Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000284878
Querying Taster for transcript #2: ENST00000400166
Querying Taster for transcript #3: ENST00000356275
Querying Taster for transcript #4: ENST00000400169
Querying Taster for transcript #5: ENST00000400165
Querying Taster for transcript #6: ENST00000306618
MT speed 2.84 s - this script 4.013436 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CXADRpolymorphism_automatic7.88074882696055e-06simple_aaeaffectedT75Asingle base exchangers437470show file
CXADRpolymorphism_automatic1.85922651709802e-05simple_aaeaffectedH195Rsingle base exchangers437470show file
CXADRpolymorphism_automatic7.94870043560048e-05simple_aaeaffectedH143Rsingle base exchangers437470show file
CXADRpolymorphism_automatic0.99999999997977without_aaeaffectedsingle base exchangers437470show file
CXADRpolymorphism_automatic0.99999999997977without_aaeaffectedsingle base exchangers437470show file
CXADRpolymorphism_automatic0.99999999997977without_aaeaffectedsingle base exchangers437470show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999992119251173 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:18937758A>GN/A show variant in all transcripts   IGV
HGNC symbol CXADR
Ensembl transcript ID ENST00000356275
Genbank transcript ID NM_001207065
UniProt peptide P78310
alteration type single base exchange
alteration region CDS
DNA changes c.223A>G
cDNA.223A>G
g.53059A>G
AA changes T75A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 75
frameshift no
known variant Reference ID: rs437470
databasehomozygous (G/G)heterozygousallele carriers
1000G123691814
ExAC14401396115401
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5680.993
-3.0170.038
(flanking)5.1991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53050wt: 0.57 / mu: 0.72wt: AGGGAAGATGTGCCA
mu: AGGGAAGATGTGCCG		 GGAA|gatg
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      75NQKVDQVGRCATSKEPYVHCQKLH
mutated  not conserved    75NQKVDQVGRCAASKEPYVHCQKL
Ptroglodytes  no alignment  ENSPTRG00000013795  n/a
Mmulatta  no alignment  ENSMMUG00000010755  n/a
Fcatus  no alignment  ENSFCAG00000002911  n/a
Mmusculus  no alignment  ENSMUSG00000022865  n/a
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000002408  n/a
Drerio  no alignment  ENSDARG00000043658  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000005780  n/a
protein features
start (aa)end (aa)featuredetails 
20134DOMAINIg-like C2-type 1.lost
20237TOPO_DOMExtracellular (Potential).lost
6875STRANDlost
7072MUTAGENVII->AID: Abolishes binding to adenovirus type 5.might get lost (downstream of altered splice site)
7880STRANDmight get lost (downstream of altered splice site)
8690TURNmight get lost (downstream of altered splice site)
9193STRANDmight get lost (downstream of altered splice site)
98100HELIXmight get lost (downstream of altered splice site)
105107STRANDmight get lost (downstream of altered splice site)
106106CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
112114HELIXmight get lost (downstream of altered splice site)
116124STRANDmight get lost (downstream of altered splice site)
120120DISULFIDmight get lost (downstream of altered splice site)
127138STRANDmight get lost (downstream of altered splice site)
141228DOMAINIg-like C2-type 2.might get lost (downstream of altered splice site)
145148STRANDmight get lost (downstream of altered splice site)
156163STRANDmight get lost (downstream of altered splice site)
162162DISULFIDBy similarity.might get lost (downstream of altered splice site)
166168STRANDmight get lost (downstream of altered splice site)
171178STRANDmight get lost (downstream of altered splice site)
185192HELIXmight get lost (downstream of altered splice site)
195201STRANDmight get lost (downstream of altered splice site)
201201CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
208215STRANDmight get lost (downstream of altered splice site)
212212DISULFIDBy similarity.might get lost (downstream of altered splice site)
221227STRANDmight get lost (downstream of altered splice site)
238258TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
259259LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
259260MUTAGENCC->AA: Loss of palmitoylation and altered localization.might get lost (downstream of altered splice site)
259365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
260260LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
293293MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
300300MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
318318MUTAGENY->A: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
323323MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
345348MUTAGENLSRM->AAAA: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
360365MOTIFPDZ-binding.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 270 / 270
position (AA) of stopcodon in wt / mu AA sequence 90 / 90
position of stopcodon in wt / mu cDNA 270 / 270
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 1 / 1
chromosome 21
strand 1
last intron/exon boundary 211
theoretical NMD boundary in CDS 160
length of CDS 270
coding sequence (CDS) position 223
cDNA position
(for ins/del: last normal base / first normal base)		 223
gDNA position
(for ins/del: last normal base / first normal base)		 53059
chromosomal position
(for ins/del: last normal base / first normal base)		 18937758
original gDNA sequence snippet CTTTGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered gDNA sequence snippet CTTTGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
original cDNA sequence snippet ATCAAGTGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered cDNA sequence snippet ATCAAGTGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
wildtype AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV GRCATSKEPY VHCQKLHRQ*
mutated AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV GRCAASKEPY VHCQKLHRQ*
speed 0.16 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999981407734829 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:18937758A>GN/A show variant in all transcripts   IGV
HGNC symbol CXADR
Ensembl transcript ID ENST00000400166
Genbank transcript ID NM_001207063
UniProt peptide P78310
alteration type single base exchange
alteration region CDS
DNA changes c.584A>G
cDNA.668A>G
g.53059A>G
AA changes H195R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 195
frameshift no
known variant Reference ID: rs437470
databasehomozygous (G/G)heterozygousallele carriers
1000G123691814
ExAC14401396115401
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5680.993
-3.0170.038
(flanking)5.1991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53050wt: 0.57 / mu: 0.72wt: AGGGAAGATGTGCCA
mu: AGGGAAGATGTGCCG		 GGAA|gatg
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      195MPTSWLAGKMCHLQRAVRPLPEAT
mutated  not conserved    195MPTSWLAGKMCRLQRAVRPLPEA
Ptroglodytes  no alignment  ENSPTRG00000013795  n/a
Mmulatta  no alignment  ENSMMUG00000010755  n/a
Fcatus  no alignment  ENSFCAG00000002911  n/a
Mmusculus  no alignment  ENSMUSG00000022865  n/a
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000002408  n/a
Drerio  no alignment  ENSDARG00000043658  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000005780  n/a
protein features
start (aa)end (aa)featuredetails 
20237TOPO_DOMExtracellular (Potential).lost
141228DOMAINIg-like C2-type 2.lost
185192HELIXmight get lost (downstream of altered splice site)
195201STRANDlost
201201CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
208215STRANDmight get lost (downstream of altered splice site)
212212DISULFIDBy similarity.might get lost (downstream of altered splice site)
221227STRANDmight get lost (downstream of altered splice site)
238258TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
259259LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
259260MUTAGENCC->AA: Loss of palmitoylation and altered localization.might get lost (downstream of altered splice site)
259365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
260260LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
293293MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
300300MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
318318MUTAGENY->A: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
323323MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
345348MUTAGENLSRM->AAAA: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
360365MOTIFPDZ-binding.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 759 / 759
position (AA) of stopcodon in wt / mu AA sequence 253 / 253
position of stopcodon in wt / mu cDNA 843 / 843
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 21
strand 1
last intron/exon boundary 656
theoretical NMD boundary in CDS 521
length of CDS 759
coding sequence (CDS) position 584
cDNA position
(for ins/del: last normal base / first normal base)		 668
gDNA position
(for ins/del: last normal base / first normal base)		 53059
chromosomal position
(for ins/del: last normal base / first normal base)		 18937758
