mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM000499)
known disease mutation: rs5422 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:39200947T>CN/A show variant in all transcripts IGV

HGNC symbol

ACTN4

Ensembl transcript ID

ENST00000390009

Genbank transcript ID

N/A

UniProt peptide

O43707

alteration type

single base exchange

alteration region

intron

DNA changes

g.62659T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121908417
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5422 (pathogenic for Focal segmental glomerulosclerosis 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000499)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000499)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000499)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.438	1
	4.392	1
(flanking)	5.303	1

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	62657	wt: 0.24 / mu: 0.29	wt: CTATGTGTCCAGCTT mu: CTATGTGCCCAGCTT	ATGT\|gtcc
Donor increased	62662	wt: 0.28 / mu: 0.36	wt: TGTCCAGCTTCTACC mu: TGCCCAGCTTCTACC	TCCA\|gctt
Donor marginally increased	62650	wt: 0.9714 / mu: 0.9786 (marginal change - not scored)	wt: TAATGACCTATGTGT mu: TAATGACCTATGTGC	ATGA\|ccta

distance from splice site

4162

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	269	DOMAIN	Actin-binding.	might get lost (downstream of altered splice site)
47	64	HELIX		might get lost (downstream of altered splice site)
50	154	DOMAIN	CH 1.	might get lost (downstream of altered splice site)
60	60	CONFLICT	C -> S (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
65	67	HELIX		might get lost (downstream of altered splice site)
74	80	TURN		might get lost (downstream of altered splice site)
82	92	HELIX		might get lost (downstream of altered splice site)
105	120	HELIX		might get lost (downstream of altered splice site)
114	114	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
121	123	TURN		might get lost (downstream of altered splice site)
131	135	HELIX		might get lost (downstream of altered splice site)
139	153	HELIX		might get lost (downstream of altered splice site)
154	157	TURN		might get lost (downstream of altered splice site)
163	269	DOMAIN	CH 2.	might get lost (downstream of altered splice site)
164	164	CONFLICT	S -> L (in Ref. 4; AL047603/AU118403).	might get lost (downstream of altered splice site)
165	177	HELIX		might get lost (downstream of altered splice site)
177	192	REGION	Polyphosphoinositide (PIP2)-binding (Potential).	might get lost (downstream of altered splice site)
187	189	STRAND		might get lost (downstream of altered splice site)
190	192	HELIX		might get lost (downstream of altered splice site)
196	205	HELIX		might get lost (downstream of altered splice site)
207	209	HELIX		might get lost (downstream of altered splice site)
212	214	HELIX		might get lost (downstream of altered splice site)
214	214	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
220	234	HELIX		might get lost (downstream of altered splice site)
243	248	HELIX		might get lost (downstream of altered splice site)
249	251	STRAND		might get lost (downstream of altered splice site)
254	267	HELIX		might get lost (downstream of altered splice site)
265	265	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
276	276	CONFLICT	T -> TET (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
292	294	CONFLICT	EHL -> CSTS (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
293	403	REPEAT	Spectrin 1.	might get lost (downstream of altered splice site)
359	360	CONFLICT	TL -> SV (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
378	378	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin).	might get lost (downstream of altered splice site)
413	518	REPEAT	Spectrin 2.	might get lost (downstream of altered splice site)
417	417	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
476	476	CONFLICT	I -> S (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
519	552	HELIX		might get lost (downstream of altered splice site)
526	526	CONFLICT	I -> II (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
528	639	REPEAT	Spectrin 3.	might get lost (downstream of altered splice site)
536	536	CONFLICT	R -> P (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
560	600	HELIX		might get lost (downstream of altered splice site)
592	592	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
606	608	STRAND		might get lost (downstream of altered splice site)
616	641	HELIX		might get lost (downstream of altered splice site)
625	625	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
645	645	CONFLICT	Q -> QQ (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
649	752	REPEAT	Spectrin 4.	might get lost (downstream of altered splice site)
673	674	CONFLICT	GR -> A (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
736	756	HELIX		might get lost (downstream of altered splice site)
765	800	DOMAIN	EF-hand 1.	might get lost (downstream of altered splice site)
778	789	CA_BIND	1 (Potential).	might get lost (downstream of altered splice site)
806	841	DOMAIN	EF-hand 2.	might get lost (downstream of altered splice site)
819	830	CA_BIND	2 (Potential).	might get lost (downstream of altered splice site)
850	850	CONFLICT	A -> T (in Ref. 3; AAC17470).	might get lost (downstream of altered splice site)
891	893	CONFLICT	AVP -> GVR (in Ref. 3; AAC17470).	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

9 / 9

chromosome

strand

last intron/exon boundary

1929

theoretical NMD boundary in CDS

1870

length of CDS

2079

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)

62659

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

39200947

original gDNA sequence snippet

AGGCCATAATGACCTATGTGTCCAGCTTCTACCATGCCTTT

altered gDNA sequence snippet

AGGCCATAATGACCTATGTGCCCAGCTTCTACCATGCCTTT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVDYHAANQS YQYGPSSAGN GAGGGGSMGD YMAQEDDWDR DLLLDPAWEK QQRKAETAAN
RICKVLAVNQ ENEHLMEDYE KLASDLLEWI RRTIPWLEDR VPQKTIQEMQ QKLEDFRDYR
RVHKPPKVQE KCQLEINFNT LQTKLRLSNR PAFMPSEGKM VSDINNGWQH LEQAEKGYEE
WLLNEIRRLE RLDHLAEKFR QKASIHEAWT DGKEAMLKHR DYETATLSDI KALIRKHEAF
ESDLAAHQDR VEQIAAIAQE LNELDYYDSH NVNTRCQKIC DQWDALGSLT HSRREALEKT
EKQLEAIDQL HLEYAKRAAP FNNWMESAME DLQDMFIVHT IEEIEGLISA HDQFKSTLPD
ADREREAILA IHKEAQRIAE SNHIKLSGSN PYTTVTPQII NSKWEKVQQL VPKRDHALLE
EQSKQQSNEH LRRQFASQAN VVGPWIQTKM EEIGRISIEM NGTLEDQLSH LKQYERSIVD
YKPNLDLLEQ QHQLIQEALI FDNKHTNYTM EHIRVGWEQL LTTIARTINE VENQILTRDA
KGISQEQMQE FRASFNHFDK DHGGALGPEE FKACLISLGY DVENDRQGEA EFNRIMSLVD
PNHSGLVTFQ AFIDFMSRET TDTDTADQVI ASFKVLAGDK NFITAEELRR ELPPDQAEYC
IARMAPYQGP DAVPGALDYK SFSTALYGES DL*

mutated AA sequence

N/A

speed

1.09 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