mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999916 (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)

chr19:43382368T>GN/A show variant in all transcripts IGV

HGNC symbol

PSG1

Ensembl transcript ID

ENST00000403380

Genbank transcript ID

N/A

UniProt peptide

P11464

alteration type

single base exchange

alteration region

CDS

DNA changes

c.127A>C
cDNA.217A>C
g.1504A>C

AA changes

T43P Score: 38 explain score(s)

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

frameshift

known variant

Reference ID: rs707745

database	homozygous (G/G)	heterozygous	allele carriers
1000G	501	1163	1664
ExAC	4195	24377	28572

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.187	0
	-0.75	0
(flanking)	-2.266	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	1503	wt: 0.27 / mu: 0.59	wt: GAGCCAACCAAAGTT mu: GAGCCACCCAAAGTT	GCCA\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000038796

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

no homologue

protein features

start (aa)	end (aa)	feature	details
35	144	DOMAIN	Ig-like V-type.	lost
41	43	CONFLICT	EPT -> QPP (in Ref. 4, 5 and 6).	lost
61	61	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
104	104	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
111	111	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
149	234	DOMAIN	Ig-like C2-type 1.	might get lost (downstream of altered splice site)
169	169	DISULFID	Probable.	might get lost (downstream of altered splice site)
199	199	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
217	217	DISULFID	Probable.	might get lost (downstream of altered splice site)
240	327	DOMAIN	Ig-like C2-type 2.	might get lost (downstream of altered splice site)
259	259	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
262	262	DISULFID	Probable.	might get lost (downstream of altered splice site)
268	268	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
303	303	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
310	310	DISULFID	Probable.	might get lost (downstream of altered splice site)
319	319	CONFLICT	I -> V (in Ref. 5 and 6).	might get lost (downstream of altered splice site)
335	410	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
354	354	DISULFID	Probable.	might get lost (downstream of altered splice site)
394	394	DISULFID	Probable.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

981 / 981

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

327 / 327

position of stopcodon in wt / mu cDNA

1071 / 1071

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

91 / 91

chromosome

strand

-1

last intron/exon boundary

1055

theoretical NMD boundary in CDS

914

length of CDS

981

coding sequence (CDS) position

127

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

217

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

1504

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

43382368

original gDNA sequence snippet

TCACGATTGAAGCCGAGCCAACCAAAGTTTCCGAGGGGAAG

altered gDNA sequence snippet

TCACGATTGAAGCCGAGCCACCCAAAGTTTCCGAGGGGAAG

original cDNA sequence snippet

TCACGATTGAAGCCGAGCCAACCAAAGTTTCCGAGGGGAAG

altered cDNA sequence snippet

TCACGATTGAAGCCGAGCCACCCAAAGTTTCCGAGGGGAAG

wildtype AA sequence

MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTAQVTIEA EPTKVSEGKD VLLLVHNLPQ
NLTGYIWYKG QMRDLYHYIT SYVVDGEIII YGPAYSGRET AYSNASLLIQ NVTREDAGSY
TLHIIKGDDG TRGVTGRFTF TLHPKLPKPY ITINNLNPRE NKDVLNFTCE PKSENYTYIW
WLNGQSLPVS PRVKRPIENR ILILPSVTRN ETGPYQCEIR DRYGGIRSDP VTLNVLYGPD
LPRIYPSFTY YRSGEVLYLS CSADSNPPAQ YSWTINEKFQ LPGQKLFIRH ITTKHSGLYV
CSVRNSATGK ESSKSMTVEV SDWTVP*

mutated AA sequence

MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTAQVTIEA EPPKVSEGKD VLLLVHNLPQ
NLTGYIWYKG QMRDLYHYIT SYVVDGEIII YGPAYSGRET AYSNASLLIQ NVTREDAGSY
TLHIIKGDDG TRGVTGRFTF TLHPKLPKPY ITINNLNPRE NKDVLNFTCE PKSENYTYIW
WLNGQSLPVS PRVKRPIENR ILILPSVTRN ETGPYQCEIR DRYGGIRSDP VTLNVLYGPD
LPRIYPSFTY YRSGEVLYLS CSADSNPPAQ YSWTINEKFQ LPGQKLFIRH ITTKHSGLYV
CSVRNSATGK ESSKSMTVEV SDWTVP*

speed

0.41 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