original gDNA sequence snippet CTTTGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered gDNA sequence snippet CTTTGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
original cDNA sequence snippet GTTAGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered cDNA sequence snippet GTTAGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
wildtype AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA GKMCHLQRAV RPLPEATSAV IIHPWGPCLL PTWKDIPRLS ITKYQVKTLN
ALLRVRLSHL LR*
mutated AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA GKMCRLQRAV RPLPEATSAV IIHPWGPCLL PTWKDIPRLS ITKYQVKTLN
ALLRVRLSHL LR*
speed 0.84 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999920512995644 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:18937758A>GN/A show variant in all transcripts   IGV
HGNC symbol CXADR
Ensembl transcript ID ENST00000400165
Genbank transcript ID NM_001207064
UniProt peptide P78310
alteration type single base exchange
alteration region CDS
DNA changes c.428A>G
cDNA.428A>G
g.53059A>G
AA changes H143R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 143
frameshift no
known variant Reference ID: rs437470
databasehomozygous (G/G)heterozygousallele carriers
1000G123691814
ExAC14401396115401
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5680.993
-3.0170.038
(flanking)5.1991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53050wt: 0.57 / mu: 0.72wt: AGGGAAGATGTGCCA
mu: AGGGAAGATGTGCCG		 GGAA|gatg
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      143KIHLVVLGKMCHLQRAVRPLPEAT
mutated  not conserved    143KIHLVVLGKMCRLQRAVRPLPEA
Ptroglodytes  no alignment  ENSPTRG00000013795  n/a
Mmulatta  no alignment  ENSMMUG00000010755  n/a
Fcatus  no alignment  ENSFCAG00000002911  n/a
Mmusculus  no alignment  ENSMUSG00000022865  n/a
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002408  144KMLLIVMVKPSKPRCH
Drerio  no alignment  ENSDARG00000043658  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000005780  n/a
protein features
start (aa)end (aa)featuredetails 
20237TOPO_DOMExtracellular (Potential).lost
141228DOMAINIg-like C2-type 2.lost
145148STRANDmight get lost (downstream of altered splice site)
156163STRANDmight get lost (downstream of altered splice site)
162162DISULFIDBy similarity.might get lost (downstream of altered splice site)
166168STRANDmight get lost (downstream of altered splice site)
171178STRANDmight get lost (downstream of altered splice site)
185192HELIXmight get lost (downstream of altered splice site)
195201STRANDmight get lost (downstream of altered splice site)
201201CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
208215STRANDmight get lost (downstream of altered splice site)
212212DISULFIDBy similarity.might get lost (downstream of altered splice site)
221227STRANDmight get lost (downstream of altered splice site)
238258TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
259259LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
259260MUTAGENCC->AA: Loss of palmitoylation and altered localization.might get lost (downstream of altered splice site)
259365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
260260LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
293293MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
300300MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
318318MUTAGENY->A: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
323323MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
345348MUTAGENLSRM->AAAA: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
360365MOTIFPDZ-binding.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 603 / 603
position (AA) of stopcodon in wt / mu AA sequence 201 / 201
position of stopcodon in wt / mu cDNA 603 / 603
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 1 / 1
chromosome 21
strand 1
last intron/exon boundary 416
theoretical NMD boundary in CDS 365
length of CDS 603
coding sequence (CDS) position 428
cDNA position
(for ins/del: last normal base / first normal base)		 428
gDNA position
(for ins/del: last normal base / first normal base)		 53059
chromosomal position
(for ins/del: last normal base / first normal base)		 18937758
original gDNA sequence snippet CTTTGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered gDNA sequence snippet CTTTGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
original cDNA sequence snippet AGTTCTTGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered cDNA sequence snippet AGTTCTTGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
wildtype AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLGK MCHLQRAVRP LPEATSAVII HPWGPCLLPT WKDIPRLSIT
KYQVKTLNAL LRVRLSHLLR *
mutated AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLGK MCRLQRAVRP LPEATSAVII HPWGPCLLPT WKDIPRLSIT
KYQVKTLNAL LRVRLSHLLR *
speed 0.92 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 2.02301697360594e-11 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:18937758A>GN/A show variant in all transcripts   IGV
HGNC symbol CXADR
Ensembl transcript ID ENST00000284878
Genbank transcript ID NM_001338
UniProt peptide P78310
alteration type single base exchange
alteration region CDS
DNA changes c.846A>G
cDNA.1594A>G
g.53059A>G
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift no
known variant Reference ID: rs437470
databasehomozygous (G/G)heterozygousallele carriers
1000G123691814
ExAC14401396115401
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5680.993
-3.0170.038
(flanking)5.1991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53050wt: 0.57 / mu: 0.72wt: AGGGAAGATGTGCCA
mu: AGGGAAGATGTGCCG		 GGAA|gatg
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
259365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
293293MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
300300MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
318318MUTAGENY->A: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
323323MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
345348MUTAGENLSRM->AAAA: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
360365MOTIFPDZ-binding.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered no
position of stopcodon in wt / mu CDS 1098 / 1098
position (AA) of stopcodon in wt / mu AA sequence 366 / 366
position of stopcodon in wt / mu cDNA 1846 / 1846
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 749 / 749
chromosome 21
strand 1
last intron/exon boundary 1582
theoretical NMD boundary in CDS 783
length of CDS 1098
coding sequence (CDS) position 846
cDNA position
(for ins/del: last normal base / first normal base)		 1594
gDNA position
(for ins/del: last normal base / first normal base)		 53059
chromosomal position
(for ins/del: last normal base / first normal base)		 18937758
original gDNA sequence snippet CTTTGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered gDNA sequence snippet CTTTGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
original cDNA sequence snippet GATATCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered cDNA sequence snippet GATATCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
wildtype AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA EMTSSVISVK NASSEYSGTY SCTVRNRVGS DQCLLRLNVV PPSNKAGLIA
GAIIGTLLAL ALIGLIIFCC RKKRREEKYE KEVHHDIRED VPPPKSRTST ARSYIGSNHS
SLGSMSPSNM EGYSKTQYNQ VPSEDFERTP QSPTLPPAKV AAPNLSRMGA IPVMIPAQSK
DGSIV*
mutated AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA EMTSSVISVK NASSEYSGTY SCTVRNRVGS DQCLLRLNVV PPSNKAGLIA
GAIIGTLLAL ALIGLIIFCC RKKRREEKYE KEVHHDIRED VPPPKSRTST ARSYIGSNHS
SLGSMSPSNM EGYSKTQYNQ VPSEDFERTP QSPTLPPAKV AAPNLSRMGA IPVMIPAQSK
DGSIV*
speed 0.14 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 2.02301697360594e-11 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:18937758A>GN/A show variant in all transcripts   IGV
HGNC symbol CXADR
Ensembl transcript ID ENST00000400169
Genbank transcript ID NM_001207066
UniProt peptide P78310
alteration type single base exchange
alteration region CDS
DNA changes c.846A>G
cDNA.846A>G
g.53059A>G
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift no
known variant Reference ID: rs437470
databasehomozygous (G/G)heterozygousallele carriers
1000G123691814
ExAC14401396115401
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5680.993
-3.0170.038
(flanking)5.1991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53050wt: 0.57 / mu: 0.72wt: AGGGAAGATGTGCCA
mu: AGGGAAGATGTGCCG		 GGAA|gatg
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
259365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
293293MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
300300MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
318318MUTAGENY->A: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
323323MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
345348MUTAGENLSRM->AAAA: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
360365MOTIFPDZ-binding.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered no
position of stopcodon in wt / mu CDS 1059 / 1059
position (AA) of stopcodon in wt / mu AA sequence 353 / 353
position of stopcodon in wt / mu cDNA 1059 / 1059
