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 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 4.378628 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PCDHA3	polymorphism_automatic	0.02567903632198	simple_aae		affected		S440I	single base exchange	rs7701755		show file
PCDHA3	polymorphism_automatic	0.02567903632198	simple_aae		affected		S440I	single base exchange	rs7701755		show file
PCDHA1	polymorphism_automatic	0.99999999997411	without_aae		affected			single base exchange	rs7701755		show file
PCDHA1	polymorphism_automatic	0.99999999997411	without_aae		affected			single base exchange	rs7701755		show file
PCDHA2	polymorphism_automatic	0.99999999997411	without_aae		affected			single base exchange	rs7701755		show file
PCDHA2	polymorphism_automatic	0.99999999997411	without_aae		affected			single base exchange	rs7701755		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.97432096367802 (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)

chr5:140182101G>TN/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.1319G>T
cDNA.1319G>T
g.1319G>T

AA changes

S440I Score: 142 explain score(s)

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

440

frameshift

known variant

Reference ID: rs7701755

database	homozygous (T/T)	heterozygous	allele carriers
1000G	910	1142	2052
ExAC	18302	-3837	14465

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.16	0.992
	1.208	0.987
(flanking)	0.323	0.959

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 gained	1330	0.42	mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC	gtgg\|AGGT

distance from splice site

1076

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

440

mutated

not conserved

440

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

all identical

ENSXETG00000032691

439

protein features

start (aa)	end (aa)	feature	details
30	697	TOPO_DOM	Extracellular (Potential).	lost
351	455	DOMAIN	Cadherin 4.	lost
456	565	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
548	548	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
581	678	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
698	718	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
719	950	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	737	REPEAT	PXXP 1.	might get lost (downstream of altered splice site)
734	894	REGION	6 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
774	777	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
799	802	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 6.	might get lost (downstream of altered splice site)
923	930	COMPBIAS	Poly-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

strand

last intron/exon boundary

2543

theoretical NMD boundary in CDS

2492

length of CDS

2853

coding sequence (CDS) position

1319

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

1319

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

1319

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

140182101

original gDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered gDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

original cDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered cDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

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 GSPSLWATAI 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 *

speed

0.90 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.97432096367802 (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)

chr5:140182101G>TN/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.1319G>T
cDNA.1319G>T
g.1319G>T

AA changes

S440I Score: 142 explain score(s)

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

440

frameshift

known variant

Reference ID: rs7701755

database	homozygous (T/T)	heterozygous	allele carriers
1000G	910	1142	2052
ExAC	18302	-3837	14465

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.16	0.992
	1.208	0.987
(flanking)	0.323	0.959

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 gained	1330	0.42	mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC	gtgg\|AGGT

distance from splice site

1157

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

440

mutated

not conserved

440

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

all identical

ENSXETG00000032691

439

protein features

start (aa)	end (aa)	feature	details
30	697	TOPO_DOM	Extracellular (Potential).	lost
351	455	DOMAIN	Cadherin 4.	lost
456	565	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
548	548	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
581	678	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
698	718	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
719	950	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	737	REPEAT	PXXP 1.	might get lost (downstream of altered splice site)
734	894	REGION	6 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
774	777	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
799	802	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 6.	might get lost (downstream of altered splice site)
923	930	COMPBIAS	Poly-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

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

2475

coding sequence (CDS) position

1319

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

1319

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

1319

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

140182101

original gDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered gDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

original cDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered cDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

wildtype AA sequence

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 GSPSLWATAI 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*

speed

0.79 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 2.58899940659565e-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)

chr5:140182101G>TN/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.16226G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7701755

database	homozygous (T/T)	heterozygous	allele carriers
1000G	910	1142	2052
ExAC	18302	-3837	14465

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.16	0.992
	1.208	0.987
(flanking)	0.323	0.959

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 gained	16237	0.42	mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC	gtgg\|AGGT

distance from splice site

13832

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
719	950	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	894	REGION	5 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
799	802	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
923	930	COMPBIAS	Poly-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

strand

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)

16226

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

140182101

original gDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered gDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

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

0.65 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 2.58899940659565e-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)

chr5:140182101G>TN/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.16226G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7701755

database	homozygous (T/T)	heterozygous	allele carriers
1000G	910	1142	2052
ExAC	18302	-3837	14465

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.16	0.992
	1.208	0.987
(flanking)	0.323	0.959

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 gained	16237	0.42	mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC	gtgg\|AGGT

distance from splice site

14624

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
30	697	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
456	565	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
548	548	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
588	678	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
698	718	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
719	950	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	737	REPEAT	PXXP 1.	might get lost (downstream of altered splice site)
734	894	REGION	5 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
799	802	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
923	930	COMPBIAS	Poly-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

strand

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)

16226

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

140182101

original gDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered gDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

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

0.41 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 2.58899940659565e-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)

chr5:140182101G>TN/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.7658G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7701755

database	homozygous (T/T)	heterozygous	allele carriers
1000G	910	1142	2052
ExAC	18302	-3837	14465

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.16	0.992
	1.208	0.987
(flanking)	0.323	0.959

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 gained	7669	0.42	mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC	gtgg\|AGGT

distance from splice site

5164

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
719	948	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	892	REGION	5 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
797	800	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
830	833	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
871	874	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
889	892	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
921	928	COMPBIAS	Poly-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

strand

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)

7658

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

140182101

original gDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered gDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

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

0.65 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 2.58899940659565e-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)

chr5:140182101G>TN/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.7658G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7701755

database	homozygous (T/T)	heterozygous	allele carriers
1000G	910	1142	2052
ExAC	18302	-3837	14465

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.16	0.992
	1.208	0.987
(flanking)	0.323	0.959

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 gained	7669	0.42	mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC	gtgg\|AGGT

distance from splice site

2544

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
719	948	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	892	REGION	5 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
797	800	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
830	833	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
871	874	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
889	892	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
921	928	COMPBIAS	Poly-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

strand

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)

7658

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

140182101

original gDNA sequence snippet

TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG

altered gDNA sequence snippet

TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.41 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems