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: ENST00000229335
Querying Taster for transcript #2: ENST00000537228
MT speed 0 s - this script 2.541823 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AICDA	disease_causing_automatic	0.999998635640785	simple_aae		affected	0	M139V	single base exchange	rs104894322		show file
AICDA	disease_causing_automatic	0.999999911347528	simple_aae		affected	0	M139V	single base exchange	rs104894322		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998635640785 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002425)
known disease mutation: rs5126 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:8757823T>CN/A show variant in all transcripts IGV

HGNC symbol

AICDA

Ensembl transcript ID

ENST00000537228

Genbank transcript ID

N/A

UniProt peptide

Q9GZX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.415A>G
cDNA.515A>G
g.7645A>G

AA changes

M139V Score: 21 explain score(s)

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

139

frameshift

known variant

Reference ID: rs104894322
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5126 (pathogenic for Hyper-IgM syndrome type 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002425)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002425)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002425)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.454	1
	4.454	1
(flanking)	2.744	1

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	7638	wt: 0.5849 / mu: 0.5938 (marginal change - not scored)	wt: CAAATAGCCATCATG mu: CAAATAGCCATCGTG	AATA\|gcca
Donor gained	7644	0.69	mu: GCCATCGTGACCTTC	CATC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

139

mutated

all conserved

139

Ptroglodytes

all identical

ENSPTRG00000004640

139

KDYFYCWNTFV

Mmulatta

all identical

ENSMMUG00000019134

138

KDYFYCWNTFV

Fcatus

all identical

ENSFCAG00000006052

KXXXXXXXXXX

Mmusculus

all identical

ENSMUSG00000040627

139

KDYFYCWNTFV

Ggallus

all identical

ENSGALG00000014280

139

KDFFYCWNTFV

Trubripes

all identical

ENSTRUG00000007079

152

YFYCWQKFVDC

Drerio

all identical

ENSDARG00000015734

151

DFFYCWQTFVA

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000023905

142

MSYKDYFYCWN

protein features

start (aa)	end (aa)	feature	details
183	198	REGION	Nuclear export signal.	might get lost (downstream of altered splice site)
193	193	MUTAGEN	F->A: Completely abolishes nuclear import; when associated with W-24 or D- 112. Little affect on nuclear import; when associated with A-10. Greatly impaired nuclear import; when associated with K-20 or G-50. Almost completely abolishes nuclear import; when associated with S-18 and V-19.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

567 / 567

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

189 / 189

position of stopcodon in wt / mu cDNA

667 / 667

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

101 / 101

chromosome

strand

-1

last intron/exon boundary

614

theoretical NMD boundary in CDS

463

length of CDS

567

coding sequence (CDS) position

415

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

515

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

7645

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

8757823

original gDNA sequence snippet

CCGGGGTGCAAATAGCCATCATGACCTTCAAAGGTGCGAAA

altered gDNA sequence snippet

CCGGGGTGCAAATAGCCATCGTGACCTTCAAAGGTGCGAAA

original cDNA sequence snippet

CCGGGGTGCAAATAGCCATCATGACCTTCAAAGAAAACCAC

altered cDNA sequence snippet

CCGGGGTGCAAATAGCCATCGTGACCTTCAAAGAAAACCAC

wildtype AA sequence

MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKENHERTFK AWEGLHENSV RLSRQLRRIL LPLYEVDDLR
DAFRTLGL*

mutated AA sequence

MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIVT FKENHERTFK AWEGLHENSV RLSRQLRRIL LPLYEVDDLR
DAFRTLGL*

speed

0.31 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: 0.999999911347528 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002425)
known disease mutation: rs5126 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:8757823T>CN/A show variant in all transcripts IGV

HGNC symbol

AICDA

Ensembl transcript ID

ENST00000229335

Genbank transcript ID

NM_020661

UniProt peptide

Q9GZX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.415A>G
cDNA.519A>G
g.7645A>G

AA changes

M139V Score: 21 explain score(s)

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

139

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.454	1
	4.454	1
(flanking)	2.744	1

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	7638	wt: 0.5849 / mu: 0.5938 (marginal change - not scored)	wt: CAAATAGCCATCATG mu: CAAATAGCCATCGTG	AATA\|gcca
Donor gained	7644	0.69	mu: GCCATCGTGACCTTC	CATC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

139

mutated

all conserved

139

Ptroglodytes

all identical

ENSPTRG00000004640

139

Mmulatta

all identical

ENSMMUG00000019134

138

Fcatus

all identical

ENSFCAG00000006052

Mmusculus

all identical

ENSMUSG00000040627

139

Ggallus

all identical

ENSGALG00000014280

139

Trubripes

all identical

ENSTRUG00000007079

152

Drerio

all identical

ENSDARG00000015734

151

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000023905

142

protein features

start (aa)	end (aa)	feature	details
183	198	REGION	Nuclear export signal.	might get lost (downstream of altered splice site)
193	193	MUTAGEN	F->A: Completely abolishes nuclear import; when associated with W-24 or D- 112. Little affect on nuclear import; when associated with A-10. Greatly impaired nuclear import; when associated with K-20 or G-50. Almost completely abolishes nuclear import; when associated with S-18 and V-19.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

597 / 597

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

199 / 199

position of stopcodon in wt / mu cDNA

701 / 701

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

105 / 105

chromosome

strand

-1

last intron/exon boundary

648

theoretical NMD boundary in CDS

493

length of CDS

597

coding sequence (CDS) position

415

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

519

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

7645

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

8757823

original gDNA sequence snippet

CCGGGGTGCAAATAGCCATCATGACCTTCAAAGGTGCGAAA

altered gDNA sequence snippet

CCGGGGTGCAAATAGCCATCGTGACCTTCAAAGGTGCGAAA

original cDNA sequence snippet

CCGGGGTGCAAATAGCCATCATGACCTTCAAAGATTATTTT

altered cDNA sequence snippet

CCGGGGTGCAAATAGCCATCGTGACCTTCAAAGATTATTTT

wildtype AA sequence

MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL
LPLYEVDDLR DAFRTLGL*

mutated AA sequence

MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIVT FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL
LPLYEVDDLR DAFRTLGL*

speed

0.29 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems