mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999933641 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM950001)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:95080803G>AN/A show variant in all transcripts IGV

HGNC symbol

SERPINA3

Ensembl transcript ID

ENST00000467132

Genbank transcript ID

N/A

UniProt peptide

P01011

alteration type

single base exchange

alteration region

CDS

DNA changes

c.25G>A
cDNA.1173G>A
g.22409G>A

AA changes

A9T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs4934

database	homozygous (A/A)	heterozygous	allele carriers
1000G	457	1086	1543
ExAC	12978	6811	19789

known disease mutation at this position, please check HGMD for details (HGMD ID CM950001)

regulatory features

H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.135	0.001
	0.035	0.002
(flanking)	0.458	0.013

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
Acc increased	22412	wt: 0.58 / mu: 0.76	wt: GAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGG mu: GAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGG	gctc\|TGGG
Acc marginally increased	22409	wt: 0.9389 / mu: 0.9511 (marginal change - not scored)	wt: AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT mu: AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT	ctgg\|CTCT
Acc marginally increased	22415	wt: 0.9308 / mu: 0.9471 (marginal change - not scored)	wt: TGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGGTTC mu: TGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGGTTC	ctgg\|GGCT

distance from splice site

619

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000023582

Mmulatta

all identical

ENSMMUG00000011218

Fcatus

no alignment

ENSFCAG00000010238

n/a

Mmusculus

all identical

ENSMUSG00000021091

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	23	SIGNAL		lost
33	33	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
50	67	HELIX		might get lost (downstream of altered splice site)
55	55	CONFLICT	D -> S (in Ref. 12; AA sequence).	might get lost (downstream of altered splice site)
69	69	CONFLICT	P -> L (in Ref. 1; AAA51543).	might get lost (downstream of altered splice site)
69	71	STRAND		might get lost (downstream of altered splice site)
73	75	STRAND		might get lost (downstream of altered splice site)
77	87	HELIX		might get lost (downstream of altered splice site)
88	90	HELIX		might get lost (downstream of altered splice site)
93	93	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
93	102	HELIX		might get lost (downstream of altered splice site)
101	101	CONFLICT	K -> R (in Ref. 5; BAD92297).	might get lost (downstream of altered splice site)
106	106	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
106	106	CONFLICT	N -> Y (in Ref. 3; AAT08028).	might get lost (downstream of altered splice site)
107	109	TURN		might get lost (downstream of altered splice site)
112	126	HELIX		might get lost (downstream of altered splice site)
127	127	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
130	132	STRAND		might get lost (downstream of altered splice site)
134	146	STRAND		might get lost (downstream of altered splice site)
151	161	HELIX		might get lost (downstream of altered splice site)
164	168	STRAND		might get lost (downstream of altered splice site)
170	172	HELIX		might get lost (downstream of altered splice site)
173	183	HELIX		might get lost (downstream of altered splice site)
185	194	STRAND		might get lost (downstream of altered splice site)
186	186	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	198	CONFLICT	D -> N (in Ref. 3; AAT08029).	might get lost (downstream of altered splice site)
199	199	CONFLICT	L -> P (in Ref. 1; AAA51543).	might get lost (downstream of altered splice site)
205	219	STRAND		might get lost (downstream of altered splice site)
223	225	HELIX		might get lost (downstream of altered splice site)
227	236	STRAND		might get lost (downstream of altered splice site)
234	234	CONFLICT	S -> N (in Ref. 3; AAT08029).	might get lost (downstream of altered splice site)
235	237	DNA_BIND		might get lost (downstream of altered splice site)
238	256	STRAND		might get lost (downstream of altered splice site)
257	260	TURN		might get lost (downstream of altered splice site)
261	279	STRAND		might get lost (downstream of altered splice site)
271	271	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
284	288	HELIX		might get lost (downstream of altered splice site)
293	301	HELIX		might get lost (downstream of altered splice site)
304	314	STRAND		might get lost (downstream of altered splice site)
316	323	STRAND		might get lost (downstream of altered splice site)
325	330	HELIX		might get lost (downstream of altered splice site)
335	337	HELIX		might get lost (downstream of altered splice site)
339	339	CONFLICT	S -> G (in Ref. 3; AAT08028).	might get lost (downstream of altered splice site)
344	347	TURN		might get lost (downstream of altered splice site)
346	346	CONFLICT	I -> S (in Ref. 3; AAT08028).	might get lost (downstream of altered splice site)
348	350	STRAND		might get lost (downstream of altered splice site)
352	365	STRAND		might get lost (downstream of altered splice site)
361	363	CONFLICT	AVL -> VVS (in Ref. 1; AAA51543).	might get lost (downstream of altered splice site)
367	373	STRAND		might get lost (downstream of altered splice site)
369	394	REGION	RCL.	might get lost (downstream of altered splice site)
383	384	SITE	Reactive bond.	might get lost (downstream of altered splice site)
392	394	STRAND		might get lost (downstream of altered splice site)
399	405	STRAND		might get lost (downstream of altered splice site)
412	418	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1272 / 1272

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

424 / 424

position of stopcodon in wt / mu cDNA

2420 / 2420

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

1149 / 1149

chromosome

strand

last intron/exon boundary

2217

theoretical NMD boundary in CDS

1018

length of CDS

1272

coding sequence (CDS) position

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

1173

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

22409

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

95080803

original gDNA sequence snippet

AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT

altered gDNA sequence snippet

AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT

original cDNA sequence snippet

AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT

altered cDNA sequence snippet

AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT

wildtype AA sequence

MERMLPLLAL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*

mutated AA sequence

MERMLPLLTL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*

speed

0.64 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