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: ENST00000372874
Querying Taster for transcript #2: ENST00000537820
MT speed 0 s - this script 3.686919 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADA	disease_causing	1	simple_aae		affected		G74V	single base exchange	rs199422328		show file
ADA	disease_causing	1	simple_aae		affected		G74V	single base exchange	rs199422328		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 1 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs1977 (probable pathogenic)
known disease mutation at this position (HGMD CM034198)
known disease mutation at this position (HGMD CM962529)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43255238C>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.221G>T
cDNA.356G>T
g.25637G>T

AA changes

G74V Score: 109 explain score(s)

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

frameshift

known variant

Reference ID: rs199422328

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

known as potential disease variant: rs1977 (probable pathogenic for Severe combined immunodeficiency due to ADA deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM962529)

known disease mutation at this position, please check HGMD for details (HGMD ID CM962529)
known disease mutation at this position, please check HGMD for details (HGMD ID CM034198)

known disease mutation at this position, please check HGMD for details (HGMD ID CM962529)
known disease mutation at this position, please check HGMD for details (HGMD ID CM034198)
known disease mutation at this position, please check HGMD for details (HGMD ID CM034198)

known disease mutation at this position, please check HGMD for details (HGMD ID CM962529)
known disease mutation at this position, please check HGMD for details (HGMD ID CM034198)
known disease mutation at this position, please check HGMD for details (HGMD ID CM034198)
known disease mutation at this position, please check HGMD for details (HGMD ID CM962529)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.392	1
	5.458	1
(flanking)	5.458	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	25634.5	sequence motif lost	-	wt: ccca\|GGGG mu: ccca.GGGT
Acc marginally increased	25633	wt: 0.9939 / mu: 0.9941 (marginal change - not scored)	wt: AACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATC mu: AACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATC	ccca\|GGGG
Acc marginally increased	25627	wt: 0.9656 / mu: 0.9666 (marginal change - not scored)	wt: GTTCCCAACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAG mu: GTTCCCAACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAG	tccc\|TTCC
Acc marginally increased	25635	wt: 0.9672 / mu: 0.9825 (marginal change - not scored)	wt: CCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCAA mu: CCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAA	cagg\|GGCT
Acc marginally increased	25628	wt: 0.8912 / mu: 0.8984 (marginal change - not scored)	wt: TTCCCAACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGG mu: TTCCCAACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGG	ccct\|TCCC
Acc marginally increased	25634	wt: 0.9630 / mu: 0.9655 (marginal change - not scored)	wt: ACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCA mu: ACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCA	ccag\|GGGC
Donor increased	25642	wt: 0.44 / mu: 0.79	wt: GCTGCCGGGAGGCTA mu: TCTGCCGGGAGGCTA	TGCC\|ggga
Acc gained	25643	0.31	mu: TTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAAGGATCG	gccg\|GGAG
Acc gained	25639	0.50	mu: TTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAAGG	gtct\|GCCG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000013524

Mmulatta

all identical

ENSMMUG00000010603

Fcatus

all identical

ENSFCAG00000002474

107

Mmusculus

all identical

ENSMUSG00000017697

Ggallus

all identical

ENSGALG00000004170

Trubripes

all identical

ENSTRUG00000010199

Drerio

all identical

ENSDARG00000003113

Dmelanogaster

no homologue

Celegans

all identical

C06G3.5

115

Xtropicalis

all identical

ENSXETG00000003459

protein features

start (aa)	end (aa)	feature	details
76	91	HELIX		might get lost (downstream of altered splice site)
92	94	TURN		might get lost (downstream of altered splice site)
95	102	STRAND		might get lost (downstream of altered splice site)
104	107	HELIX		might get lost (downstream of altered splice site)
109	111	STRAND		might get lost (downstream of altered splice site)
116	118	HELIX		might get lost (downstream of altered splice site)
126	144	HELIX		might get lost (downstream of altered splice site)
147	155	STRAND		might get lost (downstream of altered splice site)
159	161	HELIX		might get lost (downstream of altered splice site)
162	171	HELIX		might get lost (downstream of altered splice site)
172	176	TURN		might get lost (downstream of altered splice site)
177	184	STRAND		might get lost (downstream of altered splice site)
184	184	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
191	193	HELIX		might get lost (downstream of altered splice site)
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

