MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000372887
Querying Taster for transcript #2: ENST00000372882
Querying Taster for transcript #3: ENST00000372874
Querying Taster for transcript #4: ENST00000537820
MT speed 0 s - this script 3.658883 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADA	disease_causing_automatic	0.998611979645496	simple_aae			0	T233I	single base exchange	rs121908729		show file
ADA	disease_causing_automatic	0.998611979645496	simple_aae			0	T209I	single base exchange	rs121908729		show file
PKIG	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121908729		show file
PKIG	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121908729		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998611979645496 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970060)
known disease mutation: rs1980 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251552G>AN/A show variant in all transcripts IGV

HGNC symbol

ADA

Ensembl transcript ID

ENST00000372874

Genbank transcript ID

NM_000022

UniProt peptide

P00813

alteration type

single base exchange

alteration region

CDS

DNA changes

c.698C>T
cDNA.833C>T
g.29323C>T

AA changes

T233I Score: 89 explain score(s)

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

233

frameshift

known variant

Reference ID: rs121908729
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs1980 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970060)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970060)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.284	0.02
	5.468	1
(flanking)	1.944	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	29321	wt: 0.9040 / mu: 0.9056 (marginal change - not scored)	wt: CTCAAGACAGAGCGG mu: CTCAAGATAGAGCGG	CAAG\|acag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

233

mutated

not conserved

233

Ptroglodytes

all identical

ENSPTRG00000013524

233

Mmulatta

all identical

ENSMMUG00000010603

233

Fcatus

all identical

ENSFCAG00000002474

266

Mmusculus

all identical

ENSMUSG00000017697

233

Ggallus

not conserved

ENSGALG00000004170

234

Trubripes

not conserved

ENSTRUG00000010199

237

Drerio

not conserved

ENSDARG00000003113

236

Dmelanogaster

no homologue

Celegans

not conserved

C06G3.5

266

Xtropicalis

not conserved

ENSXETG00000003459

230

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1092 / 1092

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

364 / 364

position of stopcodon in wt / mu cDNA

1227 / 1227

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

136 / 136

chromosome

strand

-1

last intron/exon boundary

1214

theoretical NMD boundary in CDS

1028

length of CDS

1092

coding sequence (CDS) position

698

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

833

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

29323

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

43251552

original gDNA sequence snippet

GGCTGTGGACATACTCAAGACAGAGCGGCTGGGACACGGCT

altered gDNA sequence snippet

GGCTGTGGACATACTCAAGATAGAGCGGCTGGGACACGGCT

original cDNA sequence snippet

GGCTGTGGACATACTCAAGACAGAGCGGCTGGGACACGGCT

altered cDNA sequence snippet

GGCTGTGGACATACTCAAGATAGAGCGGCTGGGACACGGCT

wildtype AA sequence

MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*

mutated AA sequence

MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKIERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*

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

disease causing

Model: simple_aae, prob: 0.998611979645496 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970060)
known disease mutation: rs1980 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251552G>AN/A show variant in all transcripts IGV

HGNC symbol

ADA

Ensembl transcript ID

ENST00000537820

Genbank transcript ID

N/A

UniProt peptide

P00813

alteration type

single base exchange

alteration region

CDS

DNA changes

c.626C>T
cDNA.710C>T
g.29323C>T

AA changes

T209I Score: 89 explain score(s)

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

209

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.284	0.02
	5.468	1
(flanking)	1.944	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	29321	wt: 0.9040 / mu: 0.9056 (marginal change - not scored)	wt: CTCAAGACAGAGCGG mu: CTCAAGATAGAGCGG	CAAG\|acag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

209

mutated

not conserved

209

Ptroglodytes

all identical

ENSPTRG00000013524

209

QEAVKSGIHRTVHAGEVGSAEVVKE

Mmulatta

all identical

ENSMMUG00000010603

209

QEAVKSGIHRTVHAGEVGSAEVVKE

Fcatus

all identical

ENSFCAG00000002474

242

YEEAVRSGIHRTVHAGEVGSAEVVR

Mmusculus

all identical

ENSMUSG00000017697

209

YEGAVKNGIHRTVHAGEVGSPEVVR

Ggallus

not conserved

ENSGALG00000004170

210

YEEAERCGIHRTVHAGEAGPATMIK

Trubripes

not conserved

ENSTRUG00000010199

213

YEEAARCGVHRTVHAGEVGPPSVVK

Drerio

not conserved

ENSDARG00000003113

212

FEEAVRSNVHRTVHAGEVGPASVVR

Dmelanogaster

no homologue

Celegans

not conserved

C06G3.5

242

QEAHKRGIHRTVHAGESGGPKEVIK

Xtropicalis

not conserved

ENSXETG00000003459

206

YEEAVKCGIHRTVHAGEVGPSSVVK

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1020 / 1020

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

340 / 340

position of stopcodon in wt / mu cDNA

1104 / 1104

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

1091

theoretical NMD boundary in CDS

956

length of CDS

1020

coding sequence (CDS) position

626

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

710

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

29323

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

43251552

original gDNA sequence snippet

GGCTGTGGACATACTCAAGACAGAGCGGCTGGGACACGGCT

altered gDNA sequence snippet

GGCTGTGGACATACTCAAGATAGAGCGGCTGGGACACGGCT

original cDNA sequence snippet

GGCTGTGGACATACTCAAGACAGAGCGGCTGGGACACGGCT

altered cDNA sequence snippet

GGCTGTGGACATACTCAAGATAGAGCGGCTGGGACACGGCT

wildtype AA sequence

MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*

mutated AA sequence

MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKIE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*

speed

0.58 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM970060)
known disease mutation: rs1980 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251552G>AN/A show variant in all transcripts IGV

HGNC symbol

PKIG

Ensembl transcript ID

ENST00000372882

Genbank transcript ID

N/A

UniProt peptide

Q9Y2B9

alteration type

single base exchange

alteration region

intron

DNA changes

g.91127G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.284	0.02
	5.468	1
(flanking)	1.944	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
Acc increased	91130	wt: 0.65 / mu: 0.74	wt: CGTGTCCCAGCCGCTCTGTCTTGAGTATGTCCACAGCCTGT mu: CGTGTCCCAGCCGCTCTATCTTGAGTATGTCCACAGCCTGT	gtct\|TGAG
Donor increased	91132	wt: 0.26 / mu: 0.51	wt: GTCTTGAGTATGTCC mu: ATCTTGAGTATGTCC	CTTG\|agta
Donor marginally increased	91128	wt: 0.9169 / mu: 0.9294 (marginal change - not scored)	wt: CTCTGTCTTGAGTAT mu: CTCTATCTTGAGTAT	CTGT\|cttg
Donor increased	91118	wt: 0.23 / mu: 0.28	wt: GTCCCAGCCGCTCTG mu: GTCCCAGCCGCTCTA	CCCA\|gccg

distance from splice site

1022

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

no protein features affected

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

144 / 144

chromosome

strand

last intron/exon boundary

295

theoretical NMD boundary in CDS

101

length of CDS

195

coding sequence (CDS) position

N/A

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

N/A

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

91127

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

43251552

original gDNA sequence snippet

AGCCGTGTCCCAGCCGCTCTGTCTTGAGTATGTCCACAGCC

altered gDNA sequence snippet

AGCCGTGTCCCAGCCGCTCTATCTTGAGTATGTCCACAGCC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MMEVESSYSD FISCDRTGRR NAVPDIQGDS EAVSVRKLAG DMGELALEGA EMDLTMLPWL
VSNS*

mutated AA sequence

N/A

speed

0.43 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM970060)
known disease mutation: rs1980 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251552G>AN/A show variant in all transcripts IGV

HGNC symbol

PKIG

Ensembl transcript ID

ENST00000372887

Genbank transcript ID

N/A

UniProt peptide

Q9Y2B9

alteration type

single base exchange

alteration region

intron

DNA changes

g.91127G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.284	0.02
	5.468	1
(flanking)	1.944	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
Acc increased	91130	wt: 0.65 / mu: 0.74	wt: CGTGTCCCAGCCGCTCTGTCTTGAGTATGTCCACAGCCTGT mu: CGTGTCCCAGCCGCTCTATCTTGAGTATGTCCACAGCCTGT	gtct\|TGAG
Donor increased	91132	wt: 0.26 / mu: 0.51	wt: GTCTTGAGTATGTCC mu: ATCTTGAGTATGTCC	CTTG\|agta
Donor marginally increased	91128	wt: 0.9169 / mu: 0.9294 (marginal change - not scored)	wt: CTCTGTCTTGAGTAT mu: CTCTATCTTGAGTAT	CTGT\|cttg
Donor increased	91118	wt: 0.23 / mu: 0.28	wt: GTCCCAGCCGCTCTG mu: GTCCCAGCCGCTCTA	CCCA\|gccg

distance from splice site

1022

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

no protein features affected

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

304 / 304

chromosome

strand

last intron/exon boundary

455

theoretical NMD boundary in CDS

101

length of CDS

195

coding sequence (CDS) position

N/A

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

N/A

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

91127

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

43251552

original gDNA sequence snippet

AGCCGTGTCCCAGCCGCTCTGTCTTGAGTATGTCCACAGCC

altered gDNA sequence snippet

AGCCGTGTCCCAGCCGCTCTATCTTGAGTATGTCCACAGCC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MMEVESSYSD FISCDRTGRR NAVPDIQGDS EAVSVRKLAG DMGELALEGA EMDLTMLPWL
VSNS*

mutated AA sequence

N/A

speed

0.43 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems