known disease mutation: rs8235 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:88679187G>AN/A show variant in all transcripts IGV

HGNC symbol

BMPR1A

Ensembl transcript ID

ENST00000372037

Genbank transcript ID

N/A

UniProt peptide

P36894

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1127G>A
cDNA.1672G>A
g.162792G>A

AA changes

C376Y Score: 194 explain score(s)

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

376

frameshift

known variant

Reference ID: rs199476088
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8235 (pathogenic for Generalized juvenile polyposis/juvenile polyposis coli) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014519)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014519)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014519)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.832	1
	5.852	1
(flanking)	1.084	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
Donor increased	162784	wt: 0.25 / mu: 0.33	wt: AAAAATGGGAGTTGC mu: AAAAATGGGAGTTAC	AAAT\|ggga
Donor gained	162788	0.50	mu: ATGGGAGTTACTGCA	GGGA\|gtta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

376

mutated

not conserved

376

Ptroglodytes

all identical

ENSPTRG00000002706

376

Mmulatta

all identical

ENSMMUG00000011852

376

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000021796

376

Ggallus

all identical

ENSGALG00000002003

377

Trubripes

all identical

ENSTRUG00000011026

369

Drerio

all identical

ENSDARG00000019728

371

Dmelanogaster

all identical

FBgn0003716

408

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003655

381

protein features

start (aa)	end (aa)	feature	details
177	532	TOPO_DOM	Cytoplasmic (Potential).	lost
234	525	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1599 / 1599

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

533 / 533

position of stopcodon in wt / mu cDNA

2144 / 2144

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

546 / 546

chromosome

strand

last intron/exon boundary

2019

theoretical NMD boundary in CDS

1423

length of CDS

1599

coding sequence (CDS) position

1127

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

1672

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

162792

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

88679187

original gDNA sequence snippet

CATCAAGAAAAATGGGAGTTGCTGCATTGCTGACCTGGGCC

altered gDNA sequence snippet

CATCAAGAAAAATGGGAGTTACTGCATTGCTGACCTGGGCC

original cDNA sequence snippet

CATCAAGAAAAATGGGAGTTGCTGCATTGCTGACCTGGGCC

altered cDNA sequence snippet

CATCAAGAAAAATGGGAGTTACTGCATTGCTGACCTGGGCC

wildtype AA sequence

MPQLYIYIRL LGAYLFIISR VQGQNLDSML HGTGMKSDSD QKKSENGVTL APEDTLPFLK
CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR
TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IRWLVLLISM AVCIIAMIIF SSCFCYKHYC
KSISSRRRYN RDLEQDEAFI PVGESLKDLI DQSQSSGSGS GLPLLVQRTI AKQIQMVRQV
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDF LKCATLDTRA LLKLAYSAAC GLCHLHTEIY GTQGKPAIAH
RDLKSKNILI KKNGSCCIAD LGLAVKFNSD TNEVDVPLNT RVGTKRYMAP EVLDESLNKN
HFQPYIMADI YSFGLIIWEM ARRCITGGIV EEYQLPYYNM VPSDPSYEDM REVVCVKRLR
PIVSNRWNSD ECLRAVLKLM SECWAHNPAS RLTALRIKKT LAKMVESQDV KI*

mutated AA sequence

MPQLYIYIRL LGAYLFIISR VQGQNLDSML HGTGMKSDSD QKKSENGVTL APEDTLPFLK
CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR
TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IRWLVLLISM AVCIIAMIIF SSCFCYKHYC
KSISSRRRYN RDLEQDEAFI PVGESLKDLI DQSQSSGSGS GLPLLVQRTI AKQIQMVRQV
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDF LKCATLDTRA LLKLAYSAAC GLCHLHTEIY GTQGKPAIAH
RDLKSKNILI KKNGSYCIAD LGLAVKFNSD TNEVDVPLNT RVGTKRYMAP EVLDESLNKN
HFQPYIMADI YSFGLIIWEM ARRCITGGIV EEYQLPYYNM VPSDPSYEDM REVVCVKRLR
PIVSNRWNSD ECLRAVLKLM SECWAHNPAS RLTALRIKKT LAKMVESQDV KI*

speed

0.13 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: 0.999999999983472 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014519)
known disease mutation: rs8235 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:88679187G>AN/A show variant in all transcripts IGV

HGNC symbol

BMPR1A

Ensembl transcript ID

ENST00000224764

Genbank transcript ID

NM_004329

UniProt peptide

P36894

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1127G>A
cDNA.1675G>A
g.162792G>A

AA changes

C376Y Score: 194 explain score(s)

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

376

frameshift

known variant

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.832	1
	5.852	1
(flanking)	1.084	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
Donor increased	162784	wt: 0.25 / mu: 0.33	wt: AAAAATGGGAGTTGC mu: AAAAATGGGAGTTAC	AAAT\|ggga
Donor gained	162788	0.50	mu: ATGGGAGTTACTGCA	GGGA\|gtta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

376

mutated

not conserved

376

Ptroglodytes

all identical

ENSPTRG00000002706

376

Mmulatta

all identical

ENSMMUG00000011852

376

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000021796

376

Ggallus

all identical

ENSGALG00000002003

377

Trubripes

all identical

ENSTRUG00000011026

369

Drerio

all identical

ENSDARG00000019728

371

Dmelanogaster

all identical

FBgn0003716

408

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003655

381

protein features

start (aa)	end (aa)	feature	details
177	532	TOPO_DOM	Cytoplasmic (Potential).	lost
234	525	DOMAIN	Protein kinase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1599 / 1599

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

533 / 533

position of stopcodon in wt / mu cDNA

2147 / 2147

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

549 / 549

chromosome

strand

last intron/exon boundary

2022

theoretical NMD boundary in CDS

1423

length of CDS

1599

coding sequence (CDS) position

1127

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

1675

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

162792

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

88679187

original gDNA sequence snippet

CATCAAGAAAAATGGGAGTTGCTGCATTGCTGACCTGGGCC

altered gDNA sequence snippet

CATCAAGAAAAATGGGAGTTACTGCATTGCTGACCTGGGCC

original cDNA sequence snippet

CATCAAGAAAAATGGGAGTTGCTGCATTGCTGACCTGGGCC

altered cDNA sequence snippet

CATCAAGAAAAATGGGAGTTACTGCATTGCTGACCTGGGCC

wildtype AA sequence

mutated AA sequence

MPQLYIYIRL LGAYLFIISR VQGQNLDSML HGTGMKSDSD QKKSENGVTL APEDTLPFLK
CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR
TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IRWLVLLISM AVCIIAMIIF SSCFCYKHYC
KSISSRRRYN RDLEQDEAFI PVGESLKDLI DQSQSSGSGS GLPLLVQRTI AKQIQMVRQV
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDF LKCATLDTRA LLKLAYSAAC GLCHLHTEIY GTQGKPAIAH
RDLKSKNILI KKNGSYCIAD LGLAVKFNSD TNEVDVPLNT RVGTKRYMAP EVLDESLNKN
HFQPYIMADI YSFGLIIWEM ARRCITGGIV EEYQLPYYNM VPSDPSYEDM REVVCVKRLR
PIVSNRWNSD ECLRAVLKLM SECWAHNPAS RLTALRIKKT LAKMVESQDV KI*

speed

1.31 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems