mutation t@sting

Prediction

disease causing

Model: without_aae, prob: 9.78242882627092e-08 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM060829)
known disease mutation: rs18076 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:21161887G>AN/A show variant in all transcripts IGV

HGNC symbol

RNASE4

Ensembl transcript ID

ENST00000555597

Genbank transcript ID

N/A

UniProt peptide

P34096

alteration type

single base exchange

alteration region

intron

DNA changes

g.9629G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121909538
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18076 (pathogenic for Amyotrophic lateral sclerosis type 9) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM060829)

known disease mutation at this position, please check HGMD for details (HGMD ID CM060829)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060829)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.999	0
	-3.847	0
(flanking)	0.076	0

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

splice sites

splice site change before start ATG (at aa -5) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	9631	wt: 0.33 / mu: 0.79	wt: TGAGGAGACGGGGCC mu: TGAAGAGACGGGGCC	AGGA\|gacg
Donor marginally increased	9629	wt: 0.9832 / mu: 0.9939 (marginal change - not scored)	wt: CATGAGGAGACGGGG mu: CATGAAGAGACGGGG	TGAG\|gaga
Donor gained	9624	0.91	mu: AGCATCATGAAGAGA	CATC\|atga

distance from splice site

4854

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	28	SIGNAL		might get lost (downstream of altered splice site)
29	29	MOD_RES	Pyrrolidone carboxylic acid.	might get lost (downstream of altered splice site)
29	40	HELIX		might get lost (downstream of altered splice site)
38	38	BINDING	Substrate.	might get lost (downstream of altered splice site)
40	40	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
50	59	HELIX		might get lost (downstream of altered splice site)
53	53	DISULFID		might get lost (downstream of altered splice site)
54	54	CONFLICT	N -> D (in Ref. 3; AAA96750).	might get lost (downstream of altered splice site)
62	66	STRAND		might get lost (downstream of altered splice site)
67	67	DISULFID		might get lost (downstream of altered splice site)
68	72	REGION	Substrate binding.	might get lost (downstream of altered splice site)
69	74	STRAND		might get lost (downstream of altered splice site)
78	82	HELIX		might get lost (downstream of altered splice site)
83	86	HELIX		might get lost (downstream of altered splice site)
85	85	DISULFID		might get lost (downstream of altered splice site)
92	92	DISULFID		might get lost (downstream of altered splice site)
93	93	BINDING	Substrate.	might get lost (downstream of altered splice site)
99	99	DISULFID		might get lost (downstream of altered splice site)
99	111	STRAND		might get lost (downstream of altered splice site)
109	109	DISULFID		might get lost (downstream of altered splice site)
110	110	BINDING	Substrate.	might get lost (downstream of altered splice site)
113	115	STRAND		might get lost (downstream of altered splice site)
120	120	DISULFID		might get lost (downstream of altered splice site)
122	136	STRAND		might get lost (downstream of altered splice site)
135	135	DISULFID		might get lost (downstream of altered splice site)
137	140	TURN		might get lost (downstream of altered splice site)
141	147	STRAND		might get lost (downstream of altered splice site)
144	144	ACT_SITE	Proton donor.	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

111 / 111

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

444

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)

9629

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

21161887

original gDNA sequence snippet

ATACTGTGAAAGCATCATGAGGAGACGGGGCCTGACCTCAC

altered gDNA sequence snippet

ATACTGTGAAAGCATCATGAAGAGACGGGGCCTGACCTCAC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MALQRTHSLL LLLLLTLLGL GLVQPSYGQD GMYQRFLRQH VHPEETGGSD RYCNLMMQRR
KMTLYHCKRF NTFIHEDIWN IRSICSTTNI QCKNGKMNCH EGVVKVTDCR DTGSSRAPNC
RYRAIASTRR VVIACEGNPQ VPVHFDG*

mutated AA sequence

N/A

speed

1.22 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