MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000262865
MT speed 0 s - this script 2.808029 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BPI	polymorphism_automatic	1.16130438598816e-11	simple_aae		affected		A16V	single base exchange	rs1341023		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999988387 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:36932660C>TN/A show variant in all transcripts IGV

HGNC symbol

BPI

Ensembl transcript ID

ENST00000262865

Genbank transcript ID

NM_001725

UniProt peptide

P17213

alteration type

single base exchange

alteration region

CDS

DNA changes

c.47C>T
cDNA.136C>T
g.44110C>T

AA changes

A16V Score: 64 explain score(s)

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

frameshift

known variant

Reference ID: rs1341023

database	homozygous (T/T)	heterozygous	allele carriers
1000G	547	1066	1613
ExAC	16058	651	16709

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.493	0.061
	1.176	0.052
(flanking)	-2.644	0

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	44103	wt: 0.65 / mu: 0.90	wt: CGCCGAGATGGGCGT mu: CGCCGAGATGGGTGT	CCGA\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000020173

n/a

Fcatus

all identical

ENSFCAG00000004810

Mmusculus

all conserved

ENSMUSG00000052922

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000017326

n/a

protein features

start (aa)	end (aa)	feature	details
1	31	SIGNAL		lost
35	41	STRAND		might get lost (downstream of altered splice site)
42	60	HELIX		might get lost (downstream of altered splice site)
49	49	MUTAGEN	S->C: No impairment of secretion and increased propensity for dimer formation.	might get lost (downstream of altered splice site)
53	53	CONFLICT	T -> R (in Ref. 8; AA sequence).	might get lost (downstream of altered splice site)
68	71	STRAND		might get lost (downstream of altered splice site)
75	79	STRAND		might get lost (downstream of altered splice site)
81	93	STRAND		might get lost (downstream of altered splice site)
97	102	STRAND		might get lost (downstream of altered splice site)
103	105	TURN		might get lost (downstream of altered splice site)
106	126	STRAND		might get lost (downstream of altered splice site)
129	153	STRAND		might get lost (downstream of altered splice site)
154	157	TURN		might get lost (downstream of altered splice site)
158	169	STRAND		might get lost (downstream of altered splice site)
163	163	MUTAGEN	C->A: No impairment of secretion and/or biological activity. Loss of dimer formation.	might get lost (downstream of altered splice site)
166	166	MUTAGEN	C->S: Poorly secreted. Loss of LPS- binding and biological activity.	might get lost (downstream of altered splice site)
166	166	DISULFID		might get lost (downstream of altered splice site)
172	176	STRAND		might get lost (downstream of altered splice site)
180	182	HELIX		might get lost (downstream of altered splice site)
183	192	HELIX		might get lost (downstream of altered splice site)
194	215	HELIX		might get lost (downstream of altered splice site)
206	206	MUTAGEN	C->A: Not secreted.	might get lost (downstream of altered splice site)
206	206	DISULFID		might get lost (downstream of altered splice site)
217	221	HELIX		might get lost (downstream of altered splice site)
226	229	STRAND		might get lost (downstream of altered splice site)
231	233	STRAND		might get lost (downstream of altered splice site)
235	237	STRAND		might get lost (downstream of altered splice site)
240	242	STRAND		might get lost (downstream of altered splice site)
240	245	REGION	Cleavage sites for elastase (Potential).	might get lost (downstream of altered splice site)
248	255	STRAND		might get lost (downstream of altered splice site)
258	260	STRAND		might get lost (downstream of altered splice site)
282	290	STRAND		might get lost (downstream of altered splice site)
291	303	HELIX		might get lost (downstream of altered splice site)
307	312	STRAND		might get lost (downstream of altered splice site)
313	315	HELIX		might get lost (downstream of altered splice site)
326	330	HELIX		might get lost (downstream of altered splice site)
333	335	STRAND		might get lost (downstream of altered splice site)
336	339	HELIX		might get lost (downstream of altered splice site)
344	350	STRAND		might get lost (downstream of altered splice site)
355	355	CONFLICT	P -> S (in Ref. 7; AAG42844).	might get lost (downstream of altered splice site)
356	360	STRAND		might get lost (downstream of altered splice site)
363	367	STRAND		might get lost (downstream of altered splice site)
369	377	STRAND		might get lost (downstream of altered splice site)
375	375	CONFLICT	F -> L (in Ref. 2).	might get lost (downstream of altered splice site)
380	380	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
383	392	STRAND		might get lost (downstream of altered splice site)
395	401	STRAND		might get lost (downstream of altered splice site)
403	412	STRAND		might get lost (downstream of altered splice site)
411	411	CONFLICT	K -> R (in Ref. 7; AAG42844).	might get lost (downstream of altered splice site)
416	424	STRAND		might get lost (downstream of altered splice site)
429	432	HELIX		might get lost (downstream of altered splice site)
433	433	CONFLICT	Q -> L (in Ref. 4; BAG37729).	might get lost (downstream of altered splice site)
433	443	HELIX		might get lost (downstream of altered splice site)
445	454	HELIX		might get lost (downstream of altered splice site)
464	474	STRAND		might get lost (downstream of altered splice site)
477	483	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1464 / 1464

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

488 / 488

position of stopcodon in wt / mu cDNA

1553 / 1553

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

90 / 90

chromosome

strand

last intron/exon boundary

1515

theoretical NMD boundary in CDS

1375

length of CDS

1464

coding sequence (CDS) position

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

136

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

44110

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

36932660

original gDNA sequence snippet

TTGCAACGCGCCGAGATGGGCGTCCCTGATGGTGCTGGTCG

altered gDNA sequence snippet

TTGCAACGCGCCGAGATGGGTGTCCCTGATGGTGCTGGTCG

original cDNA sequence snippet

TTGCAACGCGCCGAGATGGGCGTCCCTGATGGTGCTGGTCG

altered cDNA sequence snippet

TTGCAACGCGCCGAGATGGGTGTCCCTGATGGTGCTGGTCG

wildtype AA sequence

MRENMARGPC NAPRWASLMV LVAIGTAVTA AVNPGVVVRI SQKGLDYASQ QGTAALQKEL
KRIKIPDYSD SFKIKHLGKG HYSFYSMDIR EFQLPSSQIS MVPNVGLKFS ISNANIKISG
KWKAQKRFLK MSGNFDLSIE GMSISADLKL GSNPTSGKPT ITCSSCSSHI NSVHVHISKS
KVGWLIQLFH KKIESALRNK MNSQVCEKVT NSVSSELQPY FQTLPVMTKI DSVAGINYGL
VAPPATTAET LDVQMKGEFY SENHHNPPPF APPVMEFPAA HDRMVYLGLS DYFFNTAGLV
YQEAGVLKMT LRDDMIPKES KFRLTTKFFG TFLPEVAKKF PNMKIQIHVS ASTPPHLSVQ
PTGLTFYPAV DVQAFAVLPN SSLASLFLIG MHTTGSMEVS AESNRLVGEL KLDRLLLELK
HSNIGPFPVE LLQDIMNYIV PILVLPRVNE KLQKGFPLPT PARVQLYNVV LQPHQNFLLF
GADVVYK*

mutated AA sequence

MRENMARGPC NAPRWVSLMV LVAIGTAVTA AVNPGVVVRI SQKGLDYASQ QGTAALQKEL
KRIKIPDYSD SFKIKHLGKG HYSFYSMDIR EFQLPSSQIS MVPNVGLKFS ISNANIKISG
KWKAQKRFLK MSGNFDLSIE GMSISADLKL GSNPTSGKPT ITCSSCSSHI NSVHVHISKS
KVGWLIQLFH KKIESALRNK MNSQVCEKVT NSVSSELQPY FQTLPVMTKI DSVAGINYGL
VAPPATTAET LDVQMKGEFY SENHHNPPPF APPVMEFPAA HDRMVYLGLS DYFFNTAGLV
YQEAGVLKMT LRDDMIPKES KFRLTTKFFG TFLPEVAKKF PNMKIQIHVS ASTPPHLSVQ
PTGLTFYPAV DVQAFAVLPN SSLASLFLIG MHTTGSMEVS AESNRLVGEL KLDRLLLELK
HSNIGPFPVE LLQDIMNYIV PILVLPRVNE KLQKGFPLPT PARVQLYNVV LQPHQNFLLF
GADVVYK*

speed

0.75 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems