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: ENST00000343060
Querying Taster for transcript #2: ENST00000355633
MT speed 0 s - this script 3.127997 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HOXA1	polymorphism_automatic	7.2645381044012e-08	simple_aae				R73H	single base exchange	rs10951154		show file
HOXA1	polymorphism_automatic	1.52894904958956e-07	simple_aae				R73H	single base exchange	rs10951154		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999927354619 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM005531)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:27135314C>TN/A show variant in all transcripts IGV

HGNC symbol

HOXA1

Ensembl transcript ID

ENST00000343060

Genbank transcript ID

NM_005522

UniProt peptide

P49639

alteration type

single base exchange

alteration region

CDS

DNA changes

c.218G>A
cDNA.280G>A
g.302G>A

AA changes

R73H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs10951154

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1656	598	2254
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM005531)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.31	0.932
	0.292	0.952
(flanking)	1.013	0.978

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

280

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000019010

Mmulatta

not conserved

ENSMMUG00000012807

Fcatus

not conserved

ENSFCAG00000007937

Mmusculus

not conserved

ENSMUSG00000029844

Ggallus

no alignment

ENSGALG00000011053

n/a

Trubripes

not conserved

ENSTRUG00000015937

Drerio

not conserved

ENSDARG00000057721

Dmelanogaster

no alignment

FBgn0002522

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000000715

protein features

start (aa)	end (aa)	feature	details
65	74	COMPBIAS	Poly-His.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1008 / 1008

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

336 / 336

position of stopcodon in wt / mu cDNA

1070 / 1070

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

63 / 63

chromosome

strand

-1

last intron/exon boundary

715

theoretical NMD boundary in CDS

602

length of CDS

1008

coding sequence (CDS) position

218

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

280

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

302

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

27135314

original gDNA sequence snippet

CCACCACCACCACCACCATCGCCACCCCCAGCCGGCTACCT

altered gDNA sequence snippet

CCACCACCACCACCACCATCACCACCCCCAGCCGGCTACCT

original cDNA sequence snippet

CCACCACCACCACCACCATCGCCACCCCCAGCCGGCTACCT

altered cDNA sequence snippet

CCACCACCACCACCACCATCACCACCCCCAGCCGGCTACCT

wildtype AA sequence

MDNARMNSFL EYPILSSGDS GTCSARAYPS DHRITTFQSC AVSANSCGGD DRFLVGRGVQ
IGSPHHHHHH HHRHPQPATY QTSGNLGVSY SHSSCGPSYG SQNFSAPYSP YALNQEADVS
GGYPQCAPAV YSGNLSSPMV QHHHHHQGYA GGAVGSPQYI HHSYGQEHQS LALATYNNSL
SPLHASHQEA CRSPASETSS PAQTFDWMKV KRNPPKTGKV GEYGYLGQPN AVRTNFTTKQ
LTELEKEFHF NKYLTRARRV EIAASLQLNE TQVKIWFQNR RMKQKKREKE GLLPISPATP
PGNDEKAEES SEKSSSSPCV PSPGSSTSDT LTTSH*

mutated AA sequence

MDNARMNSFL EYPILSSGDS GTCSARAYPS DHRITTFQSC AVSANSCGGD DRFLVGRGVQ
IGSPHHHHHH HHHHPQPATY QTSGNLGVSY SHSSCGPSYG SQNFSAPYSP YALNQEADVS
GGYPQCAPAV YSGNLSSPMV QHHHHHQGYA GGAVGSPQYI HHSYGQEHQS LALATYNNSL
SPLHASHQEA CRSPASETSS PAQTFDWMKV KRNPPKTGKV GEYGYLGQPN AVRTNFTTKQ
LTELEKEFHF NKYLTRARRV EIAASLQLNE TQVKIWFQNR RMKQKKREKE GLLPISPATP
PGNDEKAEES SEKSSSSPCV PSPGSSTSDT LTTSH*

speed

0.59 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: 0.999999847105095 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM005531)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:27135314C>TN/A show variant in all transcripts IGV

HGNC symbol

HOXA1

Ensembl transcript ID

ENST00000355633

Genbank transcript ID

NM_153620

UniProt peptide

P49639

alteration type

single base exchange

alteration region

CDS

DNA changes

c.218G>A
cDNA.302G>A
g.302G>A

AA changes

R73H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs10951154

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1656	598	2254
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM005531)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.31	0.932
	0.292	0.952
(flanking)	1.013	0.978

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

137

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000019010

Mmulatta

not conserved

ENSMMUG00000012807

Fcatus

not conserved

ENSFCAG00000007937

Mmusculus

not conserved

ENSMUSG00000029844

Ggallus

no alignment

ENSGALG00000011053

n/a

Trubripes

not conserved

ENSTRUG00000015937

Drerio

not conserved

ENSDARG00000057721

Dmelanogaster

not conserved

FBgn0002522

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000000715

protein features

start (aa)	end (aa)	feature	details
65	74	COMPBIAS	Poly-His.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

414 / 414

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

138 / 138

position of stopcodon in wt / mu cDNA

498 / 498

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

85 / 85

chromosome

strand

-1

last intron/exon boundary

534

theoretical NMD boundary in CDS

399

length of CDS

414

coding sequence (CDS) position

218

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

302

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

302

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

27135314

original gDNA sequence snippet

CCACCACCACCACCACCATCGCCACCCCCAGCCGGCTACCT

altered gDNA sequence snippet

CCACCACCACCACCACCATCACCACCCCCAGCCGGCTACCT

original cDNA sequence snippet

CCACCACCACCACCACCATCGCCACCCCCAGCCGGCTACCT

altered cDNA sequence snippet

CCACCACCACCACCACCATCACCACCCCCAGCCGGCTACCT

wildtype AA sequence

MDNARMNSFL EYPILSSGDS GTCSARAYPS DHRITTFQSC AVSANSCGGD DRFLVGRGVQ
IGSPHHHHHH HHRHPQPATY QTSGNLGVSY SHSSCGPSYG SQNFSAPYSP YALNQEADPP
RSLSLPRIGD IFSSADF*

mutated AA sequence

MDNARMNSFL EYPILSSGDS GTCSARAYPS DHRITTFQSC AVSANSCGGD DRFLVGRGVQ
IGSPHHHHHH HHHHPQPATY QTSGNLGVSY SHSSCGPSYG SQNFSAPYSP YALNQEADPP
RSLSLPRIGD IFSSADF*

speed

0.60 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems