mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.901957741900338 (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)

chr17:39884583G>AN/A show variant in all transcripts IGV

HGNC symbol

HAP1

Ensembl transcript ID

ENST00000393939

Genbank transcript ID

NM_001079871

UniProt peptide

P54257

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1070C>T
cDNA.1080C>T
g.6314C>T

AA changes

S357L Score: 145 explain score(s)

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

357

frameshift

known variant

Reference ID: rs4796693

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1566	740	2306
ExAC	-	-	-

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.636	0.704
	0.268	0.718
(flanking)	3.277	0.748

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	6313.5	sequence motif lost	-	wt: ccca\|GCGG mu: ccca.GTGG
Acc increased	6304	wt: 0.26 / mu: 0.37	wt: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGC mu: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGC	ctgc\|CCTC
Acc marginally increased	6313	wt: 0.9164 / mu: 0.9182 (marginal change - not scored)	wt: CCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATG mu: CCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATG	ccag\|CGGA
Acc marginally increased	6312	wt: 0.9947 / mu: 0.9967 (marginal change - not scored)	wt: ACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGAT mu: ACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGAT	ccca\|GCGG
Acc marginally increased	6316	wt: 0.8703 / mu: 0.8861 (marginal change - not scored)	wt: GTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGGCT mu: GTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGGCT	gcgg\|AGGC
Acc marginally increased	6307	wt: 0.4322 / mu: 0.4417 (marginal change - not scored)	wt: GGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAA mu: GGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAA	ccct\|CCCC
Donor marginally increased	6312	wt: 0.9986 / mu: 0.9987 (marginal change - not scored)	wt: TCCCCAGCGGAGGCC mu: TCCCCAGTGGAGGCC	CCCA\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

357

mutated

not conserved

357

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000002132

346

Mmusculus

all identical

ENSMUSG00000006930

310

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000074508

203

Dmelanogaster

all conserved

FBgn0262872

415

Celegans

not conserved

T27A3.1

232

Xtropicalis

all identical

ENSXETG00000012489

325

protein features

start (aa)	end (aa)	feature	details
106	461	DOMAIN	HAP1 N-terminal.	lost
261	601	COMPBIAS	Glu-rich.	lost
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

1785 / 1785

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

595 / 595

position of stopcodon in wt / mu cDNA

1795 / 1795

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

1342

theoretical NMD boundary in CDS

1281

length of CDS

1785

coding sequence (CDS) position

1070

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

1080

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

6314

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

39884583

original gDNA sequence snippet

CTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGG

altered gDNA sequence snippet

CTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGG

original cDNA sequence snippet

GGAGTGTGTGGAGCAGTTTTCGGAGGCCAGCCAACAGATGG

altered cDNA sequence snippet

GGAGTGTGTGGAGCAGTTTTTGGAGGCCAGCCAACAGATGG

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 ETLPGFQETL AEELRTSLRR
MISDPVYFME RNYEMPRGDT SSLRYDFRYS EDREQVRGFE AEEGLMLAAD IMRGEDFTPA
EEFVPQEELG AAKKVPAEEG VMEEAELVSE ETEGWEEVEL ELDEATRMNV VTSALEASGL
GPSHLDMNYV LQQLANWQDA HYRRQLRWKM LQKGECPHGA LPAASRTSCR SSCR*

mutated 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 ECVEQFLEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM ETLPGFQETL AEELRTSLRR
MISDPVYFME RNYEMPRGDT SSLRYDFRYS EDREQVRGFE AEEGLMLAAD IMRGEDFTPA
EEFVPQEELG AAKKVPAEEG VMEEAELVSE ETEGWEEVEL ELDEATRMNV VTSALEASGL
GPSHLDMNYV LQQLANWQDA HYRRQLRWKM LQKGECPHGA LPAASRTSCR SSCR*

speed

0.57 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