mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 1.16376132271566e-09 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980658)
known disease mutation: rs644 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:169524537C>GN/A show variant in all transcripts IGV

HGNC symbol

Ensembl transcript ID

ENST00000546081

Genbank transcript ID

N/A

UniProt peptide

P12259

alteration type

single base exchange

alteration region

CDS

DNA changes

c.590G>C
cDNA.1004G>C
g.31290G>C

AA changes

R197T Score: 71 explain score(s)

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

197

frameshift

known variant

Reference ID: rs118203906

database	homozygous (G/G)	heterozygous	allele carriers
1000G	0	1	1
ExAC	1	18	19

known disease mutation: rs644 (pathogenic for Thrombophilia due to factor V Leiden) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980658)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980658)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980658)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.023	0.081
	1.265	0.079
(flanking)	-0.125	0.05

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	31285	wt: 0.63 / mu: 0.94	wt: AAGAAAACCAGGAAT mu: AAGAAAACCACGAAT	GAAA\|acca
Donor marginally increased	31281	wt: 0.9968 / mu: 0.9982 (marginal change - not scored)	wt: CCCAAAGAAAACCAG mu: CCCAAAGAAAACCAC	CAAA\|gaaa
Donor marginally increased	31287	wt: 0.4210 / mu: 0.4272 (marginal change - not scored)	wt: GAAAACCAGGAATCT mu: GAAAACCACGAATCT	AAAC\|cagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

197

mutated

not conserved

197

Ptroglodytes

all identical

ENSPTRG00000001659

334

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026579

333

Ggallus

not conserved

ENSGALG00000015207

337

Trubripes

not conserved

ENSTRUG00000014416

334

Drerio

not conserved

ENSDARG00000055705

331

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000002423

334

protein features

start (aa)	end (aa)	feature	details
30	329	DOMAIN	F5/8 type A 1.	lost
203	329	DOMAIN	Plastocyanin-like 2.	might get lost (downstream of altered splice site)
239	239	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
248	248	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	297	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
329	329	DISULFID	By similarity.	might get lost (downstream of altered splice site)
334	335	SITE	Cleavage; by activated protein C.	might get lost (downstream of altered splice site)
348	526	DOMAIN	Plastocyanin-like 3.	might get lost (downstream of altered splice site)
348	684	DOMAIN	F5/8 type A 2.	might get lost (downstream of altered splice site)
382	382	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
460	460	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
468	468	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
500	500	DISULFID	By similarity.	might get lost (downstream of altered splice site)
526	526	DISULFID	By similarity.	might get lost (downstream of altered splice site)
534	535	SITE	Cleavage; by activated protein C.	might get lost (downstream of altered splice site)
536	684	DOMAIN	Plastocyanin-like 4.	might get lost (downstream of altered splice site)
554	554	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
603	603	DISULFID	By similarity.	might get lost (downstream of altered splice site)
640	640	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
684	684	DISULFID	By similarity.	might get lost (downstream of altered splice site)
692	1573	REGION	B.	might get lost (downstream of altered splice site)
693	693	MOD_RES	Sulfotyrosine (Potential).	might get lost (downstream of altered splice site)
707	708	SITE	Cleavage; by activated protein C.	might get lost (downstream of altered splice site)
724	724	MOD_RES	Sulfotyrosine (Potential).	might get lost (downstream of altered splice site)
726	726	MOD_RES	Sulfotyrosine (Potential).	might get lost (downstream of altered splice site)
737	738	SITE	Cleavage; by thrombin.	might get lost (downstream of altered splice site)
738	1573	PROPEP	Activation peptide (connecting region). /FTId=PRO_0000002980.	might get lost (downstream of altered splice site)
741	741	CONFLICT	N -> S (in Ref. 7; ABD23003).	might get lost (downstream of altered splice site)
741	741	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
752	752	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
760	760	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
776	776	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
782	782	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
821	821	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
895	911	REPEAT	1-1.	might get lost (downstream of altered splice site)
895	928	REGION	2 X 17 AA tandem repeats.	might get lost (downstream of altered splice site)
908	908	CONFLICT	E -> K (in Ref. 1; AAA52424 and 8; CAC82573).	might get lost (downstream of altered splice site)
912	928	REPEAT	1-2.	might get lost (downstream of altered splice site)
938	938	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
977	977	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
991	991	CONFLICT	K -> E (in Ref. 5; BAF84302).	might get lost (downstream of altered splice site)
1022	1023	SITE	Cleavage; by activated protein C.	might get lost (downstream of altered splice site)
1046	1047	SITE	Cleavage; by thrombin.	might get lost (downstream of altered splice site)
1074	1074	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1083	1083	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1103	1103	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1106	1106	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1150	1150	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1185	1193	REPEAT	2-1.	might get lost (downstream of altered splice site)
1185	1501	REGION	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.	might get lost (downstream of altered splice site)
1194	1202	REPEAT	2-2.	might get lost (downstream of altered splice site)
1203	1211	REPEAT	2-3.	might get lost (downstream of altered splice site)
1212	1220	REPEAT	2-4.	might get lost (downstream of altered splice site)
1221	1229	REPEAT	2-5.	might get lost (downstream of altered splice site)
1230	1238	REPEAT	2-6.	might get lost (downstream of altered splice site)
1239	1247	REPEAT	2-7.	might get lost (downstream of altered splice site)
1248	1256	REPEAT	2-8.	might get lost (downstream of altered splice site)
1257	1265	REPEAT	2-9.	might get lost (downstream of altered splice site)
1266	1274	REPEAT	2-10.	might get lost (downstream of altered splice site)
1275	1283	REPEAT	2-11.	might get lost (downstream of altered splice site)
1284	1292	REPEAT	2-12.	might get lost (downstream of altered splice site)
1293	1301	REPEAT	2-13.	might get lost (downstream of altered splice site)
1302	1310	REPEAT	2-14.	might get lost (downstream of altered splice site)
1311	1319	REPEAT	2-15.	might get lost (downstream of altered splice site)
1320	1328	REPEAT	2-16.	might get lost (downstream of altered splice site)
1329	1337	REPEAT	2-17.	might get lost (downstream of altered splice site)
1338	1346	REPEAT	2-18.	might get lost (downstream of altered splice site)
1347	1355	REPEAT	2-19.	might get lost (downstream of altered splice site)
1356	1364	REPEAT	2-20.	might get lost (downstream of altered splice site)
1365	1373	REPEAT	2-21.	might get lost (downstream of altered splice site)
1374	1382	REPEAT	2-22.	might get lost (downstream of altered splice site)
1383	1391	REPEAT	2-23.	might get lost (downstream of altered splice site)
1392	1400	REPEAT	2-24.	might get lost (downstream of altered splice site)
1401	1409	REPEAT	2-25.	might get lost (downstream of altered splice site)
1410	1418	REPEAT	2-26.	might get lost (downstream of altered splice site)
1419	1427	REPEAT	2-27.	might get lost (downstream of altered splice site)
1428	1436	REPEAT	2-28.	might get lost (downstream of altered splice site)
1437	1445	REPEAT	2-29.	might get lost (downstream of altered splice site)
1446	1454	REPEAT	2-30.	might get lost (downstream of altered splice site)
1455	1463	REPEAT	2-31.	might get lost (downstream of altered splice site)
1464	1472	REPEAT	2-32.	might get lost (downstream of altered splice site)
1473	1481	REPEAT	2-33.	might get lost (downstream of altered splice site)
1479	1479	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1482	1490	REPEAT	2-34.	might get lost (downstream of altered splice site)
1493	1501	REPEAT	2-35.	might get lost (downstream of altered splice site)
1499	1499	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1522	1522	MOD_RES	Sulfotyrosine (Potential).	might get lost (downstream of altered splice site)
1538	1538	MOD_RES	Sulfotyrosine (Potential).	might get lost (downstream of altered splice site)
1543	1543	MOD_RES	Sulfotyrosine (Potential).	might get lost (downstream of altered splice site)
1559	1559	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1569	1571	TURN		might get lost (downstream of altered splice site)
1573	1574	SITE	Cleavage; by thrombin.	might get lost (downstream of altered splice site)
1578	1751	DOMAIN	Plastocyanin-like 5.	might get lost (downstream of altered splice site)
1578	1907	DOMAIN	F5/8 type A 3.	might get lost (downstream of altered splice site)
1593	1593	MOD_RES	Sulfotyrosine (Potential).	might get lost (downstream of altered splice site)
1703	1703	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1725	1725	DISULFID	Probable.	might get lost (downstream of altered splice site)
1751	1751	DISULFID	Probable.	might get lost (downstream of altered splice site)
1761	1907	DOMAIN	Plastocyanin-like 6.	might get lost (downstream of altered splice site)
1843	1843	METAL	Copper (By similarity).	might get lost (downstream of altered splice site)
1845	1845	METAL	Copper (By similarity).	might get lost (downstream of altered splice site)
1907	1907	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1907	2061	DOMAIN	F5/8 type C 1.	might get lost (downstream of altered splice site)
2010	2010	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
2061	2061	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2066	2066	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2066	2221	DOMAIN	F5/8 type C 2.	might get lost (downstream of altered splice site)
2072	2074	TURN		might get lost (downstream of altered splice site)
2075	2077	STRAND		might get lost (downstream of altered splice site)
2079	2081	HELIX		might get lost (downstream of altered splice site)
2082	2085	STRAND		might get lost (downstream of altered splice site)
2093	2095	STRAND		might get lost (downstream of altered splice site)
2098	2100	HELIX		might get lost (downstream of altered splice site)
2107	2109	STRAND		might get lost (downstream of altered splice site)
2111	2113	STRAND		might get lost (downstream of altered splice site)
2123	2139	STRAND		might get lost (downstream of altered splice site)
2141	2143	STRAND		might get lost (downstream of altered splice site)
2146	2163	STRAND		might get lost (downstream of altered splice site)
2182	2185	STRAND		might get lost (downstream of altered splice site)
2188	2211	STRAND		might get lost (downstream of altered splice site)
2209	2209	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
2213	2213	CONFLICT	A -> T (in Ref. 1; AAA52424).	might get lost (downstream of altered splice site)
2213	2222	STRAND		might get lost (downstream of altered splice site)
2221	2221	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

999 / 999

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

333 / 333

position of stopcodon in wt / mu cDNA

1413 / 1413

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

415 / 415

chromosome

strand

-1

last intron/exon boundary

1611

theoretical NMD boundary in CDS

1146

length of CDS

999

coding sequence (CDS) position

590

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

1004

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

31290

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

169524537

original gDNA sequence snippet

AAACTGCCCAAAGAAAACCAGGAATCTTAAGAAAATAACTC

altered gDNA sequence snippet

AAACTGCCCAAAGAAAACCACGAATCTTAAGAAAATAACTC

original cDNA sequence snippet

AAACTGCCCAAAGAAAACCAGGAATCTTAAGAAAATAACTC

altered cDNA sequence snippet

AAACTGCCCAAAGAAAACCACGAATCTTAAGAAAATAACTC

wildtype AA sequence

MDDAVAPGRE YTYEWSISED SGPTHDDPPC LTHIYYSHEN LIEDFNSGLI GPLLICKKGT
LTEGGTQKTF DKQIVLLFAV FDESKSWSQS SSLMYTVNGY VNGTMPDITV CAHDHISWHL
LGMSSGPELF SIHFNGQVLE QNHHKVSAIT LVSATSTTAN MTVGPEGKWI ISSLTPKHLQ
AGMQAYIDIK NCPKKTRNLK KITREQRRHM KRWEYFIAAE EVIWDYAPVI PANMDKKYRS
QHLDNFSNQI GKHYKKVMYT QYEDESFTKH TVNPNMKEDG ILGPIIRAQV RDTLKIVFKN
MASRPYSIYP HGVTFSPYED EVNSSFTSGT TP*

mutated AA sequence

MDDAVAPGRE YTYEWSISED SGPTHDDPPC LTHIYYSHEN LIEDFNSGLI GPLLICKKGT
LTEGGTQKTF DKQIVLLFAV FDESKSWSQS SSLMYTVNGY VNGTMPDITV CAHDHISWHL
LGMSSGPELF SIHFNGQVLE QNHHKVSAIT LVSATSTTAN MTVGPEGKWI ISSLTPKHLQ
AGMQAYIDIK NCPKKTTNLK KITREQRRHM KRWEYFIAAE EVIWDYAPVI PANMDKKYRS
QHLDNFSNQI GKHYKKVMYT QYEDESFTKH TVNPNMKEDG ILGPIIRAQV RDTLKIVFKN
MASRPYSIYP HGVTFSPYED EVNSSFTSGT TP*

speed

1.02 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