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 1 / 1
chromosome 21
strand 1
last intron/exon boundary 1018
theoretical NMD boundary in CDS 967
length of CDS 1059
coding sequence (CDS) position 846
cDNA position
(for ins/del: last normal base / first normal base)		 846
gDNA position
(for ins/del: last normal base / first normal base)		 53059
chromosomal position
(for ins/del: last normal base / first normal base)		 18937758
original gDNA sequence snippet CTTTGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered gDNA sequence snippet CTTTGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
original cDNA sequence snippet GATATCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered cDNA sequence snippet GATATCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
wildtype AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA EMTSSVISVK NASSEYSGTY SCTVRNRVGS DQCLLRLNVV PPSNKAGLIA
GAIIGTLLAL ALIGLIIFCC RKKRREEKYE KEVHHDIRED VPPPKSRTST ARSYIGSNHS
SLGSMSPSNM EGYSKTQYNQ VPSEDFERTP QSPTLPPAKF KYPYKTDGIT VV*
mutated AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA EMTSSVISVK NASSEYSGTY SCTVRNRVGS DQCLLRLNVV PPSNKAGLIA
GAIIGTLLAL ALIGLIIFCC RKKRREEKYE KEVHHDIRED VPPPKSRTST ARSYIGSNHS
SLGSMSPSNM EGYSKTQYNQ VPSEDFERTP QSPTLPPAKF KYPYKTDGIT VV*
speed 0.60 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 2.02301697360594e-11 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:18937758A>GN/A show variant in all transcripts   IGV
HGNC symbol CXADR
Ensembl transcript ID ENST00000306618
Genbank transcript ID N/A
UniProt peptide P78310
alteration type single base exchange
alteration region CDS
DNA changes c.723A>G
cDNA.723A>G
g.53059A>G
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift no
known variant Reference ID: rs437470
databasehomozygous (G/G)heterozygousallele carriers
1000G123691814
ExAC14401396115401
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5680.993
-3.0170.038
(flanking)5.1991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53050wt: 0.57 / mu: 0.72wt: AGGGAAGATGTGCCA
mu: AGGGAAGATGTGCCG		 GGAA|gatg
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
238258TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
259259LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
259260MUTAGENCC->AA: Loss of palmitoylation and altered localization.might get lost (downstream of altered splice site)
259365TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
260260LIPIDS-palmitoyl cysteine (Probable).might get lost (downstream of altered splice site)
293293MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
300300MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
318318MUTAGENY->A: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
323323MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
345348MUTAGENLSRM->AAAA: Affects basolateral localization in airway epithelial cells.might get lost (downstream of altered splice site)
360365MOTIFPDZ-binding.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered no
position of stopcodon in wt / mu CDS 975 / 975
position (AA) of stopcodon in wt / mu AA sequence 325 / 325
position of stopcodon in wt / mu cDNA 975 / 975
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 1 / 1
chromosome 21
strand 1
last intron/exon boundary 711
theoretical NMD boundary in CDS 660
length of CDS 975
coding sequence (CDS) position 723
cDNA position
(for ins/del: last normal base / first normal base)		 723
gDNA position
(for ins/del: last normal base / first normal base)		 53059
chromosomal position
(for ins/del: last normal base / first normal base)		 18937758
original gDNA sequence snippet CTTTGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered gDNA sequence snippet CTTTGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
original cDNA sequence snippet GATATCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC
altered cDNA sequence snippet GATATCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC
wildtype AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA ASNKAGLIAG AIIGTLLALA LIGLIIFCCR KKRREEKYEK EVHHDIREDV
PPPKSRTSTA RSYIGSNHSS LGSMSPSNME GYSKTQYNQV PSEDFERTPQ SPTLPPAKVA
APNLSRMGAI PVMIPAQSKD GSIV*
mutated AA sequence MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLVK PSGARCYVDG SEEIGSDFKI KCEPKEGSLP LQYEWQKLSD
SQKMPTSWLA ASNKAGLIAG AIIGTLLALA LIGLIIFCCR KKRREEKYEK EVHHDIREDV
PPPKSRTSTA RSYIGSNHSS LGSMSPSNME GYSKTQYNQV PSEDFERTPQ SPTLPPAKVA
APNLSRMGAI PVMIPAQSKD GSIV*
speed 0.18 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

Problems