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: ENST00000374375
Querying Taster for transcript #2: ENST00000374369
Querying Taster for transcript #3: ENST00000374372
MT speed 0 s - this script 3.445329 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GDF5	disease_causing_automatic	0.999999999915199	simple_aae		affected	0	C400Y	single base exchange	rs74315387		show file
GDF5	disease_causing_automatic	0.999999999915199	simple_aae		affected	0	C400Y	single base exchange	rs74315387		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999915199 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970643)
known disease mutation: rs8379 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:34022014C>TN/A show variant in all transcripts IGV

HGNC symbol

GDF5

Ensembl transcript ID

ENST00000374369

Genbank transcript ID

NM_000557

UniProt peptide

P43026

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1199G>A
cDNA.1514G>A
g.20555G>A

AA changes

C400Y Score: 194 explain score(s)

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

400

frameshift

known variant

Reference ID: rs74315387
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8379 (pathogenic for Grebe syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970643)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970643)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970643)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.082	1
	5.588	1
(flanking)	3.05	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	20559	wt: 0.80 / mu: 0.91	wt: TGCAGTCGGAAGGCA mu: TACAGTCGGAAGGCA	CAGT\|cgga
Donor increased	20560	wt: 0.75 / mu: 0.88	wt: GCAGTCGGAAGGCAC mu: ACAGTCGGAAGGCAC	AGTC\|ggaa
Donor gained	20557	0.36	mu: GCTACAGTCGGAAGG	TACA\|gtcg

distance from splice site

568

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

400

mutated

not conserved

400

Ptroglodytes

all identical

ENSPTRG00000013439

400

Mmulatta

all identical

ENSMMUG00000007333

398

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038259

394

Ggallus

all identical

ENSGALG00000001786

399

Trubripes

no homologue

Drerio

all identical

ENSDARG00000002760

375

Dmelanogaster

all identical

FBgn0000490

492

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000021223

395

protein features

start (aa)	end (aa)	feature	details
399	403	STRAND		lost
400	400	DISULFID		lost
406	408	STRAND		might get lost (downstream of altered splice site)
410	412	HELIX		might get lost (downstream of altered splice site)
414	416	HELIX		might get lost (downstream of altered splice site)
418	420	STRAND		might get lost (downstream of altered splice site)
422	425	STRAND		might get lost (downstream of altered splice site)
428	432	STRAND		might get lost (downstream of altered splice site)
429	429	DISULFID		might get lost (downstream of altered splice site)
433	433	DISULFID		might get lost (downstream of altered splice site)
439	441	HELIX		might get lost (downstream of altered splice site)
445	456	HELIX		might get lost (downstream of altered splice site)
458	460	TURN		might get lost (downstream of altered splice site)
465	465	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
465	465	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
466	466	DISULFID		might get lost (downstream of altered splice site)
466	479	STRAND		might get lost (downstream of altered splice site)
481	483	STRAND		might get lost (downstream of altered splice site)
485	500	STRAND		might get lost (downstream of altered splice site)
498	498	DISULFID		might get lost (downstream of altered splice site)
500	500	DISULFID		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1506 / 1506

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

502 / 502

position of stopcodon in wt / mu cDNA

1821 / 1821

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

316 / 316

chromosome

strand

-1

last intron/exon boundary

947

theoretical NMD boundary in CDS

581

length of CDS

1506

coding sequence (CDS) position

1199

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

1514

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

20555

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

34022014

original gDNA sequence snippet

CAAGAACCTTAAGGCTCGCTGCAGTCGGAAGGCACTGCATG

altered gDNA sequence snippet

CAAGAACCTTAAGGCTCGCTACAGTCGGAAGGCACTGCATG

original cDNA sequence snippet

CAAGAACCTTAAGGCTCGCTGCAGTCGGAAGGCACTGCATG

altered cDNA sequence snippet

CAAGAACCTTAAGGCTCGCTACAGTCGGAAGGCACTGCATG

wildtype AA sequence

MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARC SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*

mutated AA sequence

MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARY SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*

speed

0.86 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: 0.999999999915199 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970643)
known disease mutation: rs8379 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:34022014C>TN/A show variant in all transcripts IGV

HGNC symbol

GDF5

Ensembl transcript ID

ENST00000374372

Genbank transcript ID

N/A

UniProt peptide

P43026

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1199G>A
cDNA.1703G>A
g.20555G>A

