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: ENST00000412718
Querying Taster for transcript #2: ENST00000381697
MT speed 0 s - this script 3.913942 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NUTM2D	polymorphism_automatic	3.39640537916353e-11	simple_aae		affected		H35Y	single base exchange	rs77153116		show file
NUTM2D	polymorphism_automatic	3.39640537916353e-11	simple_aae		affected		H35Y	single base exchange	rs77153116		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999966036 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:89118125C>TN/A show variant in all transcripts IGV

HGNC symbol

NUTM2D

Ensembl transcript ID

ENST00000412718

Genbank transcript ID

NM_001009610

UniProt peptide

Q5VT03

alteration type

single base exchange

alteration region

CDS

DNA changes

c.103C>T
cDNA.649C>T
g.701C>T

AA changes

H35Y Score: 83 explain score(s)

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

frameshift

known variant

Reference ID: rs77153116

database	homozygous (T/T)	heterozygous	allele carriers
1000G	186	942	1128
ExAC	1925	23436	25361

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.681	0.056
	0.786	0.049
(flanking)	0.681	0.033

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 marginally increased	701	wt: 0.9497 / mu: 0.9528 (marginal change - not scored)	wt: GTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACA mu: GTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACA	tctc\|ATTG
Acc marginally increased	703	wt: 0.9695 / mu: 0.9843 (marginal change - not scored)	wt: CTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGC mu: CTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGC	tcat\|TGTG
Acc marginally increased	705	wt: 0.8996 / mu: 0.9185 (marginal change - not scored)	wt: TACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGCGG mu: TACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGCGG	attg\|TGGA
Acc increased	699	wt: 0.24 / mu: 0.54	wt: GGGTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGA mu: GGGTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGA	tttc\|TCAT
Acc marginally increased	706	wt: 0.9897 / mu: 0.9915 (marginal change - not scored)	wt: ACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGCGGT mu: ACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGCGGT	ttgt\|GGAA
Acc marginally increased	704	wt: 0.9663 / mu: 0.9787 (marginal change - not scored)	wt: TTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGCG mu: TTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGCG	catt\|GTGG
Acc marginally increased	691	wt: 0.6510 / mu: 0.6799 (marginal change - not scored)	wt: CACTCTCTGGGTCTTACCCTTGGCTTTTCTCATTGTGGAAA mu: CACTCTCTGGGTCTTACCCTTGGCTTTTCTTATTGTGGAAA	cctt\|GGCT
Acc marginally increased	700	wt: 0.9401 / mu: 0.9412 (marginal change - not scored)	wt: GGTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGAC mu: GGTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGAC	ttct\|CATT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000019677

n/a

Fcatus

all identical

ENSFCAG00000010760

435

Mmusculus

no alignment

ENSMUSG00000071909

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
206	213	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
353	442	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1674 / 1674

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

558 / 558

position of stopcodon in wt / mu cDNA

2220 / 2220

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

547 / 547

chromosome

strand

last intron/exon boundary

2182

theoretical NMD boundary in CDS

1585

length of CDS

1674

coding sequence (CDS) position

103

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

649

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

701

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

89118125

original gDNA sequence snippet

GTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACA

altered gDNA sequence snippet

GTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACA

original cDNA sequence snippet

GTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACA

altered cDNA sequence snippet

GTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACA

wildtype AA sequence

mutated AA sequence

speed

0.81 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: 0.999999999966036 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:89118125C>TN/A show variant in all transcripts IGV

HGNC symbol

NUTM2D

Ensembl transcript ID

ENST00000381697

Genbank transcript ID

N/A

UniProt peptide

Q5VT03

alteration type

single base exchange

alteration region

CDS

DNA changes

c.103C>T
cDNA.701C>T
g.701C>T

AA changes

H35Y Score: 83 explain score(s)

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

frameshift

known variant

Reference ID: rs77153116

database	homozygous (T/T)	heterozygous	allele carriers
1000G	186	942	1128
ExAC	1925	23436	25361

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.681	0.056
	0.786	0.049
(flanking)	0.681	0.033

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 marginally increased	701	wt: 0.9497 / mu: 0.9528 (marginal change - not scored)	wt: GTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACA mu: GTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACA	tctc\|ATTG
Acc marginally increased	703	wt: 0.9695 / mu: 0.9843 (marginal change - not scored)	wt: CTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGC mu: CTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGC	tcat\|TGTG
Acc marginally increased	705	wt: 0.8996 / mu: 0.9185 (marginal change - not scored)	wt: TACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGCGG mu: TACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGCGG	attg\|TGGA
Acc increased	699	wt: 0.24 / mu: 0.54	wt: GGGTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGA mu: GGGTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGA	tttc\|TCAT
Acc marginally increased	706	wt: 0.9897 / mu: 0.9915 (marginal change - not scored)	wt: ACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGCGGT mu: ACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGCGGT	ttgt\|GGAA
Acc marginally increased	704	wt: 0.9663 / mu: 0.9787 (marginal change - not scored)	wt: TTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACAGCG mu: TTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACAGCG	catt\|GTGG
Acc marginally increased	691	wt: 0.6510 / mu: 0.6799 (marginal change - not scored)	wt: CACTCTCTGGGTCTTACCCTTGGCTTTTCTCATTGTGGAAA mu: CACTCTCTGGGTCTTACCCTTGGCTTTTCTTATTGTGGAAA	cctt\|GGCT
Acc marginally increased	700	wt: 0.9401 / mu: 0.9412 (marginal change - not scored)	wt: GGTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGAC mu: GGTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGAC	ttct\|CATT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000019677

n/a

Fcatus

all identical

ENSFCAG00000010760

435

Mmusculus

no alignment

ENSMUSG00000071909

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
206	213	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
353	442	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2421 / 2421

