mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999697441095521 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM012083)
known disease mutation: rs12742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:87017523C>TN/A show variant in all transcripts IGV

HGNC symbol

CD8A

Ensembl transcript ID

ENST00000409511

Genbank transcript ID

NM_001145873

UniProt peptide

P01732

alteration type

single base exchange

alteration region

CDS

DNA changes

c.331G>A
cDNA.1362G>A
g.17997G>A

AA changes

G111S Score: 56 explain score(s)

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

111

frameshift

known variant

Reference ID: rs121918660

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs12742 (pathogenic for Cd8 deficiency, familial) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012083)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012083)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012083)

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
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.763	0.999
	2.763	0.968
(flanking)	-0.934	0.053

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 gained	17993	0.75	mu: GAGAACGAGAGCTAC	GAAC\|gaga
Donor gained	17992	0.74	mu: AGAGAACGAGAGCTA	AGAA\|cgag
Donor gained	17997	0.83	mu: ACGAGAGCTACTATT	GAGA\|gcta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

111

mutated

not conserved

111

Ptroglodytes

all identical

ENSPTRG00000012159

152

Mmulatta

all identical

ENSMMUG00000003524

111

Fcatus

all identical

ENSFCAG00000014826

114

Mmusculus

all identical

ENSMUSG00000053977

120

Ggallus

all identical

ENSGALG00000015816

115

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
22	135	DOMAIN	Ig-like V-type.	lost
22	182	TOPO_DOM	Extracellular (Potential).	lost
107	109	HELIX		might get lost (downstream of altered splice site)
111	111	MUTAGEN	G->R: Prevents CD8 expression.	lost
111	119	STRAND		lost
115	115	DISULFID		might get lost (downstream of altered splice site)
122	125	STRAND		might get lost (downstream of altered splice site)
129	131	STRAND		might get lost (downstream of altered splice site)
183	203	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
204	235	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

708 / 708

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

236 / 236

position of stopcodon in wt / mu cDNA

1739 / 1739

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

1032 / 1032

chromosome

strand

-1

last intron/exon boundary

1688

theoretical NMD boundary in CDS

606

length of CDS

708

coding sequence (CDS) position

331

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

1362

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

17997

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

87017523

original gDNA sequence snippet

ACTTCCGCCGAGAGAACGAGGGCTACTATTTCTGCTCGGCC

altered gDNA sequence snippet

ACTTCCGCCGAGAGAACGAGAGCTACTATTTCTGCTCGGCC

original cDNA sequence snippet

ACTTCCGCCGAGAGAACGAGGGCTACTATTTCTGCTCGGCC

altered cDNA sequence snippet

ACTTCCGCCGAGAGAACGAGAGCTACTATTTCTGCTCGGCC

wildtype AA sequence

MALPVTALLL PLALLLHAAR PSQFRVSPLD RTWNLGETVE LKCQVLLSNP TSGCSWLFQP
RGAAASPTFL LYLSQNKPKA AEGLDTQRFS GKRLGDTFVL TLSDFRRENE GYYFCSALSN
SIMYFSHFVP VFLPAKPTTT PAPRPPTPAP TIASQPLSLR PEACRPAAGG AVHTRGLDFA
CDIYIWAPLA GTCGVLLLSL VITLYCNHRN RRRVCKCPRP VVKSGDKPSL SARYV*

mutated AA sequence

MALPVTALLL PLALLLHAAR PSQFRVSPLD RTWNLGETVE LKCQVLLSNP TSGCSWLFQP
RGAAASPTFL LYLSQNKPKA AEGLDTQRFS GKRLGDTFVL TLSDFRRENE SYYFCSALSN
SIMYFSHFVP VFLPAKPTTT PAPRPPTPAP TIASQPLSLR PEACRPAAGG AVHTRGLDFA
CDIYIWAPLA GTCGVLLLSL VITLYCNHRN RRRVCKCPRP VVKSGDKPSL SARYV*

speed

1.15 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