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: ENST00000367758
Querying Taster for transcript #2: ENST00000367759
MT speed 0 s - this script 3.948475 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MROH9	polymorphism_automatic	1.32005517627931e-13	simple_aae				V74A	single base exchange	rs2294740		show file
MROH9	polymorphism_automatic	1.32005517627931e-13	simple_aae				V74A	single base exchange	rs2294740		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999868 (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)

chr1:170928671T>CN/A show variant in all transcripts IGV

HGNC symbol

MROH9

Ensembl transcript ID

ENST00000367758

Genbank transcript ID

NM_025063

UniProt peptide

Q5TGP6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.221T>C
cDNA.320T>C
g.24060T>C

AA changes

V74A Score: 64 explain score(s)

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

frameshift

known variant

Reference ID: rs2294740

database	homozygous (C/C)	heterozygous	allele carriers
1000G	214	825	1039
ExAC	3520	18436	21956

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.431	0.001
	0.827	0.002
(flanking)	0.269	0.001

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	24061	wt: 0.9274 / mu: 0.9799 (marginal change - not scored)	wt: CTAGTTGTCATGCCA mu: CTAGCTGTCATGCCA	AGTT\|gtca

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

no homologue

Mmulatta

no alignment

ENSMMUG00000013380

n/a

Fcatus

not conserved

ENSFCAG00000003012

Mmusculus

not conserved

ENSMUSG00000071890

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1722 / 1722

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

574 / 574

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

100 / 100

chromosome

strand

last intron/exon boundary

1575

theoretical NMD boundary in CDS

1425

length of CDS

1722

coding sequence (CDS) position

221

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

320

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

24060

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

170928671

original gDNA sequence snippet

GTCATCCTTTGGAATGCTAGTTGTCATGCCAAGTCTTGACA

altered gDNA sequence snippet

GTCATCCTTTGGAATGCTAGCTGTCATGCCAAGTCTTGACA

original cDNA sequence snippet

GTCATCCTTTGGAATGCTAGTTGTCATGCCAAGTCTTGACA

altered cDNA sequence snippet

GTCATCCTTTGGAATGCTAGCTGTCATGCCAAGTCTTGACA

wildtype AA sequence

mutated AA sequence

speed

0.78 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: 0.999999999999868 (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)

chr1:170928671T>CN/A show variant in all transcripts IGV

HGNC symbol

MROH9

Ensembl transcript ID

ENST00000367759

Genbank transcript ID

NM_001163629

UniProt peptide

Q5TGP6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.221T>C
cDNA.375T>C
g.24060T>C

AA changes

V74A Score: 64 explain score(s)

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

frameshift

known variant

Reference ID: rs2294740

database	homozygous (C/C)	heterozygous	allele carriers
1000G	214	825	1039
ExAC	3520	18436	21956

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.431	0.001
	0.827	0.002
(flanking)	0.269	0.001

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	24061	wt: 0.9274 / mu: 0.9799 (marginal change - not scored)	wt: CTAGTTGTCATGCCA mu: CTAGCTGTCATGCCA	AGTT\|gtca

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

no homologue

Mmulatta

no alignment

ENSMMUG00000013380

n/a

Fcatus

not conserved

ENSFCAG00000003012

Mmusculus

not conserved

ENSMUSG00000071890

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2586 / 2586

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

862 / 862

position of stopcodon in wt / mu cDNA

2740 / 2740

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

155 / 155

chromosome

strand

last intron/exon boundary

2499

theoretical NMD boundary in CDS

2294

length of CDS

2586

coding sequence (CDS) position

221

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

375

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

24060

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

170928671

original gDNA sequence snippet

GTCATCCTTTGGAATGCTAGTTGTCATGCCAAGTCTTGACA

altered gDNA sequence snippet

GTCATCCTTTGGAATGCTAGCTGTCATGCCAAGTCTTGACA

original cDNA sequence snippet

GTCATCCTTTGGAATGCTAGTTGTCATGCCAAGTCTTGACA

altered cDNA sequence snippet

GTCATCCTTTGGAATGCTAGCTGTCATGCCAAGTCTTGACA

wildtype AA sequence

MLTRNPKTKS SLQILQDSVK WHHMAHKVNS LLDAYSGLLS NESMILAVNS SFVDPLLQFE
SQLKIIESSF GMLVVMPSLD KVKEMGSSYE YIEDMENLYH NILNIYENIL TSLVSKDLYK
LQILKEMLVW MSKDSSYLQE RIMVIINKVL RFTVTKVRKY ISVDAPCLGL LAAELSLLCS
HEDPSIVKQA SLGMCHLLYI ARCQNDIGTN KPTNGKSHSL QFPSSDVEFL PKEFQQDESK
IAQRVGQTLL PPLLTDFVQS LLMKLSSPDD KIASDAASIL IFTLEFHAEK VTMVSKIVDA
IYRQLCDNNC MKDVMLQVIT LLTCTSPKKV IFQLMDYPVP ADDTLIQMWK AACSQASVAP
HVLKTILLIL KGKPGEMEDT VTEGKRFSLD ITNLMPLAAC QALCTFLPLG SYRKAVAQYF
PQLLTTLMFQ VFYNSELKPI LKDRALYAQD ALRVLLNCSG LQQVDITLMK ENFWDQLSED
LCYYHGVCFI AKTLSEYNFP QFPETLSYLY KLSVEGPRRS EDTVIVLIFL TELLNNFFKD
PLPEEFLVLF INWINDSNPV VSRLILHRIV HMSPIINKTE NVSSILIAIL DAFLSKDDNV
VLQALLTLRR LLNELDKVTY SLGTRIGSSY CTLMDHINGG IRSMAIRHFG QLVRDMRQYT
WMVNDVVLEG LVPLILFLED DDKRVAEACK YTLKICTSQL KWSTSRLLKD ENYSFEMVVL
NICNNLIISH RNYITDLTSD TLRFLWSPRT YLKRASVILI GYLAKSGGHL LLRDEIEVML
DVIERLLRDE DPMIKQLAEI TYDIFKKKAH KLTSAPLKQN FQKLLKLFYI KKLKPLYNYN
SPNGQIDSPT DSKDVKNDKA L*

mutated AA sequence

MLTRNPKTKS SLQILQDSVK WHHMAHKVNS LLDAYSGLLS NESMILAVNS SFVDPLLQFE
SQLKIIESSF GMLAVMPSLD KVKEMGSSYE YIEDMENLYH NILNIYENIL TSLVSKDLYK
LQILKEMLVW MSKDSSYLQE RIMVIINKVL RFTVTKVRKY ISVDAPCLGL LAAELSLLCS
HEDPSIVKQA SLGMCHLLYI ARCQNDIGTN KPTNGKSHSL QFPSSDVEFL PKEFQQDESK
IAQRVGQTLL PPLLTDFVQS LLMKLSSPDD KIASDAASIL IFTLEFHAEK VTMVSKIVDA
IYRQLCDNNC MKDVMLQVIT LLTCTSPKKV IFQLMDYPVP ADDTLIQMWK AACSQASVAP
HVLKTILLIL KGKPGEMEDT VTEGKRFSLD ITNLMPLAAC QALCTFLPLG SYRKAVAQYF
PQLLTTLMFQ VFYNSELKPI LKDRALYAQD ALRVLLNCSG LQQVDITLMK ENFWDQLSED
LCYYHGVCFI AKTLSEYNFP QFPETLSYLY KLSVEGPRRS EDTVIVLIFL TELLNNFFKD
PLPEEFLVLF INWINDSNPV VSRLILHRIV HMSPIINKTE NVSSILIAIL DAFLSKDDNV
VLQALLTLRR LLNELDKVTY SLGTRIGSSY CTLMDHINGG IRSMAIRHFG QLVRDMRQYT
WMVNDVVLEG LVPLILFLED DDKRVAEACK YTLKICTSQL KWSTSRLLKD ENYSFEMVVL
NICNNLIISH RNYITDLTSD TLRFLWSPRT YLKRASVILI GYLAKSGGHL LLRDEIEVML
DVIERLLRDE DPMIKQLAEI TYDIFKKKAH KLTSAPLKQN FQKLLKLFYI KKLKPLYNYN
SPNGQIDSPT DSKDVKNDKA L*

speed

1.20 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems