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: ENST00000409155
Querying Taster for transcript #2: ENST00000277315
MT speed 0 s - this script 3.719764 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALAD	disease_causing	0.999999997295375	simple_aae				R240W	single base exchange	rs121912982		show file
ALAD	disease_causing	0.999999999859092	simple_aae				R223W	single base exchange	rs121912982		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999997295375 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM920013)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:116151801G>AN/A show variant in all transcripts IGV

HGNC symbol

ALAD

Ensembl transcript ID

ENST00000409155

Genbank transcript ID

NM_000031

UniProt peptide

P13716

alteration type

single base exchange

alteration region

CDS

DNA changes

c.718C>T
cDNA.915C>T
g.11813C>T

AA changes

R240W Score: 101 explain score(s)

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

240

frameshift

known variant

Reference ID: rs121912982

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation at this position, please check HGMD for details (HGMD ID CM920013)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920013)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920013)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.746	1
	3.468	1
(flanking)	0.211	0.999

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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

240

mutated

not conserved

240

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000031965

269

Fcatus

all identical

ENSFCAG00000009244

256

Mmusculus

all identical

ENSMUSG00000028393

240

Ggallus

all identical

ENSGALG00000008869

247

Trubripes

all identical

ENSTRUG00000010590

249

Drerio

all identical

ENSDARG00000052815

242

Dmelanogaster

all identical

FBgn0036271

237

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000023474

186

protein features

start (aa)	end (aa)	feature	details
231	243	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

993 / 993

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

331 / 331

position of stopcodon in wt / mu cDNA

1190 / 1190

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

198 / 198

chromosome

strand

-1

last intron/exon boundary

1129

theoretical NMD boundary in CDS

881

length of CDS

993

coding sequence (CDS) position

718

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

915

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

11813

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

116151801

original gDNA sequence snippet

ATACCCTCATCCCTTAGGACCGGGATGTACGGGAAGGAGCT

altered gDNA sequence snippet

ATACCCTCATCCCTTAGGACTGGGATGTACGGGAAGGAGCT

original cDNA sequence snippet

TGGCTCTCCGAGCTGTGGACCGGGATGTACGGGAAGGAGCT

altered cDNA sequence snippet

TGGCTCTCCGAGCTGTGGACTGGGATGTACGGGAAGGAGCT

wildtype AA sequence

MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTDV PDDIQPITSL PGVARYGVKR
LEEMLRPLVE EGLRCVLIFG VPSRVPKDER GSAADSEESP AIEAIHLLRK TFPNLLVACD
VCLCPYTSHG HCGLLSENGA FRAEESRQRL AEVALAYAKA GCQVVAPSDM MDGRVEAIKE
ALMAHGLGNR VSVMSYSAKF ASCFYGPFRD AAKSSPAFGD RRCYQLPPGA RGLALRAVDR
DVREGADMLM VKPGMPYLDI VREVKDKHPD LPLAVYHVSG EFAMLWHGAQ AGAFDLKAAV
LEAMTAFRRA GADIIITYYT PQLLQWLKEE *

mutated AA sequence

MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTDV PDDIQPITSL PGVARYGVKR
LEEMLRPLVE EGLRCVLIFG VPSRVPKDER GSAADSEESP AIEAIHLLRK TFPNLLVACD
VCLCPYTSHG HCGLLSENGA FRAEESRQRL AEVALAYAKA GCQVVAPSDM MDGRVEAIKE
ALMAHGLGNR VSVMSYSAKF ASCFYGPFRD AAKSSPAFGD RRCYQLPPGA RGLALRAVDW
DVREGADMLM VKPGMPYLDI VREVKDKHPD LPLAVYHVSG EFAMLWHGAQ AGAFDLKAAV
LEAMTAFRRA GADIIITYYT PQLLQWLKEE *

speed

0.75 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

disease causing

Model: simple_aae, prob: 0.999999999859092 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM920013)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:116151801G>AN/A show variant in all transcripts IGV

HGNC symbol

ALAD

Ensembl transcript ID

ENST00000277315

Genbank transcript ID

N/A

UniProt peptide

P13716

alteration type

single base exchange

alteration region

CDS

DNA changes

c.667C>T
cDNA.929C>T
g.11813C>T

AA changes

R223W Score: 101 explain score(s)

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

223

frameshift

known variant

Reference ID: rs121912982

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.746	1
	3.468	1
(flanking)	0.211	0.999

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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

223

mutated

not conserved

223

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000031965

269

Fcatus

all identical

ENSFCAG00000009244

256

Mmusculus

all identical

ENSMUSG00000028393

240

Ggallus

all identical

ENSGALG00000008869

247

Trubripes

all identical

ENSTRUG00000010590

249

Drerio

all identical

ENSDARG00000052815

242

Dmelanogaster

all identical

FBgn0036271

237

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000023474

186

protein features

start (aa)	end (aa)	feature	details
221	223	HELIX		lost
223	223	METAL	Zinc 2.	lost
223	223	MUTAGEN	C->A: No effect on catalytic activity; when associated with A-131.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

942 / 942

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

314 / 314

position of stopcodon in wt / mu cDNA

1204 / 1204

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

263 / 263

chromosome

strand

-1

last intron/exon boundary

1143

theoretical NMD boundary in CDS

830

length of CDS

942

coding sequence (CDS) position

667

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

929

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

11813

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

116151801

original gDNA sequence snippet

ATACCCTCATCCCTTAGGACCGGGATGTACGGGAAGGAGCT

altered gDNA sequence snippet

ATACCCTCATCCCTTAGGACTGGGATGTACGGGAAGGAGCT

original cDNA sequence snippet

TGGCTCTCCGAGCTGTGGACCGGGATGTACGGGAAGGAGCT

altered cDNA sequence snippet

TGGCTCTCCGAGCTGTGGACTGGGATGTACGGGAAGGAGCT

wildtype AA sequence

MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL
IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCGLLSE
NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS
AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDRDVREGAD MLMVKPGMPY
LDIVREVKDK HPDLPLAVYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT
YYTPQLLQWL KEE*

mutated AA sequence

MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL
IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCGLLSE
NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS
AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDWDVREGAD MLMVKPGMPY
LDIVREVKDK HPDLPLAVYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT
YYTPQLLQWL KEE*

speed

1.03 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems