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: ENST00000540418
Querying Taster for transcript #2: ENST00000303145
Querying Taster for transcript #3: ENST00000411698
MT speed 0 s - this script 3.819484 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MDM1	polymorphism_automatic	6.59472476627343e-14	simple_aae				R209H	single base exchange	rs2306393		show file
MDM1	polymorphism_automatic	6.59472476627343e-14	simple_aae				R489H	single base exchange	rs2306393		show file
MDM1	polymorphism_automatic	6.59472476627343e-14	simple_aae				R454H	single base exchange	rs2306393		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999934 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:68708761C>TN/A show variant in all transcripts IGV

HGNC symbol

MDM1

Ensembl transcript ID

ENST00000540418

Genbank transcript ID

N/A

UniProt peptide

Q8TC05

alteration type

single base exchange

alteration region

CDS

DNA changes

c.626G>A
cDNA.1142G>A
g.17401G>A

AA changes

R209H Score: 29 explain score(s)

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

209

frameshift

known variant

Reference ID: rs2306393

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1238	966	2204
ExAC	30254	-27741	2513

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.309	0.056
	0.253	0.047
(flanking)	1.447	0.044

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 marginally increased	17402	wt: 0.9890 / mu: 0.9921 (marginal change - not scored)	wt: GTACGTGAGAAATCT mu: GTACATGAGAAATCT	ACGT\|gaga
Donor marginally increased	17404	wt: 0.8492 / mu: 0.9134 (marginal change - not scored)	wt: ACGTGAGAAATCTAA mu: ACATGAGAAATCTAA	GTGA\|gaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

209

mutated

not conserved

209

Ptroglodytes

not conserved

ENSPTRG00000005196

489

Mmulatta

not conserved

ENSMMUG00000018725

490

Fcatus

no alignment

ENSFCAG00000018582

n/a

Mmusculus

not conserved

ENSMUSG00000020212

501

Ggallus

not conserved

ENSGALG00000009905

451

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000045675

477

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000001452

496

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1305 / 1305

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

435 / 435

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

517 / 517

chromosome

strand

-1

last intron/exon boundary

1709

theoretical NMD boundary in CDS

1142

length of CDS

1305

coding sequence (CDS) position

626

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

1142

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

17401

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

68708761

original gDNA sequence snippet

GCAAGAGAAGTTGGATGTACGTGAGAAATCTAAGGCAGATA

altered gDNA sequence snippet

GCAAGAGAAGTTGGATGTACATGAGAAATCTAAGGCAGATA

original cDNA sequence snippet

GCAAGAGAAGTTGGATGTACGTGAGAAATCTAAGGCAGATA

altered cDNA sequence snippet

GCAAGAGAAGTTGGATGTACATGAGAAATCTAAGGCAGATA

wildtype AA sequence

MELKDLHQPK RKLTPWKHQR LGKVNSEYRA KFLSPAQYLY KAGAWTHVKG NMPNQVKELR
EKAEFYRKRV QGTHFSRDHL NQILSDSNCC WDVSSTTSSE GTVSSNIRAL DLAGDPTSHK
TLQKCPSTEP EEKGNIVEEQ PQKNTTEKLG VSAPTIPVRR RLAWDTENTS EDVQKQPGEK
EEEDDNEEEG DRKTGKQAFM GEQEKLDVRE KSKADKMKEG SDSSVSSEKG GRLPTPKLRE
LGGIQRTHHD LTTPAVGGAV LVSPSKMKPP APEQRKRMTS QDCLETSKND FTKKESRAVS
LLTSPAAGIK TVDPLPLRED SEDNIHKFAE ATLPVSKIPK YPTNPPGQLP SPPHVPSYWH
PSRRIQGSLR DPEFQHNVGK ARMNNLQLPQ HEAFNDEDED RLSEISARSA ASSLRAFQTL
ARAKKRKENF WGKT*

mutated AA sequence

MELKDLHQPK RKLTPWKHQR LGKVNSEYRA KFLSPAQYLY KAGAWTHVKG NMPNQVKELR
EKAEFYRKRV QGTHFSRDHL NQILSDSNCC WDVSSTTSSE GTVSSNIRAL DLAGDPTSHK
TLQKCPSTEP EEKGNIVEEQ PQKNTTEKLG VSAPTIPVRR RLAWDTENTS EDVQKQPGEK
EEEDDNEEEG DRKTGKQAFM GEQEKLDVHE KSKADKMKEG SDSSVSSEKG GRLPTPKLRE
LGGIQRTHHD LTTPAVGGAV LVSPSKMKPP APEQRKRMTS QDCLETSKND FTKKESRAVS
LLTSPAAGIK TVDPLPLRED SEDNIHKFAE ATLPVSKIPK YPTNPPGQLP SPPHVPSYWH
PSRRIQGSLR DPEFQHNVGK ARMNNLQLPQ HEAFNDEDED RLSEISARSA ASSLRAFQTL
ARAKKRKENF WGKT*

speed

0.76 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

polymorphism

Model: simple_aae, prob: 0.999999999999934 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:68708761C>TN/A show variant in all transcripts IGV

HGNC symbol

MDM1

Ensembl transcript ID

ENST00000303145

Genbank transcript ID

NM_017440

UniProt peptide

Q8TC05

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1466G>A
cDNA.1553G>A
g.17401G>A

AA changes

R489H Score: 29 explain score(s)

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

489

frameshift

known variant

Reference ID: rs2306393

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1238	966	2204
ExAC	30254	-27741	2513

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.309	0.056
	0.253	0.047
(flanking)	1.447	0.044

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 marginally increased	17402	wt: 0.9890 / mu: 0.9921 (marginal change - not scored)	wt: GTACGTGAGAAATCT mu: GTACATGAGAAATCT	ACGT\|gaga
Donor marginally increased	17404	wt: 0.8492 / mu: 0.9134 (marginal change - not scored)	wt: ACGTGAGAAATCTAA mu: ACATGAGAAATCTAA	GTGA\|gaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

489

mutated

not conserved

489

Ptroglodytes

not conserved

ENSPTRG00000005196

489

Mmulatta

not conserved

ENSMMUG00000018725

494

Fcatus

no alignment

ENSFCAG00000018582

n/a

Mmusculus

not conserved

ENSMUSG00000020212

499

Ggallus

not conserved

ENSGALG00000009905

451

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000045675

484

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000001452

493

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2145 / 2145

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

715 / 715

position of stopcodon in wt / mu cDNA

2232 / 2232

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

88 / 88

chromosome

strand

-1

last intron/exon boundary

2120

theoretical NMD boundary in CDS

1982

length of CDS

2145

coding sequence (CDS) position

1466

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

1553

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

17401

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

68708761

original gDNA sequence snippet

GCAAGAGAAGTTGGATGTACGTGAGAAATCTAAGGCAGATA

altered gDNA sequence snippet

GCAAGAGAAGTTGGATGTACATGAGAAATCTAAGGCAGATA

original cDNA sequence snippet

GCAAGAGAAGTTGGATGTACGTGAGAAATCTAAGGCAGATA

altered cDNA sequence snippet

GCAAGAGAAGTTGGATGTACATGAGAAATCTAAGGCAGATA

wildtype AA sequence

MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVTQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGLDRL LRKKAGLTVV
PSYNALRNSE YQRQFVWKTS KETAPAFAAN QVFHNKSQFV PPFKGNSVIH ETEYKRNFKG
LSPVKEPKLR NDLRENRNLE TVSPERKSNK IDDRLKLEAE MELKDLHQPK RKLTPWKHQR
LGKVNSEYRA KFLSPAQYLY KAGAWTHVKG NMPNQVKELR EKAEFYRKRV QGTHFSRDHL
NQILSDSNCC WDVSSTTSSE GTVSSNIRAL DLAGDPTSHK TLQKCPSTEP EEKGNIVEEQ
PQKNTTEKLG VSAPTIPVRR RLAWDTENTS EDVQKQPGEK EEEDDNEEEG DRKTGKQAFM
GEQEKLDVRE KSKADKMKEG SDSSVSSEKG GRLPTPKLRE LGGIQRTHHD LTTPAVGGAV
LVSPSKMKPP APEQRKRMTS QDCLETSKND FTKKESRAVS LLTSPAAGIK TVDPLPLRED
SEDNIHKFAE ATLPVSKIPK YPTNPPGQLP SPPHVPSYWH PSRRIQGSLR DPEFQHNVGK
ARMNNLQLPQ HEAFNDEDED RLSEISARSA ASSLRAFQTL ARAKKRKENF WGKT*

mutated AA sequence

MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVTQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGLDRL LRKKAGLTVV
PSYNALRNSE YQRQFVWKTS KETAPAFAAN QVFHNKSQFV PPFKGNSVIH ETEYKRNFKG
LSPVKEPKLR NDLRENRNLE TVSPERKSNK IDDRLKLEAE MELKDLHQPK RKLTPWKHQR
LGKVNSEYRA KFLSPAQYLY KAGAWTHVKG NMPNQVKELR EKAEFYRKRV QGTHFSRDHL
NQILSDSNCC WDVSSTTSSE GTVSSNIRAL DLAGDPTSHK TLQKCPSTEP EEKGNIVEEQ
PQKNTTEKLG VSAPTIPVRR RLAWDTENTS EDVQKQPGEK EEEDDNEEEG DRKTGKQAFM
GEQEKLDVHE KSKADKMKEG SDSSVSSEKG GRLPTPKLRE LGGIQRTHHD LTTPAVGGAV
LVSPSKMKPP APEQRKRMTS QDCLETSKND FTKKESRAVS LLTSPAAGIK TVDPLPLRED
SEDNIHKFAE ATLPVSKIPK YPTNPPGQLP SPPHVPSYWH PSRRIQGSLR DPEFQHNVGK
ARMNNLQLPQ HEAFNDEDED RLSEISARSA ASSLRAFQTL ARAKKRKENF WGKT*

speed

0.92 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999934 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:68708761C>TN/A show variant in all transcripts IGV

HGNC symbol

MDM1

Ensembl transcript ID

ENST00000411698

Genbank transcript ID

NM_001205028

UniProt peptide

Q8TC05

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1361G>A
cDNA.1402G>A
g.17401G>A

AA changes

R454H Score: 29 explain score(s)

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

454

frameshift

known variant

Reference ID: rs2306393

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1238	966	2204
ExAC	30254	-27741	2513

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.309	0.056
	0.253	0.047
(flanking)	1.447	0.044

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 marginally increased	17402	wt: 0.9890 / mu: 0.9921 (marginal change - not scored)	wt: GTACGTGAGAAATCT mu: GTACATGAGAAATCT	ACGT\|gaga
Donor marginally increased	17404	wt: 0.8492 / mu: 0.9134 (marginal change - not scored)	wt: ACGTGAGAAATCTAA mu: ACATGAGAAATCTAA	GTGA\|gaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

454

mutated

not conserved

454

Ptroglodytes

not conserved

ENSPTRG00000005196

489

Mmulatta

not conserved

ENSMMUG00000018725

494

Fcatus

no alignment

ENSFCAG00000018582

n/a

Mmusculus

not conserved

ENSMUSG00000020212

499

Ggallus

not conserved

ENSGALG00000009905

451

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000045675

478

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000001452

492

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2040 / 2040

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

680 / 680

position of stopcodon in wt / mu cDNA

2081 / 2081

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

-1

last intron/exon boundary

1969

theoretical NMD boundary in CDS

1877

length of CDS

2040

coding sequence (CDS) position

1361

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

1402

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

17401

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

68708761

original gDNA sequence snippet

GCAAGAGAAGTTGGATGTACGTGAGAAATCTAAGGCAGATA

altered gDNA sequence snippet

GCAAGAGAAGTTGGATGTACATGAGAAATCTAAGGCAGATA

original cDNA sequence snippet

GCAAGAGAAGTTGGATGTACGTGAGAAATCTAAGGCAGATA

altered cDNA sequence snippet

GCAAGAGAAGTTGGATGTACATGAGAAATCTAAGGCAGATA

wildtype AA sequence

MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVTQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGVFHN KSQFVPPFKG
NSVIHETEYK RNFKGLSPVK EPKLRNDLRE NRNLETVSPE RKSNKIDDRL KLEAEMELKD
LHQPKRKLTP WKHQRLGKVN SEYRAKFLSP AQYLYKAGAW THVKGNMPNQ GSLNAMWYAE
VKELREKAEF YRKRVQGTHF SRDHLNQILS DSNCCWDVSS TTSSEGTVSS NIRALDLAGD
PTSHKTLQKC PSTEPEEKGN IVEEQPQKNT TEKLGVSAPT IPVRRRLAWD TENTSEDVQK
QPGEKEEEDD NEEEGDRKTG KQAFMGEQEK LDVREKSKAD KMKEGSDSSV SSEKGGRLPT
PKLRELGGIQ RTHHDLTTPA VGGAVLVSPS KMKPPAPEQR KRMTSQDCLE TSKNDFTKKE
SRAVSLLTSP AAGIKTVDPL PLREDSEDNI HKFAEATLPV SKIPKYPTNP PGQLPSPPHV
PSYWHPSRRI QGSLRDPEFQ HNVGKARMNN LQLPQHEAFN DEDEDRLSEI SARSAASSLR
AFQTLARAKK RKENFWGKT*

mutated AA sequence

MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVTQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGVFHN KSQFVPPFKG
NSVIHETEYK RNFKGLSPVK EPKLRNDLRE NRNLETVSPE RKSNKIDDRL KLEAEMELKD
LHQPKRKLTP WKHQRLGKVN SEYRAKFLSP AQYLYKAGAW THVKGNMPNQ GSLNAMWYAE
VKELREKAEF YRKRVQGTHF SRDHLNQILS DSNCCWDVSS TTSSEGTVSS NIRALDLAGD
PTSHKTLQKC PSTEPEEKGN IVEEQPQKNT TEKLGVSAPT IPVRRRLAWD TENTSEDVQK
QPGEKEEEDD NEEEGDRKTG KQAFMGEQEK LDVHEKSKAD KMKEGSDSSV SSEKGGRLPT
PKLRELGGIQ RTHHDLTTPA VGGAVLVSPS KMKPPAPEQR KRMTSQDCLE TSKNDFTKKE
SRAVSLLTSP AAGIKTVDPL PLREDSEDNI HKFAEATLPV SKIPKYPTNP PGQLPSPPHV
PSYWHPSRRI QGSLRDPEFQ HNVGKARMNN LQLPQHEAFN DEDEDRLSEI SARSAASSLR
AFQTLARAKK RKENFWGKT*

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems