mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999936752 (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)

chr4:113352397G>AN/A show variant in all transcripts IGV

HGNC symbol

ALPK1

Ensembl transcript ID

ENST00000458497

Genbank transcript ID

NM_001102406

UniProt peptide

Q96QP1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1694G>A
cDNA.1973G>A
g.145733G>A

AA changes

G565D Score: 94 explain score(s)

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

565

frameshift

known variant

Reference ID: rs2074388

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1014	1114	2128
ExAC	23754	-14741	9013

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.445	0
	0.354	0
(flanking)	-2.048	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	145736	wt: 0.63 / mu: 0.82	wt: TGGTGAGGGAGCTGT mu: TGATGAGGGAGCTGT	GTGA\|ggga
Donor marginally increased	145731	wt: 0.9252 / mu: 0.9778 (marginal change - not scored)	wt: AGCAATGGTGAGGGA mu: AGCAATGATGAGGGA	CAAT\|ggtg
Donor gained	145729	0.71	mu: ACAGCAATGATGAGG	AGCA\|atga

distance from splice site

794

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

565

mutated

not conserved

565

Ptroglodytes

all identical

ENSPTRG00000016375

565

Mmulatta

no alignment

ENSMMUG00000014073

n/a

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028028

565

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000059741

561

Dmelanogaster

no homologue

Celegans

no alignment

F42A10.4

n/a

Xtropicalis

not conserved

ENSXETG00000024103

548

protein features

start (aa)	end (aa)	feature	details
921	960	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
1017	1237	DOMAIN	Alpha-type protein kinase.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3735 / 3735

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

1245 / 1245

position of stopcodon in wt / mu cDNA

4014 / 4014

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

280 / 280

chromosome

strand

last intron/exon boundary

4007

theoretical NMD boundary in CDS

3677

length of CDS

3735

coding sequence (CDS) position

1694

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

1973

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

145733

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

113352397

original gDNA sequence snippet

GCCATCGGACTACAGCAATGGTGAGGGAGCTGTTTTCAACA

altered gDNA sequence snippet

GCCATCGGACTACAGCAATGATGAGGGAGCTGTTTTCAACA

original cDNA sequence snippet

GCCATCGGACTACAGCAATGGTGAGGGAGCTGTTTTCAACA

altered cDNA sequence snippet

GCCATCGGACTACAGCAATGATGAGGGAGCTGTTTTCAACA

wildtype AA sequence

MNNQKVVAVL LQECKQVLDQ LLLEAPDVSE EDKSEDQRCR ALLPSELRTL IQEAKEMKWP
FVPEKWQYKQ AVGPEDKTNL KDVIGAGLQQ LLASLRASIL ARDCAAAAAI VFLVDRFLYG
LDVSGKLLQV AKGLHKLQPA TPIAPQVVIR QARISVNSGK LLKAEYILSS LISNNGATGT
WLYRNESDKV LVQSVCIQIR GQILQKLGMW YEAAELIWAS IVGYLALPQP DKKGLSTSLG
ILADIFVSMS KNDYEKFKNN PQINLSLLKE FDHHLLSAAE ACKLAAAFSA YTPLFVLTAV
NIRGTCLLSY SSSNDCPPEL KNLHLCEAKE AFEIGLLTKR DDEPVTGKQE LHSFVKAAFG
LTTVHRRLHG ETGTVHAASQ LCKEAMGKLY NFSTSSRSQD REALSQEVMS VIAQVKEHLQ
VQSFSNVDDR SYVPESFECR LDKLILHGQG DFQKILDTYS QHHTSVCEVF ESDCGNNKNE
QKDAKTGVCI TALKTEIKNI DTVSTTQEKP HCQRDTGISS SLMGKNVQRE LRRGGRRNWT
HSDAFRVSLD QDVETETEPS DYSNGEGAVF NKSLSGSQTS SAWSNLSGFS SSASWEEVNY
HVDDRSARKE PGKEHLVDTQ CSTALSEELE NDREGRAMHS LHSQLHDLSL QEPNNDNLEP
SQNQPQQQMP LTPFSPHNTP GIFLAPGAGL LEGAPEGIQE VRNMGPRNTS AHSRPSYRSA
SWSSDSGRPK NMGTHPSVQK EEAFEIIVEF PETNCDVKDR QGKEQGEEIS ERGAGPTFKA
SPSWVDPEGE TAESTEDAPL DFHRVLHNSL GNISMLPCSS FTPNWPVQNP DSRKSGGPVA
EQGIDPDAST VDEEGQLLDS MDVPCTNGHG SHRLCILRQP PGQRAETPNS SVSGNILFPV
LSEDCTTTEE GNQPGNMLNC SQNSSSSSVW WLKSPAFSSG SSEGDSPWSY LNSSGSSWVS
LPGKMRKEIL EARTLQPDDF EKLLAGVRHD WLFQRLENTG VFKPSQLHRA HSALLLKYSK
KSELWTAQET IVYLGDYLTV KKKGRQRNAF WVHHLHQEEI LGRYVGKDYK EQKGLWHHFT
DVERQMTAQH YVTEFNKRLY EQNIPTQIFY IPSTILLILE DKTIKGCISV EPYILGEFVK
LSNNTKVVKT EYKATEYGLA YGHFSYEFSN HRDVVVDLQG WVTGNGKGLI YLTDPQIHSV
DQKVFTTNFG KRGIFYFFNN QHVECNEICH RLSLTRPSME KPCT*

mutated AA sequence

MNNQKVVAVL LQECKQVLDQ LLLEAPDVSE EDKSEDQRCR ALLPSELRTL IQEAKEMKWP
FVPEKWQYKQ AVGPEDKTNL KDVIGAGLQQ LLASLRASIL ARDCAAAAAI VFLVDRFLYG
LDVSGKLLQV AKGLHKLQPA TPIAPQVVIR QARISVNSGK LLKAEYILSS LISNNGATGT
WLYRNESDKV LVQSVCIQIR GQILQKLGMW YEAAELIWAS IVGYLALPQP DKKGLSTSLG
ILADIFVSMS KNDYEKFKNN PQINLSLLKE FDHHLLSAAE ACKLAAAFSA YTPLFVLTAV
NIRGTCLLSY SSSNDCPPEL KNLHLCEAKE AFEIGLLTKR DDEPVTGKQE LHSFVKAAFG
LTTVHRRLHG ETGTVHAASQ LCKEAMGKLY NFSTSSRSQD REALSQEVMS VIAQVKEHLQ
VQSFSNVDDR SYVPESFECR LDKLILHGQG DFQKILDTYS QHHTSVCEVF ESDCGNNKNE
QKDAKTGVCI TALKTEIKNI DTVSTTQEKP HCQRDTGISS SLMGKNVQRE LRRGGRRNWT
HSDAFRVSLD QDVETETEPS DYSNDEGAVF NKSLSGSQTS SAWSNLSGFS SSASWEEVNY
HVDDRSARKE PGKEHLVDTQ CSTALSEELE NDREGRAMHS LHSQLHDLSL QEPNNDNLEP
SQNQPQQQMP LTPFSPHNTP GIFLAPGAGL LEGAPEGIQE VRNMGPRNTS AHSRPSYRSA
SWSSDSGRPK NMGTHPSVQK EEAFEIIVEF PETNCDVKDR QGKEQGEEIS ERGAGPTFKA
SPSWVDPEGE TAESTEDAPL DFHRVLHNSL GNISMLPCSS FTPNWPVQNP DSRKSGGPVA
EQGIDPDAST VDEEGQLLDS MDVPCTNGHG SHRLCILRQP PGQRAETPNS SVSGNILFPV
LSEDCTTTEE GNQPGNMLNC SQNSSSSSVW WLKSPAFSSG SSEGDSPWSY LNSSGSSWVS
LPGKMRKEIL EARTLQPDDF EKLLAGVRHD WLFQRLENTG VFKPSQLHRA HSALLLKYSK
KSELWTAQET IVYLGDYLTV KKKGRQRNAF WVHHLHQEEI LGRYVGKDYK EQKGLWHHFT
DVERQMTAQH YVTEFNKRLY EQNIPTQIFY IPSTILLILE DKTIKGCISV EPYILGEFVK
LSNNTKVVKT EYKATEYGLA YGHFSYEFSN HRDVVVDLQG WVTGNGKGLI YLTDPQIHSV
DQKVFTTNFG KRGIFYFFNN QHVECNEICH RLSLTRPSME KPCT*

speed

1.09 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