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 8 transcript(s)...
Querying Taster for transcript #1: ENST00000555835
Querying Taster for transcript #2: ENST00000397995
Querying Taster for transcript #3: ENST00000555597
Querying Taster for transcript #4: ENST00000336811
Querying Taster for transcript #5: ENST00000397990
Querying Taster for transcript #6: ENST00000398001
Querying Taster for transcript #7: ENST00000304704
Querying Taster for transcript #8: ENST00000397999
MT speed 0 s - this script 3.543096 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ANG	disease_causing_automatic	0.498488126753551	simple_aae		affected	0	K64I	single base exchange	rs121909540		show file
ANG	disease_causing_automatic	0.498488126753551	simple_aae		affected	0	K64I	single base exchange	rs121909540		show file
RNASE4	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121909540		show file
RNASE4	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121909540		show file
RNASE4	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121909540		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.498488126753551 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM060828)
known disease mutation: rs18078 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:21161914A>TN/A show variant in all transcripts IGV

HGNC symbol

ANG

Ensembl transcript ID

ENST00000336811

Genbank transcript ID

NM_001145

UniProt peptide

P03950

alteration type

single base exchange

alteration region

CDS

DNA changes

c.191A>T
cDNA.791A>T
g.9579A>T

AA changes

K64I Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs121909540
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18078 (pathogenic for Amyotrophic lateral sclerosis type 9) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM060828)

known disease mutation at this position, please check HGMD for details (HGMD ID CM060828)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060828)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.378	1
	2.456	1
(flanking)	0.65	0.988

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	9577	wt: 0.30 / mu: 0.69	wt: CGGGGCCTGACCTCACCCTGCAAAGACATCAACACATTTAT mu: CGGGGCCTGACCTCACCCTGCATAGACATCAACACATTTAT	ctgc\|AAAG

distance from splice site

209

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000034128

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000072115

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
60	63	TURN		might get lost (downstream of altered splice site)
63	63	DISULFID		might get lost (downstream of altered splice site)
64	64	MUTAGEN	K->Q: Significantly decreases binding affinity for RNH1.	lost
64	68	REGION	Substrate binding.	lost
65	70	STRAND		might get lost (downstream of altered splice site)
74	78	HELIX		might get lost (downstream of altered splice site)
79	81	HELIX		might get lost (downstream of altered splice site)
81	81	DISULFID		might get lost (downstream of altered splice site)
83	85	TURN		might get lost (downstream of altered splice site)
86	89	STRAND		might get lost (downstream of altered splice site)
90	92	TURN		might get lost (downstream of altered splice site)
92	92	MUTAGEN	N->A: Slightly decreases binding affinity for RNH1.	might get lost (downstream of altered splice site)
93	98	STRAND		might get lost (downstream of altered splice site)
100	110	STRAND		might get lost (downstream of altered splice site)
105	105	DISULFID		might get lost (downstream of altered splice site)
109	110	MUTAGEN	GG->RR: Significantly decreases binding affinity for RNH1.	might get lost (downstream of altered splice site)
112	115	STRAND		might get lost (downstream of altered splice site)
116	116	DISULFID		might get lost (downstream of altered splice site)
117	125	STRAND		might get lost (downstream of altered splice site)
128	132	STRAND		might get lost (downstream of altered splice site)
131	131	DISULFID		might get lost (downstream of altered splice site)
132	132	MUTAGEN	E->A: Slightly decreases binding affinity for RNH1.	might get lost (downstream of altered splice site)
135	139	STRAND		might get lost (downstream of altered splice site)
138	138	ACT_SITE	Proton donor.	might get lost (downstream of altered splice site)
140	140	MUTAGEN	D->H,S,A: 15- to 18-fold increase in RNase activity.	might get lost (downstream of altered splice site)
141	141	MUTAGEN	Q->G: Over 18-fold increase in RNase activity.	might get lost (downstream of altered splice site)
141	144	HELIX		might get lost (downstream of altered splice site)
143	144	MUTAGEN	IF->AA: 3- to 5-fold increase in RNase activity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