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

221

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

356

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

25637

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

43255238

original gDNA sequence snippet

CCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCAAAA

altered gDNA sequence snippet

CCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAA

original cDNA sequence snippet

CTACATGCCTGCTATCGCGGGCTGCCGGGAGGCTATCAAAA

altered cDNA sequence snippet

CTACATGCCTGCTATCGCGGTCTGCCGGGAGGCTATCAAAA

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 AIAVCREAIK 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*

speed

0.90 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: 1 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs1977 (probable pathogenic)
known disease mutation at this position (HGMD CM034198)
known disease mutation at this position (HGMD CM962529)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:43255238C>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.221G>T
cDNA.305G>T
g.25637G>T

AA changes

G74V Score: 109 explain score(s)

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

frameshift

known variant

Reference ID: rs199422328

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)	0.392	1
	5.458	1
(flanking)	5.458	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	25634.5	sequence motif lost	-	wt: ccca\|GGGG mu: ccca.GGGT
Acc marginally increased	25633	wt: 0.9939 / mu: 0.9941 (marginal change - not scored)	wt: AACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATC mu: AACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATC	ccca\|GGGG
Acc marginally increased	25627	wt: 0.9656 / mu: 0.9666 (marginal change - not scored)	wt: GTTCCCAACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAG mu: GTTCCCAACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAG	tccc\|TTCC
Acc marginally increased	25635	wt: 0.9672 / mu: 0.9825 (marginal change - not scored)	wt: CCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCAA mu: CCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAA	cagg\|GGCT
Acc marginally increased	25628	wt: 0.8912 / mu: 0.8984 (marginal change - not scored)	wt: TTCCCAACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGG mu: TTCCCAACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGG	ccct\|TCCC
Acc marginally increased	25634	wt: 0.9630 / mu: 0.9655 (marginal change - not scored)	wt: ACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCA mu: ACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCA	ccag\|GGGC
Donor increased	25642	wt: 0.44 / mu: 0.79	wt: GCTGCCGGGAGGCTA mu: TCTGCCGGGAGGCTA	TGCC\|ggga
Acc gained	25643	0.31	mu: TTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAAGGATCG	gccg\|GGAG
Acc gained	25639	0.50	mu: TTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAAGG	gtct\|GCCG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000013524

Mmulatta

all identical

ENSMMUG00000010603

Fcatus

all identical

ENSFCAG00000002474

107

Mmusculus

all identical

ENSMUSG00000017697

Ggallus

all identical

ENSGALG00000004170

Trubripes

all identical

ENSTRUG00000010199

Drerio

all identical

ENSDARG00000003113

Dmelanogaster

no homologue

Celegans

all identical

C06G3.5

115

Xtropicalis

all identical

ENSXETG00000003459

protein features

start (aa)	end (aa)	feature	details
76	91	HELIX		might get lost (downstream of altered splice site)
92	94	TURN		might get lost (downstream of altered splice site)
95	102	STRAND		might get lost (downstream of altered splice site)
104	107	HELIX		might get lost (downstream of altered splice site)
109	111	STRAND		might get lost (downstream of altered splice site)
116	118	HELIX		might get lost (downstream of altered splice site)
126	144	HELIX		might get lost (downstream of altered splice site)
147	155	STRAND		might get lost (downstream of altered splice site)
159	161	HELIX		might get lost (downstream of altered splice site)
162	171	HELIX		might get lost (downstream of altered splice site)
172	176	TURN		might get lost (downstream of altered splice site)
177	184	STRAND		might get lost (downstream of altered splice site)
184	184	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
191	193	HELIX		might get lost (downstream of altered splice site)
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

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

221

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

305

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

25637

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

43255238

original gDNA sequence snippet

CCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCAAAA

altered gDNA sequence snippet

CCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAA

original cDNA sequence snippet

CTACATGCCTGCTATCGCGGGCTGCCGGGAGGCTATCAAAA

altered cDNA sequence snippet

CTACATGCCTGCTATCGCGGTCTGCCGGGAGGCTATCAAAA

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 AIAVCREAIK 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*

speed

0.75 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems