mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999986327 (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)

chr17:39890715A>TN/A show variant in all transcripts IGV

HGNC symbol

HAP1

Ensembl transcript ID

ENST00000347901

Genbank transcript ID

NM_177977

UniProt peptide

P54257

alteration type

single base exchange

alteration region

CDS

DNA changes

c.172T>A
cDNA.182T>A
g.182T>A

AA changes

S58T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs4796603

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1570	716	2286
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
TAF7, Transcription Factor, TAF7 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.112	0.003
	0.79	0.003
(flanking)	-0.186	0.002

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	181	wt: 0.20 / mu: 0.31	wt: TCTGGATCCCAGTTC mu: TCTGGAACCCAGTTC	TGGA\|tccc

distance from splice site

182

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000002132

Mmusculus

all identical

ENSMUSG00000006930

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074508

n/a

Dmelanogaster

not conserved

FBgn0262872

1157

Celegans

no alignment

T27A3.1

n/a

Xtropicalis

no alignment

ENSXETG00000012489

n/a

protein features

start (aa)	end (aa)	feature	details
106	461	DOMAIN	HAP1 N-terminal.	might get lost (downstream of altered splice site)
184	199	CONFLICT	Missing (in Ref. 6; CAB82785).	might get lost (downstream of altered splice site)
261	601	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)
573	573	CONFLICT	P -> L (in Ref. 3; BAB13952).	might get lost (downstream of altered splice site)
579	579	CONFLICT	M -> V (in Ref. 1; AAC39861).	might get lost (downstream of altered splice site)
611	611	CONFLICT	A -> T (in Ref. 7; AAC50297).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1860 / 1860

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

620 / 620

position of stopcodon in wt / mu cDNA

1870 / 1870

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

11 / 11

chromosome

strand

-1

last intron/exon boundary

1417

theoretical NMD boundary in CDS

1356

length of CDS

1860

coding sequence (CDS) position

172

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

182

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

182

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

39890715

original gDNA sequence snippet

GATCCCGAGCCACCTCTGGATCCCAGTTCCTCTCGGAAGCC

altered gDNA sequence snippet

GATCCCGAGCCACCTCTGGAACCCAGTTCCTCTCGGAAGCC

original cDNA sequence snippet

GATCCCGAGCCACCTCTGGATCCCAGTTCCTCTCGGAAGCC

altered cDNA sequence snippet

GATCCCGAGCCACCTCTGGAACCCAGTTCCTCTCGGAAGCC

wildtype AA sequence

MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFSEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM YGAETEKLQK QLASEKEIQM
QLQEEETLPG FQETLAEELR TSLRRMISDP VYFMERNYEM PRGDTSSLRY DFRYSEDREQ
VRGFEAEEGL MLAADIMRGE DFTPAEEFVP QEELGAAKKV PAEEGVMEEA ELVSEETEGW
EEVELELDEA TRMNVVTSAL EASGLGPSHL DMNYVLQQLA NWQDAHYRRQ LRWKMLQKGE
CPHGALPAAS RTSCRSSCR*

mutated AA sequence

MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGTQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFSEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM YGAETEKLQK QLASEKEIQM
QLQEEETLPG FQETLAEELR TSLRRMISDP VYFMERNYEM PRGDTSSLRY DFRYSEDREQ
VRGFEAEEGL MLAADIMRGE DFTPAEEFVP QEELGAAKKV PAEEGVMEEA ELVSEETEGW
EEVELELDEA TRMNVVTSAL EASGLGPSHL DMNYVLQQLA NWQDAHYRRQ LRWKMLQKGE
CPHGALPAAS RTSCRSSCR*

speed

1.31 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