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: ENST00000504120
Querying Taster for transcript #2: ENST00000394633
Querying Taster for transcript #3: ENST00000520672
Querying Taster for transcript #4: ENST00000526136
Querying Taster for transcript #5: ENST00000522353
Querying Taster for transcript #6: ENST00000532566
MT speed 0 s - this script 4.935567 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PCDHA3polymorphism_automatic0.031978237182374simple_aaeaffectedC759Ysingle base exchangers2240694show file
PCDHA3polymorphism_automatic0.031978237182374simple_aaeaffectedC759Ysingle base exchangers2240694show file
PCDHA1polymorphism_automatic1without_aaeaffectedsingle base exchangers2240694show file
PCDHA2polymorphism_automatic1without_aaeaffectedsingle base exchangers2240694show file
PCDHA1polymorphism_automatic1without_aaeaffectedsingle base exchangers2240694show file
PCDHA2polymorphism_automatic1without_aaeaffectedsingle base exchangers2240694show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.968021762817626 (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) chr5:140183058G>AN/A show variant in all transcripts   IGV
HGNC symbol PCDHA3
Ensembl transcript ID ENST00000522353
Genbank transcript ID NM_018906
UniProt peptide Q9Y5H8
alteration type single base exchange
alteration region CDS
DNA changes c.2276G>A
cDNA.2276G>A
g.2276G>A
AA changes C759Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 759
frameshift no
known variant Reference ID: rs2240694
databasehomozygous (A/A)heterozygousallele carriers
1000G71711971914
ExAC16867-96715900
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.040.922
3.2690.921
(flanking)-0.3550.194
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2281wt: 0.60 / mu: 0.77wt: GCTCTGGAGAGGGGT
mu: ACTCTGGAGAGGGGT		 TCTG|gaga
Donor marginally increased2268wt: 0.2619 / mu: 0.2827 (marginal change - not scored)wt: CAGCAGAGGGTGTGC
mu: CAGCAGAGGGTGTAC		 GCAG|aggg
Donor increased2278wt: 0.37 / mu: 0.73wt: TGTGCTCTGGAGAGG
mu: TGTACTCTGGAGAGG		 TGCT|ctgg
Donor marginally increased2280wt: 0.9168 / mu: 0.9607 (marginal change - not scored)wt: TGCTCTGGAGAGGGG
mu: TACTCTGGAGAGGGG		 CTCT|ggag
distance from splice site 119
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      759WSYSQQRQQRVCSGEGLPKTDLMA
mutated  not conserved    759WSYSQQRQQRVYSGEGLPKTDLM
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000032691  750WTYSQQRQYKVHLNGTPLKNDLI
protein features
start (aa)end (aa)featuredetails 
719950TOPO_DOMCytoplasmic (Potential).lost
734894REGION6 X 4 AA repeats of P-X-X-P.lost
774777REPEATPXXP 2.might get lost (downstream of altered splice site)
799802REPEATPXXP 3.might get lost (downstream of altered splice site)
832835REPEATPXXP 4.might get lost (downstream of altered splice site)
873876REPEATPXXP 5.might get lost (downstream of altered splice site)
891894REPEATPXXP 6.might get lost (downstream of altered splice site)
923930COMPBIASPoly-Lys.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2853 / 2853
position (AA) of stopcodon in wt / mu AA sequence 951 / 951
position of stopcodon in wt / mu cDNA 2853 / 2853
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 5
strand 1
last intron/exon boundary 2543
theoretical NMD boundary in CDS 2492
length of CDS 2853
coding sequence (CDS) position 2276
cDNA position
(for ins/del: last normal base / first normal base)		 2276
gDNA position
(for ins/del: last normal base / first normal base)		 2276
chromosomal position
(for ins/del: last normal base / first normal base)		 140183058
original gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
original cDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered cDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
wildtype AA sequence MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVCS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *
mutated AA sequence MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVYS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *
speed 0.40 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: 0.968021762817626 (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) chr5:140183058G>AN/A show variant in all transcripts   IGV
HGNC symbol PCDHA3
Ensembl transcript ID ENST00000532566
Genbank transcript ID NM_031497
UniProt peptide Q9Y5H8
alteration type single base exchange
alteration region CDS
DNA changes c.2276G>A
cDNA.2276G>A
g.2276G>A
AA changes C759Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 759
frameshift no
known variant Reference ID: rs2240694