444 / 444

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

148 / 148

position of stopcodon in wt / mu cDNA

1044 / 1044

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

601 / 601

chromosome

strand

last intron/exon boundary

583

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

444

coding sequence (CDS) position

191

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

791

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

9579

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

21161914

original gDNA sequence snippet

GGGCCTGACCTCACCCTGCAAAGACATCAACACATTTATTC

altered gDNA sequence snippet

GGGCCTGACCTCACCCTGCATAGACATCAACACATTTATTC

original cDNA sequence snippet

GGGCCTGACCTCACCCTGCAAAGACATCAACACATTTATTC

altered cDNA sequence snippet

GGGCCTGACCTCACCCTGCATAGACATCAACACATTTATTC

wildtype AA sequence

MVMGLGVLLL VFVLGLGLTP PTLAQDNSRY THFLTQHYDA KPQGRDDRYC ESIMRRRGLT
SPCKDINTFI HGNKRSIKAI CENKNGNPHR ENLRISKSSF QVTTCKLHGG SPWPPCQYRA
TAGFRNVVVA CENGLPVHLD QSIFRRP*

mutated AA sequence

MVMGLGVLLL VFVLGLGLTP PTLAQDNSRY THFLTQHYDA KPQGRDDRYC ESIMRRRGLT
SPCIDINTFI HGNKRSIKAI CENKNGNPHR ENLRISKSSF QVTTCKLHGG SPWPPCQYRA
TAGFRNVVVA CENGLPVHLD QSIFRRP*

speed

0.68 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: 0.498488126753551 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM060828)
known disease mutation: rs18078 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:21161914A>TN/A show variant in all transcripts IGV

HGNC symbol

ANG

Ensembl transcript ID

ENST00000397990

Genbank transcript ID

NM_001097577

UniProt peptide

P03950

alteration type

single base exchange

alteration region

CDS

DNA changes

c.191A>T
cDNA.311A>T
g.9579A>T

AA changes

K64I Score: 102 explain score(s)

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

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.378	1
	2.456	1
(flanking)	0.65	0.988

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	9577	wt: 0.30 / mu: 0.69	wt: CGGGGCCTGACCTCACCCTGCAAAGACATCAACACATTTAT mu: CGGGGCCTGACCTCACCCTGCATAGACATCAACACATTTAT	ctgc\|AAAG

distance from splice site

209

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000034128

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000072115

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
60	63	TURN		might get lost (downstream of altered splice site)
63	63	DISULFID		might get lost (downstream of altered splice site)
64	64	MUTAGEN	K->Q: Significantly decreases binding affinity for RNH1.	lost
64	68	REGION	Substrate binding.	lost
65	70	STRAND		might get lost (downstream of altered splice site)
74	78	HELIX		might get lost (downstream of altered splice site)
79	81	HELIX		might get lost (downstream of altered splice site)
81	81	DISULFID		might get lost (downstream of altered splice site)
83	85	TURN		might get lost (downstream of altered splice site)
86	89	STRAND		might get lost (downstream of altered splice site)
90	92	TURN		might get lost (downstream of altered splice site)
92	92	MUTAGEN	N->A: Slightly decreases binding affinity for RNH1.	might get lost (downstream of altered splice site)
93	98	STRAND		might get lost (downstream of altered splice site)
100	110	STRAND		might get lost (downstream of altered splice site)
105	105	DISULFID		might get lost (downstream of altered splice site)
109	110	MUTAGEN	GG->RR: Significantly decreases binding affinity for RNH1.	might get lost (downstream of altered splice site)
112	115	STRAND		might get lost (downstream of altered splice site)
116	116	DISULFID		might get lost (downstream of altered splice site)
117	125	STRAND		might get lost (downstream of altered splice site)
128	132	STRAND		might get lost (downstream of altered splice site)
131	131	DISULFID		might get lost (downstream of altered splice site)
132	132	MUTAGEN	E->A: Slightly decreases binding affinity for RNH1.	might get lost (downstream of altered splice site)
135	139	STRAND		might get lost (downstream of altered splice site)
138	138	ACT_SITE	Proton donor.	might get lost (downstream of altered splice site)
140	140	MUTAGEN	D->H,S,A: 15- to 18-fold increase in RNase activity.	might get lost (downstream of altered splice site)
141	141	MUTAGEN	Q->G: Over 18-fold increase in RNase activity.	might get lost (downstream of altered splice site)
141	144	HELIX		might get lost (downstream of altered splice site)
143	144	MUTAGEN	IF->AA: 3- to 5-fold increase in RNase activity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

444 / 444

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

148 / 148

position of stopcodon in wt / mu cDNA

564 / 564

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

121 / 121

chromosome

strand

last intron/exon boundary

103

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

444

coding sequence (CDS) position

191

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

311

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

9579

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

21161914

original gDNA sequence snippet

GGGCCTGACCTCACCCTGCAAAGACATCAACACATTTATTC

altered gDNA sequence snippet

GGGCCTGACCTCACCCTGCATAGACATCAACACATTTATTC

original cDNA sequence snippet

GGGCCTGACCTCACCCTGCAAAGACATCAACACATTTATTC

altered cDNA sequence snippet

GGGCCTGACCTCACCCTGCATAGACATCAACACATTTATTC

wildtype AA sequence

MVMGLGVLLL VFVLGLGLTP PTLAQDNSRY THFLTQHYDA KPQGRDDRYC ESIMRRRGLT
SPCKDINTFI HGNKRSIKAI CENKNGNPHR ENLRISKSSF QVTTCKLHGG SPWPPCQYRA
TAGFRNVVVA CENGLPVHLD QSIFRRP*

mutated AA sequence

MVMGLGVLLL VFVLGLGLTP PTLAQDNSRY THFLTQHYDA KPQGRDDRYC ESIMRRRGLT
SPCIDINTFI HGNKRSIKAI CENKNGNPHR ENLRISKSSF QVTTCKLHGG SPWPPCQYRA
TAGFRNVVVA CENGLPVHLD QSIFRRP*

speed

0.62 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 CM060828)
known disease mutation: rs18078 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:21161914A>TN/A show variant in all transcripts IGV

HGNC symbol

RNASE4

Ensembl transcript ID

ENST00000555835

Genbank transcript ID

NM_002937

UniProt peptide

P34096

alteration type

single base exchange

alteration region

intron

DNA changes

g.9656A>T

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)	2.378	1
	2.456	1
(flanking)	0.65	0.988

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

splice sites

splice site change before start ATG (at aa -5) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	9654	wt: 0.30 / mu: 0.69	wt: CGGGGCCTGACCTCACCCTGCAAAGACATCAACACATTTAT mu: CGGGGCCTGACCTCACCCTGCATAGACATCAACACATTTAT	ctgc\|AAAG

distance from splice site

5600

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	28	SIGNAL		might get lost (downstream of altered splice site)
29	29	MOD_RES	Pyrrolidone carboxylic acid.	might get lost (downstream of altered splice site)
29	40	HELIX		might get lost (downstream of altered splice site)
38	38	BINDING	Substrate.	might get lost (downstream of altered splice site)
40	40	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
50	59	HELIX		might get lost (downstream of altered splice site)
53	53	DISULFID		might get lost (downstream of altered splice site)
54	54	CONFLICT	N -> D (in Ref. 3; AAA96750).	might get lost (downstream of altered splice site)
62	66	STRAND		might get lost (downstream of altered splice site)
67	67	DISULFID		might get lost (downstream of altered splice site)
68	72	REGION	Substrate binding.	might get lost (downstream of altered splice site)
69	74	STRAND		might get lost (downstream of altered splice site)
78	82	HELIX		might get lost (downstream of altered splice site)
83	86	HELIX		might get lost (downstream of altered splice site)
85	85	DISULFID		might get lost (downstream of altered splice site)
92	92	DISULFID		might get lost (downstream of altered splice site)
93	93	BINDING	Substrate.	might get lost (downstream of altered splice site)
99	99	DISULFID		might get lost (downstream of altered splice site)
99	111	STRAND		might get lost (downstream of altered splice site)
109	109	DISULFID		might get lost (downstream of altered splice site)
110	110	BINDING	Substrate.	might get lost (downstream of altered splice site)
113	115	STRAND		might get lost (downstream of altered splice site)
120	120	DISULFID		might get lost (downstream of altered splice site)
122	136	STRAND		might get lost (downstream of altered splice site)
135	135	DISULFID		might get lost (downstream of altered splice site)
137	140	TURN		might get lost (downstream of altered splice site)
141	147	STRAND		might get lost (downstream of altered splice site)
144	144	ACT_SITE	Proton donor.	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

