mutation t@sting

Prediction

disease causing

Model: without_aae, prob: 0.999999999658292 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM023571)
known disease mutation: rs7760 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:202141631C>TN/A show variant in all transcripts IGV

HGNC symbol

CASP8

Ensembl transcript ID

ENST00000264274

Genbank transcript ID

N/A

UniProt peptide

Q14790

alteration type

single base exchange

alteration region

intron

DNA changes

g.43466C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs17860424

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs7760 (pathogenic for Autoimmune lymphoproliferative syndrome type 2B) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023571)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023571)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023571)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.229	0.945
	0.654	0.941
(flanking)	2.834	0.936

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	43462	wt: 0.23 / mu: 0.57	wt: GCAAAAGCACGGGAG mu: GCAAAAGCATGGGAG	AAAA\|gcac
Donor marginally increased	43469	wt: 0.9913 / mu: 0.9916 (marginal change - not scored)	wt: CACGGGAGAAAGTGC mu: CATGGGAGAAAGTGC	CGGG\|agaa
Donor increased	43470	wt: 0.34 / mu: 0.38	wt: ACGGGAGAAAGTGCC mu: ATGGGAGAAAGTGCC	GGGA\|gaaa

distance from splice site

4132

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	216	PROPEP	/FTId=PRO_0000004628.	might get lost (downstream of altered splice site)
188	188	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
219	219	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
230	232	STRAND		might get lost (downstream of altered splice site)
235	240	STRAND		might get lost (downstream of altered splice site)
246	249	HELIX		might get lost (downstream of altered splice site)
252	254	HELIX		might get lost (downstream of altered splice site)
255	257	STRAND		might get lost (downstream of altered splice site)
263	276	HELIX		might get lost (downstream of altered splice site)
280	286	STRAND		might get lost (downstream of altered splice site)
289	301	HELIX		might get lost (downstream of altered splice site)
294	294	CONFLICT	E -> D (in Ref. 5; AAD24962).	might get lost (downstream of altered splice site)
310	316	STRAND		might get lost (downstream of altered splice site)
317	317	ACT_SITE		might get lost (downstream of altered splice site)
322	324	STRAND		might get lost (downstream of altered splice site)
326	328	STRAND		might get lost (downstream of altered splice site)
330	332	STRAND		might get lost (downstream of altered splice site)
331	331	CONFLICT	A -> P (in Ref. 2; AAC50602 and 5; AAD24962).	might get lost (downstream of altered splice site)
333	337	HELIX		might get lost (downstream of altered splice site)
334	334	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
338	340	HELIX		might get lost (downstream of altered splice site)
342	344	TURN		might get lost (downstream of altered splice site)
343	344	CONFLICT	LK -> FG (in Ref. 8; AAL87631).	might get lost (downstream of altered splice site)
346	348	HELIX		might get lost (downstream of altered splice site)
353	359	STRAND		might get lost (downstream of altered splice site)
360	360	ACT_SITE		might get lost (downstream of altered splice site)
362	364	STRAND		might get lost (downstream of altered splice site)
375	384	PROPEP	/FTId=PRO_0000004630.	might get lost (downstream of altered splice site)
377	379	STRAND		might get lost (downstream of altered splice site)
387	387	MUTAGEN	S->A: Impaired CDK1-mediated phosphorylation and enhanced apoptosis.	might get lost (downstream of altered splice site)
387	387	MOD_RES	Phosphoserine; by CDK1.	might get lost (downstream of altered splice site)
395	405	STRAND		might get lost (downstream of altered splice site)
412	414	STRAND		might get lost (downstream of altered splice site)
415	417	TURN		might get lost (downstream of altered splice site)
420	432	HELIX		might get lost (downstream of altered splice site)
433	435	HELIX		might get lost (downstream of altered splice site)
439	451	HELIX		might get lost (downstream of altered splice site)
456	459	TURN		might get lost (downstream of altered splice site)
465	468	STRAND		might get lost (downstream of altered splice site)
471	473	STRAND		might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

236 / 236

chromosome

strand

last intron/exon boundary

1288

theoretical NMD boundary in CDS

1002

length of CDS

1188

coding sequence (CDS) position

N/A

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

N/A

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

43466

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

202141631

original gDNA sequence snippet

ATCACAATTTTGCAAAAGCACGGGAGAAAGTGCCCAAACTT

altered gDNA sequence snippet

ATCACAATTTTGCAAAAGCATGGGAGAAAGTGCCCAAACTT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MDFSRNLYDI GEQLDSEDLA SLKFLSLDYI PQRKQEPIKD ALMLFQRLQE KRMLEESNLS
FLKELLFRIN RLDLLITYLN TRKEEMEREL QTPGRAQISA YRVMLYQISE EVSRSELRSF
KFLLQEEISK CKLDDDMNLL DIFIEMEKRV ILGEGKLDIL KRVCAQINKS LLKIINDYEE
FSKGALTTTF EELHFEIKPH DDCTVEQIYE ILKIYQLMDH SNMDCFICCI LSHGDKGIIY
GTDGQEAPIY ELTSQFTGLK CPSLAGKPKV FFIQACQGDN YQKGIPVETD SEEQPYLEMD
LSSPQTRYIP DEADFLLGMA TVNNCVSYRN PAEGTWYIQS LCQSLRERCP RGDDILTILT
EVNYEVSNKD DKKNMGKQMP QPTFTLRKKL VFPSD*

mutated AA sequence

N/A

speed

0.47 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