MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000367425
Querying Taster for transcript #2: ENST00000391985
MT speed 1.68 s - this script 4.356813 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CFHR3	polymorphism_automatic	3.55380169736463e-11	simple_aae		affected		P241S	single base exchange	rs138675433		show file
CFHR3	polymorphism_automatic	3.55380169736463e-11	simple_aae		affected		P180S	single base exchange	rs138675433		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999964462 (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)

chr1:196759282C>TN/A show variant in all transcripts IGV

HGNC symbol

CFHR3

Ensembl transcript ID

ENST00000367425

Genbank transcript ID

NM_021023

UniProt peptide

Q02985

alteration type

single base exchange

alteration region

CDS

DNA changes

c.721C>T
cDNA.813C>T
g.15358C>T

AA changes

P241S Score: 74 explain score(s)

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

241

frameshift

known variant

Reference ID: rs138675433

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	144	202	346

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.216	0.27
	-3.892	0
(flanking)	-0.593	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 gained	15351	0.49	mu: TACCAATGCCAGTCC	CCAA\|tgcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

241

mutated

not conserved

241

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000092786

276

DRPSY

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
208	266	DOMAIN	Sushi 4.	lost
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	CONFLICT	P -> S (in Ref. 1; CAA48639).	lost
253	253	DISULFID	By similarity.	might get lost (downstream of altered splice site)
260	260	CONFLICT	E -> A (in Ref. 1; CAA48639).	might get lost (downstream of altered splice site)
264	264	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	330	DOMAIN	Sushi 5.	might get lost (downstream of altered splice site)
268	268	DISULFID	By similarity.	might get lost (downstream of altered splice site)
302	302	DISULFID	By similarity.	might get lost (downstream of altered splice site)
309	309	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
319	319	DISULFID	By similarity.	might get lost (downstream of altered splice site)
329	329	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

993 / 993

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

331 / 331

position of stopcodon in wt / mu cDNA

1085 / 1085

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

93 / 93

chromosome

strand

last intron/exon boundary

889

theoretical NMD boundary in CDS

746

length of CDS

993

coding sequence (CDS) position

721

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

813

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

15358

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

196759282

original gDNA sequence snippet

GAGTCGAGTACCAATGCCAGCCCTACTATGAACTTCAGGGT

altered gDNA sequence snippet

GAGTCGAGTACCAATGCCAGTCCTACTATGAACTTCAGGGT

original cDNA sequence snippet

GAGTCGAGTACCAATGCCAGCCCTACTATGAACTTCAGGGT

altered cDNA sequence snippet

GAGTCGAGTACCAATGCCAGTCCTACTATGAACTTCAGGGT

wildtype AA sequence

MLLLINVILT LWVSCANGQV KPCDFPDIKH GGLFHENMRR PYFPVAVGKY YSYYCDEHFE
TPSGSYWDYI HCTQNGWSPA VPCLRKCYFP YLENGYNQNY GRKFVQGNST EVACHPGYGL
PKAQTTVTCT EKGWSPTPRC IRVRTCSKSD IEIENGFISE SSSIYILNKE IQYKCKPGYA
TADGNSSGSI TCLQNGWSAQ PICINSSEKC GPPPPISNGD TTSFLLKVYV PQSRVEYQCQ
PYYELQGSNY VTCSNGEWSE PPRCIHPCII TEENMNKNNI KLKGRSDRKY YAKTGDTIEF
MCKLGYNANT SILSFQAVCR EGIVEYPRCE *

mutated AA sequence

MLLLINVILT LWVSCANGQV KPCDFPDIKH GGLFHENMRR PYFPVAVGKY YSYYCDEHFE
TPSGSYWDYI HCTQNGWSPA VPCLRKCYFP YLENGYNQNY GRKFVQGNST EVACHPGYGL
PKAQTTVTCT EKGWSPTPRC IRVRTCSKSD IEIENGFISE SSSIYILNKE IQYKCKPGYA
TADGNSSGSI TCLQNGWSAQ PICINSSEKC GPPPPISNGD TTSFLLKVYV PQSRVEYQCQ
SYYELQGSNY VTCSNGEWSE PPRCIHPCII TEENMNKNNI KLKGRSDRKY YAKTGDTIEF
MCKLGYNANT SILSFQAVCR EGIVEYPRCE *

speed

1.05 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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999964462 (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)

chr1:196759282C>TN/A show variant in all transcripts IGV

HGNC symbol

CFHR3

Ensembl transcript ID

ENST00000391985

Genbank transcript ID

NM_001166624

UniProt peptide

Q02985

alteration type

single base exchange

alteration region

CDS

DNA changes

c.538C>T
cDNA.609C>T
g.15358C>T

AA changes

P180S Score: 74 explain score(s)

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

180

frameshift

known variant

Reference ID: rs138675433

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	144	202	346

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.216	0.27
	-3.892	0
(flanking)	-0.593	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 gained	15351	0.49	mu: TACCAATGCCAGTCC	CCAA\|tgcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

180

mutated

not conserved

180

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000092786

276

DRPSY

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
144	205	DOMAIN	Sushi 3.	lost
185	185	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
192	192	DISULFID	By similarity.	might get lost (downstream of altered splice site)
194	194	CONFLICT	Q -> R (in Ref. 1; CAA48639).	might get lost (downstream of altered splice site)
203	203	DISULFID	By similarity.	might get lost (downstream of altered splice site)
205	205	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
208	266	DOMAIN	Sushi 4.	might get lost (downstream of altered splice site)
210	210	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	CONFLICT	P -> S (in Ref. 1; CAA48639).	might get lost (downstream of altered splice site)
253	253	DISULFID	By similarity.	might get lost (downstream of altered splice site)
260	260	CONFLICT	E -> A (in Ref. 1; CAA48639).	might get lost (downstream of altered splice site)
264	264	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	330	DOMAIN	Sushi 5.	might get lost (downstream of altered splice site)
268	268	DISULFID	By similarity.	might get lost (downstream of altered splice site)
302	302	DISULFID	By similarity.	might get lost (downstream of altered splice site)
309	309	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
319	319	DISULFID	By similarity.	might get lost (downstream of altered splice site)
329	329	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

810 / 810

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

270 / 270

position of stopcodon in wt / mu cDNA

881 / 881

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

72 / 72

chromosome

strand

last intron/exon boundary

685

theoretical NMD boundary in CDS

563

length of CDS

810

coding sequence (CDS) position

538

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

609

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

15358

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

196759282

original gDNA sequence snippet

GAGTCGAGTACCAATGCCAGCCCTACTATGAACTTCAGGGT

altered gDNA sequence snippet

GAGTCGAGTACCAATGCCAGTCCTACTATGAACTTCAGGGT

original cDNA sequence snippet

GAGTCGAGTACCAATGCCAGCCCTACTATGAACTTCAGGGT

altered cDNA sequence snippet

GAGTCGAGTACCAATGCCAGTCCTACTATGAACTTCAGGGT

wildtype AA sequence

MLLLINVILT LWVSCANGQV KPCDFPDIKH GGLFHENMRR PYFPVAVGKY YSYYCDEHFE
TPSGSYWDYI HCTQNGWSPA VPCLRKCYFP YLENGYNQNY GRKFVQGNST EVACHPGYGL
PKAQTTVTCT EKGWSPTPRC IRVNSSEKCG PPPPISNGDT TSFLLKVYVP QSRVEYQCQP
YYELQGSNYV TCSNGEWSEP PRCIHPCIIT EENMNKNNIK LKGRSDRKYY AKTGDTIEFM
CKLGYNANTS ILSFQAVCRE GIVEYPRCE*

mutated AA sequence

MLLLINVILT LWVSCANGQV KPCDFPDIKH GGLFHENMRR PYFPVAVGKY YSYYCDEHFE
TPSGSYWDYI HCTQNGWSPA VPCLRKCYFP YLENGYNQNY GRKFVQGNST EVACHPGYGL
PKAQTTVTCT EKGWSPTPRC IRVNSSEKCG PPPPISNGDT TSFLLKVYVP QSRVEYQCQS
YYELQGSNYV TCSNGEWSEP PRCIHPCIIT EENMNKNNIK LKGRSDRKYY AKTGDTIEFM
CKLGYNANTS ILSFQAVCRE GIVEYPRCE*

speed

0.63 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems