mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999983 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

Kozak consensus sequence changed
amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes
start ATG shifted

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:219903258T>GN/A show variant in all transcripts IGV

HGNC symbol

CFAP65

Ensembl transcript ID

ENST00000410037

Genbank transcript ID

N/A

UniProt peptide

Q6ZU64

alteration type

single base exchange

alteration region

CDS
alteration spans start ATG, i.e. might be located in 5'UTR and CDS

DNA changes

c.1A>C
cDNA.118A>C
g.2992A>C

AA changes

M1? initiating Methionine lost
possible effect: activation of potential downstream translation initiation site with same reading frame resulting in shortened AA sequence, 1 AA at beginning of AA sequence are missing
M1- Score: - explain score(s)

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

1-1

frameshift

known variant

Reference ID: rs6736922

database	homozygous (G/G)	heterozygous	allele carriers
1000G	921	1110	2031
ExAC	30220	-27673	2547

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.59	0
	-0.766	0
(flanking)	-0.102	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
Acc increased	2987	wt: 0.60 / mu: 0.67	wt: TCCCTTTGGACTGTGTCCCAAGGACATGATGCTCACCCAGG mu: TCCCTTTGGACTGTGTCCCAAGGACCTGATGCTCACCCAGG	ccaa\|GGAC
Donor increased	2991	wt: 0.24 / mu: 0.48	wt: AAGGACATGATGCTC mu: AAGGACCTGATGCTC	GGAC\|atga

distance from splice site

Kozak consensus sequence altered?

yes

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all conserved

ENSPTRG00000012937

Mmulatta

all conserved

ENSMMUG00000000783

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000047021

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000006863

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000013869

n/a

protein features

start (aa)	end (aa)	feature	details
129	129	CONFLICT	H -> R (in Ref. 1; BAC86878).	might get lost (downstream of altered splice site)
188	208	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
320	320	CONFLICT	T -> A (in Ref. 1; BAC86878).	might get lost (downstream of altered splice site)
665	665	CONFLICT	G -> W (in Ref. 1; BAC86878).	might get lost (downstream of altered splice site)
877	986	DOMAIN	MSP.	might get lost (downstream of altered splice site)
1525	1550	COILED	Potential.	might get lost (downstream of altered splice site)
1574	1574	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
1761	1848	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)

length of protein

delayed start of translation

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2193 / 2190

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

731 / 730

position of stopcodon in wt / mu cDNA

2310 / 2307

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

118 / 121

chromosome

strand

-1

last intron/exon boundary

1774

theoretical NMD boundary in CDS

1606

length of CDS

2193

coding sequence (CDS) position

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

118

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

2992

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

219903258

original gDNA sequence snippet

TTGGACTGTGTCCCAAGGACATGATGCTCACCCAGGCTCCA

altered gDNA sequence snippet

TTGGACTGTGTCCCAAGGACCTGATGCTCACCCAGGCTCCA

original cDNA sequence snippet

TTGGACTGTGTCCCAAGGACATGATGCTCACCCAGGCTCCA

altered cDNA sequence snippet

TTGGACTGTGTCCCAAGGACCTGATGCTCACCCAGGCTCCA

wildtype AA sequence

MMLTQAPSSV VRSRNSRNHT VNSGGSCLSA STVAIPAIND SSAAMSACST ISAQPASSMD
TQMHSPKKQE RVNKRVIWGI EVAEELHWKG WELGKETTRN LVLKNRSLKL QKMKYRPPKT
KFFFTVIPQP IFLSPGITLT LPIVFRPLEA KEYMDQLWFE KAEGMFCVGL RATLPCHRLI
CRPPSLQLPM CAVGDTTEAF FCLDNVGDLP TFFTWEFSSP FQMLPATGLL EPGQASQIKV
TFQPLTAVIY EVQATCWYGA GSRQRSSIQL QAVAKCAQLL VSIKHKCPED QDAEGFQKLL
YFGSVAVGCT SERQIRLHNP SAVNAPFRIE ISPDELAEDQ AFSCPTAHGI VLPGEKKCVS
VFFHPKTLDT RTVDYCSIMP SGCASKTLLK VVGFCRGPAV SLQHYCVNFS WVNLGERSEQ
PLWIENQSDC TAHFQFAIDC LESVFTIRPA FGTLVGKARM TLHCAFQPTH PIICFRRVAC
LIHHQDPLFL DLMGTCHSDS TKPAILKPQH LTWYRTHLAR GLTLYPPDIL DAMLKEKKLA
QDQNGALMIP IQDLEDMPAP QYPYIPPMTE FFFDGTSDIT IFPPPISVEP VEVDFGACPG
PEAPNPVPLC LMNHTKGKIM VVWTRRSDCP FWVTPESCDV PPLKSMAMRL HFQPPHPNCL
YTVELEAFAI YKVCARNERE ECGVSARSLS GLVGWQEVTE GSFRLHPLRA RLSLGWTVTP
MSLSPPKLLA *

mutated AA sequence

MLTQAPSSVV RSRNSRNHTV NSGGSCLSAS TVAIPAINDS SAAMSACSTI SAQPASSMDT
QMHSPKKQER VNKRVIWGIE VAEELHWKGW ELGKETTRNL VLKNRSLKLQ KMKYRPPKTK
FFFTVIPQPI FLSPGITLTL PIVFRPLEAK EYMDQLWFEK AEGMFCVGLR ATLPCHRLIC
RPPSLQLPMC AVGDTTEAFF CLDNVGDLPT FFTWEFSSPF QMLPATGLLE PGQASQIKVT
FQPLTAVIYE VQATCWYGAG SRQRSSIQLQ AVAKCAQLLV SIKHKCPEDQ DAEGFQKLLY
FGSVAVGCTS ERQIRLHNPS AVNAPFRIEI SPDELAEDQA FSCPTAHGIV LPGEKKCVSV
FFHPKTLDTR TVDYCSIMPS GCASKTLLKV VGFCRGPAVS LQHYCVNFSW VNLGERSEQP
LWIENQSDCT AHFQFAIDCL ESVFTIRPAF GTLVGKARMT LHCAFQPTHP IICFRRVACL
IHHQDPLFLD LMGTCHSDST KPAILKPQHL TWYRTHLARG LTLYPPDILD AMLKEKKLAQ
DQNGALMIPI QDLEDMPAPQ YPYIPPMTEF FFDGTSDITI FPPPISVEPV EVDFGACPGP
EAPNPVPLCL MNHTKGKIMV VWTRRSDCPF WVTPESCDVP PLKSMAMRLH FQPPHPNCLY
TVELEAFAIY KVCARNEREE CGVSARSLSG LVGWQEVTEG SFRLHPLRAR LSLGWTVTPM
SLSPPKLLA*

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