AA changes

C400Y Score: 194 explain score(s)

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

400

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)	2.082	1
	5.588	1
(flanking)	3.05	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	20559	wt: 0.80 / mu: 0.91	wt: TGCAGTCGGAAGGCA mu: TACAGTCGGAAGGCA	CAGT\|cgga
Donor increased	20560	wt: 0.75 / mu: 0.88	wt: GCAGTCGGAAGGCAC mu: ACAGTCGGAAGGCAC	AGTC\|ggaa
Donor gained	20557	0.36	mu: GCTACAGTCGGAAGG	TACA\|gtcg

distance from splice site

568

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

400

mutated

not conserved

400

Ptroglodytes

all identical

ENSPTRG00000013439

400

Mmulatta

all identical

ENSMMUG00000007333

398

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038259

394

Ggallus

all identical

ENSGALG00000001786

399

Trubripes

no homologue

Drerio

all identical

ENSDARG00000002760

375

Dmelanogaster

all identical

FBgn0000490

492

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000021223

395

protein features

start (aa)	end (aa)	feature	details
399	403	STRAND		lost
400	400	DISULFID		lost
406	408	STRAND		might get lost (downstream of altered splice site)
410	412	HELIX		might get lost (downstream of altered splice site)
414	416	HELIX		might get lost (downstream of altered splice site)
418	420	STRAND		might get lost (downstream of altered splice site)
422	425	STRAND		might get lost (downstream of altered splice site)
428	432	STRAND		might get lost (downstream of altered splice site)
429	429	DISULFID		might get lost (downstream of altered splice site)
433	433	DISULFID		might get lost (downstream of altered splice site)
439	441	HELIX		might get lost (downstream of altered splice site)
445	456	HELIX		might get lost (downstream of altered splice site)
458	460	TURN		might get lost (downstream of altered splice site)
465	465	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
465	465	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
466	466	DISULFID		might get lost (downstream of altered splice site)
466	479	STRAND		might get lost (downstream of altered splice site)
481	483	STRAND		might get lost (downstream of altered splice site)
485	500	STRAND		might get lost (downstream of altered splice site)
498	498	DISULFID		might get lost (downstream of altered splice site)
500	500	DISULFID		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1506 / 1506

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

502 / 502

position of stopcodon in wt / mu cDNA

2010 / 2010

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

505 / 505

chromosome

strand

-1

last intron/exon boundary

1136

theoretical NMD boundary in CDS

581

length of CDS

1506

coding sequence (CDS) position

1199

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

1703

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

20555

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

34022014

original gDNA sequence snippet

CAAGAACCTTAAGGCTCGCTGCAGTCGGAAGGCACTGCATG

altered gDNA sequence snippet

CAAGAACCTTAAGGCTCGCTACAGTCGGAAGGCACTGCATG

original cDNA sequence snippet

CAAGAACCTTAAGGCTCGCTGCAGTCGGAAGGCACTGCATG

altered cDNA sequence snippet

CAAGAACCTTAAGGCTCGCTACAGTCGGAAGGCACTGCATG

wildtype AA sequence

mutated AA sequence

MRLPKLLTFL LWYLAWLDLE FICTVLGAPD LGQRPQGTRP GLAKAEAKER PPLARNVFRP
GGHSYGGGAT NANARAKGGT GQTGGLTQPK KDEPKKLPPR PGGPEPKPGH PPQTRQATAR
TVTPKGQLPG GKAPPKAGSV PSSFLLKKAR EPGPPREPKE PFRPPPITPH EYMLSLYRTL
SDADRKGGNS SVKLEAGLAN TITSFIDKGQ DDRGPVVRKQ RYVFDISALE KDGLLGAELR
ILRKKPSDTA KPAAPGGGRA AQLKLSSCPS GRQPASLLDV RSVPGLDGSG WEVFDIWKLF
RNFKNSAQLC LELEAWERGR AVDLRGLGFD RAARQVHEKA LFLVFGRTKK RDLFFNEIKA
RSGQDDKTVY EYLFSQRRKR RAPLATRQGK RPSKNLKARY SRKALHVNFK DMGWDDWIIA
PLEYEAFHCE GLCEFPLRSH LEPTNHAVIQ TLMNSMDPES TPPTCCVPTR LSPISILFID
SANNVVYKQY EDMVVESCGC R*

speed

1.38 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table