databasehomozygous (A/A)heterozygousallele carriers
1000G71711971914
ExAC16867-96715900
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.040.922
3.2690.921
(flanking)-0.3550.194
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2281wt: 0.60 / mu: 0.77wt: GCTCTGGAGAGGGGT
mu: ACTCTGGAGAGGGGT		 TCTG|gaga
Donor marginally increased2268wt: 0.2619 / mu: 0.2827 (marginal change - not scored)wt: CAGCAGAGGGTGTGC
mu: CAGCAGAGGGTGTAC		 GCAG|aggg
Donor increased2278wt: 0.37 / mu: 0.73wt: TGTGCTCTGGAGAGG
mu: TGTACTCTGGAGAGG		 TGCT|ctgg
Donor marginally increased2280wt: 0.9168 / mu: 0.9607 (marginal change - not scored)wt: TGCTCTGGAGAGGGG
mu: TACTCTGGAGAGGGG		 CTCT|ggag
distance from splice site 200
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      759WSYSQQRQQRVCSGEGLPKTDLMA
mutated  not conserved    759WSYSQQRQQRVYSGEGLPKTDLM
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000032691  750WTYSQQRQYKVHLNGTPLKNDLI
protein features
start (aa)end (aa)featuredetails 
719950TOPO_DOMCytoplasmic (Potential).lost
734894REGION6 X 4 AA repeats of P-X-X-P.lost
774777REPEATPXXP 2.might get lost (downstream of altered splice site)
799802REPEATPXXP 3.might get lost (downstream of altered splice site)
832835REPEATPXXP 4.might get lost (downstream of altered splice site)
873876REPEATPXXP 5.might get lost (downstream of altered splice site)
891894REPEATPXXP 6.might get lost (downstream of altered splice site)
923930COMPBIASPoly-Lys.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2475 / 2475
position (AA) of stopcodon in wt / mu AA sequence 825 / 825
position of stopcodon in wt / mu cDNA 2475 / 2475
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 5
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 2475
coding sequence (CDS) position 2276
cDNA position
(for ins/del: last normal base / first normal base)		 2276
gDNA position
(for ins/del: last normal base / first normal base)		 2276
chromosomal position
(for ins/del: last normal base / first normal base)		 140183058
original gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
original cDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered cDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
wildtype AA sequence MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVCS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKVS NFYLFFPKCL CFSFLNVSTP LEIH*
mutated AA sequence MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVYS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKVS NFYLFFPKCL CFSFLNVSTP LEIH*
speed 1.16 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: without_aae, prob: 3.65108307097496e-22 (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) chr5:140183058G>AN/A show variant in all transcripts   IGV
HGNC symbol PCDHA1
Ensembl transcript ID ENST00000504120
Genbank transcript ID NM_018900
UniProt peptide Q9Y5I3
alteration type single base exchange
alteration region intron
DNA changes g.17183G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2240694
databasehomozygous (A/A)heterozygousallele carriers
1000G71711971914
ExAC16867-96715900
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.040.922
3.2690.921
(flanking)-0.3550.194
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased17187wt: 0.9168 / mu: 0.9607 (marginal change - not scored)wt: TGCTCTGGAGAGGGG
mu: TACTCTGGAGAGGGG		 CTCT|ggag
Donor marginally increased17175wt: 0.2619 / mu: 0.2827 (marginal change - not scored)wt: CAGCAGAGGGTGTGC
mu: CAGCAGAGGGTGTAC		 GCAG|aggg
Donor increased17188wt: 0.60 / mu: 0.77wt: GCTCTGGAGAGGGGT
mu: ACTCTGGAGAGGGGT		 TCTG|gaga
Donor increased17185wt: 0.37 / mu: 0.73wt: TGTGCTCTGGAGAGG
mu: TGTACTCTGGAGAGG		 TGCT|ctgg
distance from splice site 14789
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
719950TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
734894REGION5 X 4 AA repeats of P-X-X-P.might get lost (downstream of altered splice site)
799802REPEATPXXP 2.might get lost (downstream of altered splice site)
832835REPEATPXXP 3.might get lost (downstream of altered splice site)
873876REPEATPXXP 4.might get lost (downstream of altered splice site)
891894REPEATPXXP 5.might get lost (downstream of altered splice site)
923930COMPBIASPoly-Lys.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 1 / 1
chromosome 5
strand 1
last intron/exon boundary 2543
theoretical NMD boundary in CDS 2492
length of CDS 2853
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)		 17183
chromosomal position
(for ins/del: last normal base / first normal base)		 140183058
original gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSVPPTEG AYVPGKPTLV CSSALGSWSN SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL
NTSERNEQPE ANLDLSGNPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *
mutated AA sequence N/A
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: 3.65108307097496e-22 (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) chr5:140183058G>AN/A show variant in all transcripts   IGV
HGNC symbol PCDHA2
Ensembl transcript ID ENST00000520672
Genbank transcript ID N/A
UniProt peptide Q9Y5H9
alteration type single base exchange
alteration region intron
DNA changes g.8615G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2240694
databasehomozygous (A/A)heterozygousallele carriers
1000G71711971914
ExAC16867-96715900
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.040.922
3.2690.921
(flanking)-0.3550.194
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased8620wt: 0.60 / mu: 0.77wt: GCTCTGGAGAGGGGT
mu: ACTCTGGAGAGGGGT		 TCTG|gaga
Donor marginally increased8607wt: 0.2619 / mu: 0.2827 (marginal change - not scored)wt: CAGCAGAGGGTGTGC
mu: CAGCAGAGGGTGTAC		 GCAG|aggg
Donor marginally increased8619wt: 0.9168 / mu: 0.9607 (marginal change - not scored)wt: TGCTCTGGAGAGGGG
mu: TACTCTGGAGAGGGG		 CTCT|ggag
Donor increased8617wt: 0.37 / mu: 0.73wt: TGTGCTCTGGAGAGG
mu: TGTACTCTGGAGAGG		 TGCT|ctgg
distance from splice site 1587
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
719948TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
734892REGION5 X 4 AA repeats of P-X-X-P.might get lost (downstream of altered splice site)
797800REPEATPXXP 2.might get lost (downstream of altered splice site)
830833REPEATPXXP 3.might get lost (downstream of altered splice site)
871874REPEATPXXP 4.might get lost (downstream of altered splice site)
889892REPEATPXXP 5.might get lost (downstream of altered splice site)
921928COMPBIASPoly-Lys.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 107 / 107
chromosome 5
strand 1
last intron/exon boundary 2495
theoretical NMD boundary in CDS 2338
length of CDS 2427
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)		 8615
chromosomal position
(for ins/del: last normal base / first normal base)		 140183058
original gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MASSIRRGRG AWTRLLSLLL LAAWEVGSGQ LRYSVPEEAK HGTFVGRIAQ DLGLELEELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHVEVIV DRPLQVFHVE
VEVKDINDNP PIFPMTVKTI RFPESRLLDS RFPLEGASDA DIGVNALLSY KLSSSEFFFL
DIQANDELSE SLSLVLGKSL DREETAEVNL LLVATDGGKP ELTGTVQILI KVLDVNDNEP
TFAQSVYKVK LLENTANGTL VVKLNASDAD EGPNSEIVYS LGSDVSSTIQ TKFTIDPISG
EIRTKGKLDY EEAKSYEIQV TATDKGTPSM SGHCKISLKL VDINDNTPEV SITSLSLPIS
ENASLGTVIA LITVSDRDSG TNGHVTCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATTS VSIEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEEVEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRA GTAAGAVSEL VPWSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQLGTGSARI PFRVGLYTGE ISTTRALDEA DSPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RAWVGAAGSE ATLVDVNVYL IIAICAVSSL LVLTVLLYTA
LRCSVPPTEG ARAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEDPPKTDLM AFSPSLSQGP
DSAEEKQLSE SEYVGKIWNF NLQIQLAS*
mutated AA sequence N/A
speed 0.83 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: 3.65108307097496e-22 (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) chr5:140183058G>AN/A show variant in all transcripts   IGV
HGNC symbol PCDHA1
Ensembl transcript ID ENST00000394633
Genbank transcript ID NM_031411
UniProt peptide Q9Y5I3
alteration type single base exchange
alteration region intron
DNA changes g.17183G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2240694
databasehomozygous (A/A)heterozygousallele carriers
1000G71711971914
ExAC16867-96715900
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.040.922
3.2690.921
(flanking)-0.3550.194
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased17187wt: 0.9168 / mu: 0.9607 (marginal change - not scored)wt: TGCTCTGGAGAGGGG
mu: TACTCTGGAGAGGGG		 CTCT|ggag
Donor marginally increased17175wt: 0.2619 / mu: 0.2827 (marginal change - not scored)wt: CAGCAGAGGGTGTGC
mu: CAGCAGAGGGTGTAC		 GCAG|aggg
Donor increased17188wt: 0.60 / mu: 0.77wt: GCTCTGGAGAGGGGT
mu: ACTCTGGAGAGGGGT		 TCTG|gaga
Donor increased17185wt: 0.37 / mu: 0.73wt: TGTGCTCTGGAGAGG
mu: TGTACTCTGGAGAGG		 TGCT|ctgg
distance from splice site 15581
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
30697TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
456565DOMAINCadherin 5.might get lost (downstream of altered splice site)
548548CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
588678DOMAINCadherin 6.might get lost (downstream of altered splice site)
698718TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
719950TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
734737REPEATPXXP 1.might get lost (downstream of altered splice site)
734894REGION5 X 4 AA repeats of P-X-X-P.might get lost (downstream of altered splice site)
799802REPEATPXXP 2.might get lost (downstream of altered splice site)
832835REPEATPXXP 3.might get lost (downstream of altered splice site)
873876REPEATPXXP 4.might get lost (downstream of altered splice site)
891894REPEATPXXP 5.might get lost (downstream of altered splice site)
923930COMPBIASPoly-Lys.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 1 / 1
chromosome 5
strand 1
last intron/exon boundary 1751
theoretical NMD boundary in CDS 1700
length of CDS 2061
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)		 17183
chromosomal position
(for ins/del: last normal base / first normal base)		 140183058
original gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQPRQPNP
DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV SPPVGAGVNS
NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI TFGKKEETKK
KKKKKKGNKT QEKKEKGNST TDNSDQ*
mutated AA sequence N/A
speed 1.05 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: 3.65108307097496e-22 (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) chr5:140183058G>AN/A show variant in all transcripts   IGV
HGNC symbol PCDHA2
Ensembl transcript ID ENST00000526136
Genbank transcript ID NM_018905
UniProt peptide Q9Y5H9
alteration type single base exchange
alteration region intron
DNA changes g.8615G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2240694
databasehomozygous (A/A)heterozygousallele carriers
1000G71711971914
ExAC16867-96715900
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.040.922
3.2690.921
(flanking)-0.3550.194
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased8620wt: 0.60 / mu: 0.77wt: GCTCTGGAGAGGGGT
mu: ACTCTGGAGAGGGGT		 TCTG|gaga
Donor marginally increased8607wt: 0.2619 / mu: 0.2827 (marginal change - not scored)wt: CAGCAGAGGGTGTGC
mu: CAGCAGAGGGTGTAC		 GCAG|aggg
Donor marginally increased8619wt: 0.9168 / mu: 0.9607 (marginal change - not scored)wt: TGCTCTGGAGAGGGG
mu: TACTCTGGAGAGGGG		 CTCT|ggag
Donor increased8617wt: 0.37 / mu: 0.73wt: TGTGCTCTGGAGAGG
mu: TGTACTCTGGAGAGG		 TGCT|ctgg
distance from splice site 6121
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
719948TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
734892REGION5 X 4 AA repeats of P-X-X-P.might get lost (downstream of altered splice site)
797800REPEATPXXP 2.might get lost (downstream of altered splice site)
830833REPEATPXXP 3.might get lost (downstream of altered splice site)
871874REPEATPXXP 4.might get lost (downstream of altered splice site)
889892REPEATPXXP 5.might get lost (downstream of altered splice site)
921928COMPBIASPoly-Lys.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 1 / 1
chromosome 5
strand 1
last intron/exon boundary 2537
theoretical NMD boundary in CDS 2486
length of CDS 2847
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)		 8615
chromosomal position
(for ins/del: last normal base / first normal base)		 140183058
original gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MASSIRRGRG AWTRLLSLLL LAAWEVGSGQ LRYSVPEEAK HGTFVGRIAQ DLGLELEELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHVEVIV DRPLQVFHVE
VEVKDINDNP PIFPMTVKTI RFPESRLLDS RFPLEGASDA DIGVNALLSY KLSSSEFFFL
DIQANDELSE SLSLVLGKSL DREETAEVNL LLVATDGGKP ELTGTVQILI KVLDVNDNEP
TFAQSVYKVK LLENTANGTL VVKLNASDAD EGPNSEIVYS LGSDVSSTIQ TKFTIDPISG
EIRTKGKLDY EEAKSYEIQV TATDKGTPSM SGHCKISLKL VDINDNTPEV SITSLSLPIS
ENASLGTVIA LITVSDRDSG TNGHVTCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATTS VSIEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEEVEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRA GTAAGAVSEL VPWSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQLGTGSARI PFRVGLYTGE ISTTRALDEA DSPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RAWVGAAGSE ATLVDVNVYL IIAICAVSSL LVLTVLLYTA
LRCSVPPTEG ARAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEDPPKTDLM AFSPSLSQGP
DSAEEKQLSE SEYVGKPRQP NPDWRYSASL RAGMHSSVHL EEAGILRAGP GGPDQQWPTV
SSATPEPEAG EVSPPVGAGV NSNSWTFKYG PGNPKQSGPG ELPDKFIIPG SPAIISIRQE
PTNSQIDKSD FITFGKKEET KKKKKKKKGN KTQEKKEKGN STTDNSDQ*
mutated AA sequence N/A
speed 0.34 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