677 / 677

chromosome

strand

last intron/exon boundary

660

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

444

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)

9656

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

21161914

original gDNA sequence snippet

GGGCCTGACCTCACCCTGCAAAGACATCAACACATTTATTC

altered gDNA sequence snippet

GGGCCTGACCTCACCCTGCATAGACATCAACACATTTATTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MALQRTHSLL LLLLLTLLGL GLVQPSYGQD GMYQRFLRQH VHPEETGGSD RYCNLMMQRR
KMTLYHCKRF NTFIHEDIWN IRSICSTTNI QCKNGKMNCH EGVVKVTDCR DTGSSRAPNC
RYRAIASTRR VVIACEGNPQ VPVHFDG*

mutated AA sequence

N/A

speed

0.50 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 CM060828)
known disease mutation: rs18078 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:21161914A>TN/A show variant in all transcripts IGV

HGNC symbol

RNASE4

Ensembl transcript ID

ENST00000397995

Genbank transcript ID

N/A

UniProt peptide

P34096

alteration type

single base exchange

alteration region

intron

DNA changes

g.9656A>T

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)	2.378	1
	2.456	1
(flanking)	0.65	0.988

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

splice sites

splice site change before start ATG (at aa -5) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	9654	wt: 0.30 / mu: 0.69	wt: CGGGGCCTGACCTCACCCTGCAAAGACATCAACACATTTAT mu: CGGGGCCTGACCTCACCCTGCATAGACATCAACACATTTAT	ctgc\|AAAG

distance from splice site

5600

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	28	SIGNAL		might get lost (downstream of altered splice site)
29	29	MOD_RES	Pyrrolidone carboxylic acid.	might get lost (downstream of altered splice site)
29	40	HELIX		might get lost (downstream of altered splice site)
38	38	BINDING	Substrate.	might get lost (downstream of altered splice site)
40	40	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
50	59	HELIX		might get lost (downstream of altered splice site)
53	53	DISULFID		might get lost (downstream of altered splice site)
54	54	CONFLICT	N -> D (in Ref. 3; AAA96750).	might get lost (downstream of altered splice site)
62	66	STRAND		might get lost (downstream of altered splice site)
67	67	DISULFID		might get lost (downstream of altered splice site)
68	72	REGION	Substrate binding.	might get lost (downstream of altered splice site)
69	74	STRAND		might get lost (downstream of altered splice site)
78	82	HELIX		might get lost (downstream of altered splice site)
83	86	HELIX		might get lost (downstream of altered splice site)
85	85	DISULFID		might get lost (downstream of altered splice site)
92	92	DISULFID		might get lost (downstream of altered splice site)
93	93	BINDING	Substrate.	might get lost (downstream of altered splice site)
99	99	DISULFID		might get lost (downstream of altered splice site)
99	111	STRAND		might get lost (downstream of altered splice site)
109	109	DISULFID		might get lost (downstream of altered splice site)
110	110	BINDING	Substrate.	might get lost (downstream of altered splice site)
113	115	STRAND		might get lost (downstream of altered splice site)
120	120	DISULFID		might get lost (downstream of altered splice site)
122	136	STRAND		might get lost (downstream of altered splice site)
135	135	DISULFID		might get lost (downstream of altered splice site)
137	140	TURN		might get lost (downstream of altered splice site)
141	147	STRAND		might get lost (downstream of altered splice site)
144	144	ACT_SITE	Proton donor.	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

132 / 132

chromosome

strand

last intron/exon boundary

115

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

444

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)

9656

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

21161914

original gDNA sequence snippet

GGGCCTGACCTCACCCTGCAAAGACATCAACACATTTATTC

altered gDNA sequence snippet

GGGCCTGACCTCACCCTGCATAGACATCAACACATTTATTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MALQRTHSLL LLLLLTLLGL GLVQPSYGQD GMYQRFLRQH VHPEETGGSD RYCNLMMQRR
KMTLYHCKRF NTFIHEDIWN IRSICSTTNI QCKNGKMNCH EGVVKVTDCR DTGSSRAPNC
RYRAIASTRR VVIACEGNPQ VPVHFDG*

mutated AA sequence

N/A

speed

0.52 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 CM060828)
known disease mutation: rs18078 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:21161914A>TN/A show variant in all transcripts IGV

HGNC symbol

RNASE4

Ensembl transcript ID

ENST00000555597

Genbank transcript ID

N/A

UniProt peptide

P34096

alteration type

single base exchange

alteration region

intron

DNA changes

g.9656A>T

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)	2.378	1
	2.456	1
(flanking)	0.65	0.988

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

splice sites

splice site change before start ATG (at aa -5) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	9654	wt: 0.30 / mu: 0.69	wt: CGGGGCCTGACCTCACCCTGCAAAGACATCAACACATTTAT mu: CGGGGCCTGACCTCACCCTGCATAGACATCAACACATTTAT	ctgc\|AAAG

distance from splice site

4881

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	28	SIGNAL		might get lost (downstream of altered splice site)
29	29	MOD_RES	Pyrrolidone carboxylic acid.	might get lost (downstream of altered splice site)
29	40	HELIX		might get lost (downstream of altered splice site)
38	38	BINDING	Substrate.	might get lost (downstream of altered splice site)
40	40	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
50	59	HELIX		might get lost (downstream of altered splice site)
53	53	DISULFID		might get lost (downstream of altered splice site)
54	54	CONFLICT	N -> D (in Ref. 3; AAA96750).	might get lost (downstream of altered splice site)
62	66	STRAND		might get lost (downstream of altered splice site)
67	67	DISULFID		might get lost (downstream of altered splice site)
68	72	REGION	Substrate binding.	might get lost (downstream of altered splice site)
69	74	STRAND		might get lost (downstream of altered splice site)
78	82	HELIX		might get lost (downstream of altered splice site)
83	86	HELIX		might get lost (downstream of altered splice site)
85	85	DISULFID		might get lost (downstream of altered splice site)
92	92	DISULFID		might get lost (downstream of altered splice site)
93	93	BINDING	Substrate.	might get lost (downstream of altered splice site)
99	99	DISULFID		might get lost (downstream of altered splice site)
99	111	STRAND		might get lost (downstream of altered splice site)
109	109	DISULFID		might get lost (downstream of altered splice site)
110	110	BINDING	Substrate.	might get lost (downstream of altered splice site)
113	115	STRAND		might get lost (downstream of altered splice site)
120	120	DISULFID		might get lost (downstream of altered splice site)
122	136	STRAND		might get lost (downstream of altered splice site)
135	135	DISULFID		might get lost (downstream of altered splice site)
137	140	TURN		might get lost (downstream of altered splice site)
141	147	STRAND		might get lost (downstream of altered splice site)
144	144	ACT_SITE	Proton donor.	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

111 / 111

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

444

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)

9656

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

21161914

original gDNA sequence snippet

GGGCCTGACCTCACCCTGCAAAGACATCAACACATTTATTC

altered gDNA sequence snippet

GGGCCTGACCTCACCCTGCATAGACATCAACACATTTATTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MALQRTHSLL LLLLLTLLGL GLVQPSYGQD GMYQRFLRQH VHPEETGGSD RYCNLMMQRR
KMTLYHCKRF NTFIHEDIWN IRSICSTTNI QCKNGKMNCH EGVVKVTDCR DTGSSRAPNC
RYRAIASTRR VVIACEGNPQ VPVHFDG*

mutated AA sequence

N/A

speed

0.54 s

Problems

data problem

No NCBI gene ID found for this transcript

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data problem

No NCBI gene ID found for this transcript

back to results table

data problem

No NCBI gene ID found for this transcript

back to results table