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: ENST00000512183
Querying Taster for transcript #2: ENST00000338148
Querying Taster for transcript #3: ENST00000409841
MT speed 0 s - this script 2.923358 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C2orf15	polymorphism_automatic	5.65225252402435e-06	simple_aae		affected		A130T	single base exchange	rs1044575		show file
MRPL30	polymorphism_automatic	5.65225252402435e-06	simple_aae		affected		A130T	single base exchange	rs1044575		show file
MRPL30	polymorphism_automatic	5.65225252402435e-06	simple_aae		affected		A130T	single base exchange	rs1044575		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999994347747476 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:99812070G>AN/A show variant in all transcripts IGV

HGNC symbol

C2orf15

Ensembl transcript ID

ENST00000512183

Genbank transcript ID

N/A

UniProt peptide

Q8WU43

alteration type

single base exchange

alteration region

CDS

DNA changes

c.388G>A
cDNA.550G>A
g.54123G>A

AA changes

A130T Score: 58 explain score(s)

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

130

frameshift

known variant

Reference ID: rs1044575

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1076	1073	2149
ExAC	25034	-17301	7733

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.36	0.542
	-0.759	0.528
(flanking)	1.709	0.946

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 increased	54113	wt: 0.22 / mu: 0.27	wt: AAGCCCTTGAAGTTGCCACAAGGACTTCCAGCAGAGGAGAA mu: AAGCCCTTGAAGTTGCCACAAGGACTTCCAACAGAGGAGAA	acaa\|GGAC
Donor increased	54128	wt: 0.48 / mu: 0.63	wt: GCAGAGGAGAACATG mu: ACAGAGGAGAACATG	AGAG\|gaga
Donor increased	54127	wt: 0.57 / mu: 0.65	wt: AGCAGAGGAGAACAT mu: AACAGAGGAGAACAT	CAGA\|ggag
Donor marginally increased	54125	wt: 0.9978 / mu: 0.9984 (marginal change - not scored)	wt: CCAGCAGAGGAGAAC mu: CCAACAGAGGAGAAC	AGCA\|gagg
Donor gained	54123	0.54	mu: TTCCAACAGAGGAGA	CCAA\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

130

mutated

not conserved

130

Ptroglodytes

not conserved

ENSPTRG00000012275

160

Mmulatta

no alignment

ENSMMUG00000000571

n/a

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000026087

130

Ggallus

not conserved

ENSGALG00000016760

128

Trubripes

no homologue

Drerio

all identical

ENSDARG00000069850

123

Dmelanogaster

not conserved

FBgn0029718

122

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000026571

131

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

486 / 486

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

162 / 162

position of stopcodon in wt / mu cDNA

648 / 648

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

163 / 163

chromosome

strand

last intron/exon boundary

516

theoretical NMD boundary in CDS

303

length of CDS

486

coding sequence (CDS) position

388

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

550

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

54123

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

99812070

original gDNA sequence snippet

AGTTGCCACAAGGACTTCCAGCAGAGGAGAACATGTCTAAC

altered gDNA sequence snippet

AGTTGCCACAAGGACTTCCAACAGAGGAGAACATGTCTAAC

original cDNA sequence snippet

AGTTGCCACAAGGACTTCCAGCAGAGGAGAACATGTCTAAC

altered cDNA sequence snippet

AGTTGCCACAAGGACTTCCAACAGAGGAGAACATGTCTAAC

wildtype AA sequence

MAGILRLVVQ WPPGRLQTVT KGVESLICTD WIRHKFTRSR IPEKVFQASP EDHEKYGGDP
QNPHKLHIVT RIKSTRRRPY WEKDIIKMLG LEKAHTPQVH KNIPSVNAKL KVVKHLIRIK
PLKLPQGLPA EENMSNTCLK STGELVVQWH LKPVEQKAHE S*

mutated AA sequence

MAGILRLVVQ WPPGRLQTVT KGVESLICTD WIRHKFTRSR IPEKVFQASP EDHEKYGGDP
QNPHKLHIVT RIKSTRRRPY WEKDIIKMLG LEKAHTPQVH KNIPSVNAKL KVVKHLIRIK
PLKLPQGLPT EENMSNTCLK STGELVVQWH LKPVEQKAHE S*

speed

0.47 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: 0.999994347747476 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:99812070G>AN/A show variant in all transcripts IGV

HGNC symbol

MRPL30

Ensembl transcript ID

ENST00000338148

Genbank transcript ID

NM_145212

UniProt peptide

Q8WU43

alteration type

single base exchange

alteration region

CDS

DNA changes

c.388G>A
cDNA.586G>A
g.40610G>A

AA changes

A130T Score: 58 explain score(s)

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

130

frameshift

known variant

Reference ID: rs1044575

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1076	1073	2149
ExAC	25034	-17301	7733

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.36	0.542
	-0.759	0.528
(flanking)	1.709	0.946

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 increased	40600	wt: 0.22 / mu: 0.27	wt: AAGCCCTTGAAGTTGCCACAAGGACTTCCAGCAGAGGAGAA mu: AAGCCCTTGAAGTTGCCACAAGGACTTCCAACAGAGGAGAA	acaa\|GGAC
Donor marginally increased	40612	wt: 0.9978 / mu: 0.9984 (marginal change - not scored)	wt: CCAGCAGAGGAGAAC mu: CCAACAGAGGAGAAC	AGCA\|gagg
Donor increased	40614	wt: 0.57 / mu: 0.65	wt: AGCAGAGGAGAACAT mu: AACAGAGGAGAACAT	CAGA\|ggag
Donor increased	40615	wt: 0.48 / mu: 0.63	wt: GCAGAGGAGAACATG mu: ACAGAGGAGAACATG	AGAG\|gaga
Donor gained	40610	0.54	mu: TTCCAACAGAGGAGA	CCAA\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

130

mutated

not conserved

130

Ptroglodytes

not conserved

ENSPTRG00000012275

160

Mmulatta

no alignment

ENSMMUG00000000571

n/a

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000026087

130

Ggallus

not conserved

ENSGALG00000016760

128

Trubripes

no homologue

Drerio

all identical

ENSDARG00000069850

123

Dmelanogaster

not conserved

FBgn0029718

122

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000026571

131

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

486 / 486

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

162 / 162

position of stopcodon in wt / mu cDNA

684 / 684

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

199 / 199

chromosome

strand

last intron/exon boundary

552

theoretical NMD boundary in CDS

303

length of CDS

486

coding sequence (CDS) position

388

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

586

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

40610

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

99812070

original gDNA sequence snippet

AGTTGCCACAAGGACTTCCAGCAGAGGAGAACATGTCTAAC

altered gDNA sequence snippet

AGTTGCCACAAGGACTTCCAACAGAGGAGAACATGTCTAAC

original cDNA sequence snippet

AGTTGCCACAAGGACTTCCAGCAGAGGAGAACATGTCTAAC

altered cDNA sequence snippet

AGTTGCCACAAGGACTTCCAACAGAGGAGAACATGTCTAAC

wildtype AA sequence

MAGILRLVVQ WPPGRLQTVT KGVESLICTD WIRHKFTRSR IPEKVFQASP EDHEKYGGDP
QNPHKLHIVT RIKSTRRRPY WEKDIIKMLG LEKAHTPQVH KNIPSVNAKL KVVKHLIRIK
PLKLPQGLPA EENMSNTCLK STGELVVQWH LKPVEQKAHE S*

mutated AA sequence

MAGILRLVVQ WPPGRLQTVT KGVESLICTD WIRHKFTRSR IPEKVFQASP EDHEKYGGDP
QNPHKLHIVT RIKSTRRRPY WEKDIIKMLG LEKAHTPQVH KNIPSVNAKL KVVKHLIRIK
PLKLPQGLPT EENMSNTCLK STGELVVQWH LKPVEQKAHE S*

speed

0.50 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999994347747476 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:99812070G>AN/A show variant in all transcripts IGV

HGNC symbol

MRPL30

Ensembl transcript ID

ENST00000409841

Genbank transcript ID

N/A

UniProt peptide

Q8WU43

alteration type

single base exchange

alteration region

CDS

DNA changes

c.388G>A
cDNA.416G>A
g.40610G>A

AA changes

A130T Score: 58 explain score(s)

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

130

frameshift

known variant

Reference ID: rs1044575

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1076	1073	2149
ExAC	25034	-17301	7733

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.36	0.542
	-0.759	0.528
(flanking)	1.709	0.946

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 increased	40600	wt: 0.22 / mu: 0.27	wt: AAGCCCTTGAAGTTGCCACAAGGACTTCCAGCAGAGGAGAA mu: AAGCCCTTGAAGTTGCCACAAGGACTTCCAACAGAGGAGAA	acaa\|GGAC
Donor marginally increased	40612	wt: 0.9978 / mu: 0.9984 (marginal change - not scored)	wt: CCAGCAGAGGAGAAC mu: CCAACAGAGGAGAAC	AGCA\|gagg
Donor increased	40614	wt: 0.57 / mu: 0.65	wt: AGCAGAGGAGAACAT mu: AACAGAGGAGAACAT	CAGA\|ggag
Donor increased	40615	wt: 0.48 / mu: 0.63	wt: GCAGAGGAGAACATG mu: ACAGAGGAGAACATG	AGAG\|gaga
Donor gained	40610	0.54	mu: TTCCAACAGAGGAGA	CCAA\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

130

mutated

not conserved

130

Ptroglodytes

not conserved

ENSPTRG00000012275

160

Mmulatta

no alignment

ENSMMUG00000000571

n/a

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000026087

130

Ggallus

not conserved

ENSGALG00000016760

128

Trubripes

no homologue

Drerio

all identical

ENSDARG00000069850

123

Dmelanogaster

not conserved

FBgn0029718

122

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000026571

131

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

486 / 486

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

162 / 162

position of stopcodon in wt / mu cDNA

514 / 514

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

29 / 29

chromosome

strand

last intron/exon boundary

633

theoretical NMD boundary in CDS

554

length of CDS

486

coding sequence (CDS) position

388

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

416

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

40610

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

99812070

original gDNA sequence snippet

AGTTGCCACAAGGACTTCCAGCAGAGGAGAACATGTCTAAC

altered gDNA sequence snippet

AGTTGCCACAAGGACTTCCAACAGAGGAGAACATGTCTAAC

original cDNA sequence snippet

AGTTGCCACAAGGACTTCCAGCAGAGGAGAACATGTCTAAC

altered cDNA sequence snippet

AGTTGCCACAAGGACTTCCAACAGAGGAGAACATGTCTAAC

wildtype AA sequence

MAGILRLVVQ WPPGRLQTVT KGVESLICTD WIRHKFTRSR IPEKVFQASP EDHEKYGGDP
QNPHKLHIVT RIKSTRRRPY WEKDIIKMLG LEKAHTPQVH KNIPSVNAKL KVVKHLIRIK
PLKLPQGLPA EENMSNTCLK STGELVVQWH LKPVEQKAHE S*

mutated AA sequence

MAGILRLVVQ WPPGRLQTVT KGVESLICTD WIRHKFTRSR IPEKVFQASP EDHEKYGGDP
QNPHKLHIVT RIKSTRRRPY WEKDIIKMLG LEKAHTPQVH KNIPSVNAKL KVVKHLIRIK
PLKLPQGLPT EENMSNTCLK STGELVVQWH LKPVEQKAHE S*

speed

0.45 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