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

807 / 807

position of stopcodon in wt / mu cDNA

3019 / 3019

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

599 / 599

chromosome

strand

last intron/exon boundary

2234

theoretical NMD boundary in CDS

1585

length of CDS

2421

coding sequence (CDS) position

103

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

701

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

701

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

89118125

original gDNA sequence snippet

GTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACA

altered gDNA sequence snippet

GTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACA

original cDNA sequence snippet

GTCTTACCCTTGGCTTTTCTCATTGTGGAAACTGCCAGACA

altered cDNA sequence snippet

GTCTTACCCTTGGCTTTTCTTATTGTGGAAACTGCCAGACA

wildtype AA sequence

MFQEPVYFQI FLFQLDSGAS GEPGHSLGLT LGFSHCGNCQ TAVVSAQPEG MASNGAYPAL
GPGVTANPGT SLSVFTALPF TTPAPGPAHG PLLVTAGAPP GGPLVLSNFP STPLVTEQDG
CGPSGAGASN VFVQMRTEVG PVKAAQAQTL VLTQTPLVWQ APGALCGGVV CPPPLLLAAA
PVVPVMAAQV VGGTQACEGG WSQGLPLPPP PPPAAQLPPI VSQGNAGPWP QGAHGEGSLA
SSQAKAPPDD SCNPRSVYEN FRLWQHYKPL ARRHLPQSPD TEALSCFLIP VLRSLARRKP
TMTLEEGLWR AMREWQHTSN FDRMIFYEMA EKFLEFEAEE EMQIQKSQWM KGPQCLPPPA
TPRLEPRGPP APEVVKQPVY LPSKAGPKAP TACLPPPRPQ RPVTKARRPP PRPHRRAETK
ARLPPPRPQR PAETKVPEEI PPEVVQEYVD IMEELLGPSL GATGEPEKQR EEGEVKQPQE
EDWTPPDPGL LSYTDKLCSQ KDFVTKVEAV IHPQFLEELL SPDPQMDFLA LSQELEQEEG
LTLAQLVEKR LLPLKEKQHA RAAPSRGTAR LDSSSSKFAA GQGAERDVPD PQQGVGMETC
PPQTTARDSQ GRGRAHTGMA RSKDSVVLLG CQDSPGLRAA RPTSPPQDHR PTCPGVGTKD
ALDLPGGSPV RESHGLAQGS SEEEELPSLA FLLGSQHKLL PWWLPQSPVP ASGLLSPEKW
GPQGTHQSPS AERRGLNLAP SPANKAKKRP LFGSLSPAEK TPHPGPGLRV SGEQSLTWGL
GGPSQSQKRK GDPLVSRKEK KQRCSQ*

mutated AA sequence

MFQEPVYFQI FLFQLDSGAS GEPGHSLGLT LGFSYCGNCQ TAVVSAQPEG MASNGAYPAL
GPGVTANPGT SLSVFTALPF TTPAPGPAHG PLLVTAGAPP GGPLVLSNFP STPLVTEQDG
CGPSGAGASN VFVQMRTEVG PVKAAQAQTL VLTQTPLVWQ APGALCGGVV CPPPLLLAAA
PVVPVMAAQV VGGTQACEGG WSQGLPLPPP PPPAAQLPPI VSQGNAGPWP QGAHGEGSLA
SSQAKAPPDD SCNPRSVYEN FRLWQHYKPL ARRHLPQSPD TEALSCFLIP VLRSLARRKP
TMTLEEGLWR AMREWQHTSN FDRMIFYEMA EKFLEFEAEE EMQIQKSQWM KGPQCLPPPA
TPRLEPRGPP APEVVKQPVY LPSKAGPKAP TACLPPPRPQ RPVTKARRPP PRPHRRAETK
ARLPPPRPQR PAETKVPEEI PPEVVQEYVD IMEELLGPSL GATGEPEKQR EEGEVKQPQE
EDWTPPDPGL LSYTDKLCSQ KDFVTKVEAV IHPQFLEELL SPDPQMDFLA LSQELEQEEG
LTLAQLVEKR LLPLKEKQHA RAAPSRGTAR LDSSSSKFAA GQGAERDVPD PQQGVGMETC
PPQTTARDSQ GRGRAHTGMA RSKDSVVLLG CQDSPGLRAA RPTSPPQDHR PTCPGVGTKD
ALDLPGGSPV RESHGLAQGS SEEEELPSLA FLLGSQHKLL PWWLPQSPVP ASGLLSPEKW
GPQGTHQSPS AERRGLNLAP SPANKAKKRP LFGSLSPAEK TPHPGPGLRV SGEQSLTWGL
GGPSQSQKRK GDPLVSRKEK KQRCSQ*

speed

1.05 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems