mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999874 (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)

chr5:140230370A>CN/A show variant in all transcripts IGV

HGNC symbol

PCDHA9

Ensembl transcript ID

ENST00000532602

Genbank transcript ID

NM_031857

UniProt peptide

Q9Y5H5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2290A>C
cDNA.3323A>C
g.3323A>C

AA changes

K764Q Score: 53 explain score(s)

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

764

frameshift

known variant

Reference ID: rs369636

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1070	996	2066
ExAC	25467	-18167	7300

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

	PhyloP	PhastCons
(flanking)	-0.74	0.001
	-0.673	0
(flanking)	-0.021	0

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
Donor increased	3327	wt: 0.26 / mu: 0.56	wt: TAAGCAGAAGACCGA mu: TCAGCAGAAGACCGA	AGCA\|gaag
Donor marginally increased	3324	wt: 0.8948 / mu: 0.9022 (marginal change - not scored)	wt: GGGTAAGCAGAAGAC mu: GGGTCAGCAGAAGAC	GTAA\|gcag
Donor increased	3314	wt: 0.52 / mu: 0.77	wt: GCTCTGGCGAGGGTA mu: GCTCTGGCGAGGGTC	TCTG\|gcga

distance from splice site

105

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

764

mutated

all conserved

764

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

755

protein features

start (aa)	end (aa)	feature	details
719	950	TOPO_DOM	Cytoplasmic (Potential).	lost
734	894	REGION	5 X 4 AA repeats of P-X-X-P.	lost
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

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

3886 / 3886

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

1034 / 1034

chromosome

strand

last intron/exon boundary

3576

theoretical NMD boundary in CDS

2492

length of CDS

2853

coding sequence (CDS) position

2290

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

3323

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

3323

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

140230370

original gDNA sequence snippet

GGGTGTGCTCTGGCGAGGGTAAGCAGAAGACCGACCTCATG

altered gDNA sequence snippet

GGGTGTGCTCTGGCGAGGGTCAGCAGAAGACCGACCTCATG

original cDNA sequence snippet

GGGTGTGCTCTGGCGAGGGTAAGCAGAAGACCGACCTCATG

altered cDNA sequence snippet

GGGTGTGCTCTGGCGAGGGTCAGCAGAAGACCGACCTCATG

wildtype AA sequence

MLYSSRGDPE GQPLLLSLLI LAMWVVGSGQ LHYSVPEEAE HGTFVGRIAQ DLGLELAELV
PRLFQLDSKG RGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVKDINDNP PVFPATQKNL FIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFFL
DVPTSNQQVK PLGLVLRKLL DREETPELHL LLTATDGGKP ELTGTVQLLI TVLDNNDNAP
VFDRTLYTVK LPENVSIGTL VIHPNASDLD EGLNGDIIYS FSSDVSPDIK SKFHMDPLSG
AITVIGHMDF EESRAHKIPV EAVDKGFPPL AGHCTLLVEV VDVNDNAPQL TIKTLSVPVK
EDAQLGTVIA LISVIDLDAD ANGQVTCSLT PHVPFKLVST YKNYYSLVLD RALDRESVSA
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRLG ERSLSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLTPRM RGTDGAVSEM VLRSVGAGVV VGKVRAVDAD
SGYNAWLSYE LQPETASASI PFRVGLYTGE ISTTRALDET DAPRQRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKSSS RASVGATGPE VTLVDVNVYL IIAICAVSSL LVLTLLLYTV
LRCSAMPTEG ECAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEGKQKTDLM AFSPGLSPCA
GSTERTGEPS ASSDSTGKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

mutated AA sequence

MLYSSRGDPE GQPLLLSLLI LAMWVVGSGQ LHYSVPEEAE HGTFVGRIAQ DLGLELAELV
PRLFQLDSKG RGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVKDINDNP PVFPATQKNL FIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFFL
DVPTSNQQVK PLGLVLRKLL DREETPELHL LLTATDGGKP ELTGTVQLLI TVLDNNDNAP
VFDRTLYTVK LPENVSIGTL VIHPNASDLD EGLNGDIIYS FSSDVSPDIK SKFHMDPLSG
AITVIGHMDF EESRAHKIPV EAVDKGFPPL AGHCTLLVEV VDVNDNAPQL TIKTLSVPVK
EDAQLGTVIA LISVIDLDAD ANGQVTCSLT PHVPFKLVST YKNYYSLVLD RALDRESVSA
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRLG ERSLSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLTPRM RGTDGAVSEM VLRSVGAGVV VGKVRAVDAD
SGYNAWLSYE LQPETASASI PFRVGLYTGE ISTTRALDET DAPRQRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKSSS RASVGATGPE VTLVDVNVYL IIAICAVSSL LVLTLLLYTV
LRCSAMPTEG ECAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEGQQKTDLM AFSPGLSPCA
GSTERTGEPS ASSDSTGKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

speed

1.01 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