MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
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 3.949456 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADA	disease_causing_automatic	0.999999985627252	simple_aae		affected	0	R211H	single base exchange	rs121908716		show file
PKIG	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121908716		show file
PKIG	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121908716		show file
ADA	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121908716		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999985627252 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM880002)
known disease mutation: rs1957 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251694C>TN/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.632G>A
cDNA.767G>A
g.29181G>A

AA changes

R211H Score: 29 explain score(s)

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

211

frameshift

known variant

Reference ID: rs121908716

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	8	8

known disease mutation: rs1957 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM880002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM880002)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.754	1
	3.516	1
(flanking)	2.295	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 gained	29186	0.37	mu: ATACTGTCCACGCCG	ACTG\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

211

mutated

not conserved

211

Ptroglodytes

all identical

ENSPTRG00000013524

211

Mmulatta

all identical

ENSMMUG00000010603

211

Fcatus

all identical

ENSFCAG00000002474

244

Mmusculus

all identical

ENSMUSG00000017697

211

Ggallus

all identical

ENSGALG00000004170

212

Trubripes

all identical

ENSTRUG00000010199

215

Drerio

all identical

ENSDARG00000003113

214

Dmelanogaster

no homologue

Celegans

all identical

C06G3.5

244

Xtropicalis

all identical

ENSXETG00000003459

208

protein features

start (aa)	end (aa)	feature	details
210	219	STRAND		lost
214	214	METAL	Zinc; catalytic.	might get lost (downstream of altered splice site)
217	217	ACT_SITE	Proton donor (Probable).	might get lost (downstream of altered splice site)
221	229	HELIX		might get lost (downstream of altered splice site)
232	232	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
234	238	STRAND		might get lost (downstream of altered splice site)
238	238	SITE	Important for catalytic activity (By similarity).	might get lost (downstream of altered splice site)
240	244	HELIX		might get lost (downstream of altered splice site)
246	254	HELIX		might get lost (downstream of altered splice site)
258	261	STRAND		might get lost (downstream of altered splice site)
263	268	HELIX		might get lost (downstream of altered splice site)
270	272	STRAND		might get lost (downstream of altered splice site)
279	285	HELIX		might get lost (downstream of altered splice site)
290	292	STRAND		might get lost (downstream of altered splice site)
295	295	METAL	Zinc; catalytic.	might get lost (downstream of altered splice site)
296	296	BINDING	Substrate.	might get lost (downstream of altered splice site)
297	300	HELIX		might get lost (downstream of altered splice site)
304	315	HELIX		might get lost (downstream of altered splice site)
319	331	HELIX		might get lost (downstream of altered splice site)
333	335	STRAND		might get lost (downstream of altered splice site)
337	351	HELIX		might get lost (downstream of altered splice site)
340	340	CONFLICT	K -> R (in Ref. 5; BAD97117).	might get lost (downstream of altered splice site)
355	362	HELIX		might get lost (downstream of altered splice site)

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

632

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

767

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

29181

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

43251694

original gDNA sequence snippet

TGTGAAGAGCGGCATTCACCGTACTGTCCACGCCGGGGAGG

altered gDNA sequence snippet

TGTGAAGAGCGGCATTCACCATACTGTCCACGCCGGGGAGG

original cDNA sequence snippet

TGTGAAGAGCGGCATTCACCGTACTGTCCACGCCGGGGAGG

altered cDNA sequence snippet

TGTGAAGAGCGGCATTCACCATACTGTCCACGCCGGGGAGG

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 HTVHAGEVGS AEVVKEAVDI LKTERLGHGY
HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF
KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG
QNL*

speed

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

Summary

known disease mutation at this position (HGMD CM880002)
known disease mutation: rs1957 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251694C>TN/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.91269C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121908716

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	8	8

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.754	1
	3.516	1
(flanking)	2.295	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	91260	wt: 0.64 / mu: 0.72	wt: CCGAGCCCACCTCCCCGGCGTGGACAGTACGGTGAATGCCG mu: CCGAGCCCACCTCCCCGGCGTGGACAGTATGGTGAATGCCG	gcgt\|GGAC
Donor increased	91265	wt: 0.52 / mu: 0.76	wt: TGGACAGTACGGTGA mu: TGGACAGTATGGTGA	GACA\|gtac

distance from splice site

880

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)

91269

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

43251694

original gDNA sequence snippet

CCTCCCCGGCGTGGACAGTACGGTGAATGCCGCTCTTCACA

altered gDNA sequence snippet

CCTCCCCGGCGTGGACAGTATGGTGAATGCCGCTCTTCACA

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

0.72 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 CM880002)
known disease mutation: rs1957 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251694C>TN/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.91269C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121908716

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	8	8

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.754	1
	3.516	1
(flanking)	2.295	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	91260	wt: 0.64 / mu: 0.72	wt: CCGAGCCCACCTCCCCGGCGTGGACAGTACGGTGAATGCCG mu: CCGAGCCCACCTCCCCGGCGTGGACAGTATGGTGAATGCCG	gcgt\|GGAC
Donor increased	91265	wt: 0.52 / mu: 0.76	wt: TGGACAGTACGGTGA mu: TGGACAGTATGGTGA	GACA\|gtac

distance from splice site

880

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)

91269

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

43251694

original gDNA sequence snippet

CCTCCCCGGCGTGGACAGTACGGTGAATGCCGCTCTTCACA

altered gDNA sequence snippet

CCTCCCCGGCGTGGACAGTATGGTGAATGCCGCTCTTCACA

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

0.66 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 CM880002)
known disease mutation: rs1957 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43251694C>TN/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

intron

DNA changes

g.29181G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121908716

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	8	8

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.754	1
	3.516	1
(flanking)	2.295	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 gained	29186	0.37	mu: ATACTGTCCACGCCG	ACTG\|tcca

distance from splice site

123

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
195	207	HELIX		might get lost (downstream of altered splice site)
210	219	STRAND		might get lost (downstream of altered splice site)
214	214	METAL	Zinc; catalytic.	might get lost (downstream of altered splice site)
217	217	ACT_SITE	Proton donor (Probable).	might get lost (downstream of altered splice site)
221	229	HELIX		might get lost (downstream of altered splice site)
232	232	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
234	238	STRAND		might get lost (downstream of altered splice site)
238	238	SITE	Important for catalytic activity (By similarity).	might get lost (downstream of altered splice site)
240	244	HELIX		might get lost (downstream of altered splice site)
246	254	HELIX		might get lost (downstream of altered splice site)
258	261	STRAND		might get lost (downstream of altered splice site)
263	268	HELIX		might get lost (downstream of altered splice site)
270	272	STRAND		might get lost (downstream of altered splice site)
279	285	HELIX		might get lost (downstream of altered splice site)
290	292	STRAND		might get lost (downstream of altered splice site)
295	295	METAL	Zinc; catalytic.	might get lost (downstream of altered splice site)
296	296	BINDING	Substrate.	might get lost (downstream of altered splice site)
297	300	HELIX		might get lost (downstream of altered splice site)
304	315	HELIX		might get lost (downstream of altered splice site)
319	331	HELIX		might get lost (downstream of altered splice site)
333	335	STRAND		might get lost (downstream of altered splice site)
337	351	HELIX		might get lost (downstream of altered splice site)
340	340	CONFLICT	K -> R (in Ref. 5; BAD97117).	might get lost (downstream of altered splice site)
355	362	HELIX		might get lost (downstream of altered splice site)

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

85 / 85

chromosome

strand

-1

last intron/exon boundary

1091

theoretical NMD boundary in CDS

956

length of CDS

1020

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)

29181

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

43251694

original gDNA sequence snippet

TGTGAAGAGCGGCATTCACCGTACTGTCCACGCCGGGGAGG

altered gDNA sequence snippet

TGTGAAGAGCGGCATTCACCATACTGTCCACGCCGGGGAGG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

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

N/A

speed

0.58 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