MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000229554
Querying Taster for transcript #2: ENST00000368580
Querying Taster for transcript #3: ENST00000368581
MT speed 0 s - this script 3.831337 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RSPH4A	polymorphism_automatic	0.99999682226439	simple_aae				R309H	single base exchange	rs6927567		show file
RSPH4A	polymorphism_automatic	0.999999952313582	simple_aae				R556H	single base exchange	rs6927567		show file
RSPH4A	polymorphism_automatic	1	without_aae					single base exchange	rs6927567		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 3.17773560972929e-06 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116950734G>AN/A show variant in all transcripts IGV

HGNC symbol

RSPH4A

Ensembl transcript ID

ENST00000368580

Genbank transcript ID

N/A

UniProt peptide

Q5TD94

alteration type

single base exchange

alteration region

CDS

DNA changes

c.926G>A
cDNA.926G>A
g.13093G>A

AA changes

R309H Score: 29 explain score(s)

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

309

frameshift

known variant

Reference ID: rs6927567

database	homozygous (A/A)	heterozygous	allele carriers
1000G	113	800	913
ExAC	2877	20109	22986

regulatory features

Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
SP1, Transcription Factor, SP1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.279	1
	3.702	1
(flanking)	0.655	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
Acc marginally decreased	13088	wt: 0.3542 / mu: 0.3312 (marginal change - not scored)	wt: TCTTGCAACATTCATTCCCAGGGTCGCTGTAATTGGTTCAA mu: TCTTGCAACATTCATTCCCAGGGTCACTGTAATTGGTTCAA	ccag\|GGTC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

309

mutated

not conserved

309

Ptroglodytes

all identical

ENSPTRG00000018535

556

Mmulatta

all identical

ENSMMUG00000001805

556

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000039552

308

Ggallus

all identical

ENSGALG00000013281

385

Trubripes

all identical

ENSTRUG00000007282

324

SAHL

Drerio

all identical

ENSDARG00000067606

363

KPVD

Dmelanogaster

not conserved

FBgn0034957

549

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000019096

363

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1410 / 1410

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

470 / 470

position of stopcodon in wt / mu cDNA

1410 / 1410

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

1 / 1

chromosome

strand

last intron/exon boundary

1176

theoretical NMD boundary in CDS

1125

length of CDS

1410

coding sequence (CDS) position

926

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

926

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

13093

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

116950734

original gDNA sequence snippet

CAACATTCATTCCCAGGGTCGCTGTAATTGGTTCAACTCCA

altered gDNA sequence snippet

CAACATTCATTCCCAGGGTCACTGTAATTGGTTCAACTCCA

original cDNA sequence snippet

ATTGGAAGATGAAATAGGTCGCTGTAATTGGTTCAACTCCA

altered cDNA sequence snippet

ATTGGAAGATGAAATAGGTCACTGTAATTGGTTCAACTCCA

wildtype AA sequence

mutated AA sequence

speed

0.49 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: 4.7686418181811e-08 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116950734G>AN/A show variant in all transcripts IGV

HGNC symbol

RSPH4A

Ensembl transcript ID

ENST00000229554

Genbank transcript ID

NM_001010892

UniProt peptide

Q5TD94

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1667G>A
cDNA.1804G>A
g.13093G>A

AA changes

R556H Score: 29 explain score(s)

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

556

frameshift

known variant

Reference ID: rs6927567

database	homozygous (A/A)	heterozygous	allele carriers
1000G	113	800	913
ExAC	2877	20109	22986

regulatory features

Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
SP1, Transcription Factor, SP1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.279	1
	3.702	1
(flanking)	0.655	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
Acc marginally decreased	13088	wt: 0.3542 / mu: 0.3312 (marginal change - not scored)	wt: TCTTGCAACATTCATTCCCAGGGTCGCTGTAATTGGTTCAA mu: TCTTGCAACATTCATTCCCAGGGTCACTGTAATTGGTTCAA	ccag\|GGTC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

556

mutated

not conserved

556

Ptroglodytes

all identical

ENSPTRG00000018535

556

Mmulatta

all identical

ENSMMUG00000001805

556

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000039552

554

KDE

Ggallus

all identical

ENSGALG00000013281

385

Trubripes

all identical

ENSTRUG00000007282

323

SAHL

Drerio

all identical

ENSDARG00000067606

366

Dmelanogaster

all identical

FBgn0034957

510

EKARKEREKALALYLKMQMLG

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000019096

364

protein features

start (aa)	end (aa)	feature	details
507	586	COMPBIAS	Glu-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2151 / 2151

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

717 / 717

position of stopcodon in wt / mu cDNA

2288 / 2288

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

138 / 138

chromosome

strand

last intron/exon boundary

2054

theoretical NMD boundary in CDS

1866

length of CDS

2151

coding sequence (CDS) position

1667

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

1804

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

13093

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

116950734

original gDNA sequence snippet

CAACATTCATTCCCAGGGTCGCTGTAATTGGTTCAACTCCA

altered gDNA sequence snippet

CAACATTCATTCCCAGGGTCACTGTAATTGGTTCAACTCCA

original cDNA sequence snippet

GCATATTCTCTCTCAGGGTCGCTGTAATTGGTTCAACTCCA

altered cDNA sequence snippet

GCATATTCTCTCTCAGGGTCACTGTAATTGGTTCAACTCCA

wildtype AA sequence

MEDSTSPKQE KENQEELGET RRPWEGKTAA SPQYSEPESS EPLEAKQGPE TGRQSRSSRP
WSPQSRAKTP LGGPAGPETS SPAPVSPREP SSSPSPLAPA RQDLAAPPQS DRTTSVIPEA
GTPYPDPLEQ SSDKRESTPH HTSQSEGNTF QQSQQPKPHL CGRRDVSYNN AKQKELRFDV
FQEEDSNSDY DLQQPAPGGS EVAPSMLEIT IQNAKAYLLK TSSNSGFNLY DHLSNMLTKI
LNERPENAVD IFENISQDVK MAHFSKKFDA LQNENELLPT YEIAEKQKAL FLQGHLEGVD
QELEDEIAEN ALPNVMESAF YFEQAGVGLG TDETYRIFLA LKQLTDTHPI QRCRFWGKIL
GLEMNYIVAE VEFREGEDEE EVEEEDVAEE RDNGESEAHE DEEDELPKSF YKAPQAIPKE
ESRTGANKYV YFVCNEPGRP WVKLPPVIPA QIVIARKIKK FFTGRLDAPI ISYPPFPGNE
SNYLRAQIAR ISAGTHVSPL GFYQFGEEEG EEEEEAEGGR NSFEENPDFE GIQVIDLVES
LSNWVHHVQH ILSQGRCNWF NSIQKNEEEE EEEDEEKDDS DYIEQEVGLP LLTPISEDLE
IQNIPPWTTR LSSNLIPQYA IAVLQSNLWP GAYAFSNGKK FENFYIGWGH KYSPDNYTPP
VPPPVYQEYP SGPEITEMDD PSVEEEQAFR AAQEAVLLAA ENEESEEDED EEDDYD*

mutated AA sequence

MEDSTSPKQE KENQEELGET RRPWEGKTAA SPQYSEPESS EPLEAKQGPE TGRQSRSSRP
WSPQSRAKTP LGGPAGPETS SPAPVSPREP SSSPSPLAPA RQDLAAPPQS DRTTSVIPEA
GTPYPDPLEQ SSDKRESTPH HTSQSEGNTF QQSQQPKPHL CGRRDVSYNN AKQKELRFDV
FQEEDSNSDY DLQQPAPGGS EVAPSMLEIT IQNAKAYLLK TSSNSGFNLY DHLSNMLTKI
LNERPENAVD IFENISQDVK MAHFSKKFDA LQNENELLPT YEIAEKQKAL FLQGHLEGVD
QELEDEIAEN ALPNVMESAF YFEQAGVGLG TDETYRIFLA LKQLTDTHPI QRCRFWGKIL
GLEMNYIVAE VEFREGEDEE EVEEEDVAEE RDNGESEAHE DEEDELPKSF YKAPQAIPKE
ESRTGANKYV YFVCNEPGRP WVKLPPVIPA QIVIARKIKK FFTGRLDAPI ISYPPFPGNE
SNYLRAQIAR ISAGTHVSPL GFYQFGEEEG EEEEEAEGGR NSFEENPDFE GIQVIDLVES
LSNWVHHVQH ILSQGHCNWF NSIQKNEEEE EEEDEEKDDS DYIEQEVGLP LLTPISEDLE
IQNIPPWTTR LSSNLIPQYA IAVLQSNLWP GAYAFSNGKK FENFYIGWGH KYSPDNYTPP
VPPPVYQEYP SGPEITEMDD PSVEEEQAFR AAQEAVLLAA ENEESEEDED EEDDYD*

speed

1.34 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 3.44262273421701e-40 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:116950734G>AN/A show variant in all transcripts IGV

HGNC symbol

RSPH4A

Ensembl transcript ID

ENST00000368581

Genbank transcript ID

NM_001161664

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.13093G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6927567

database	homozygous (A/A)	heterozygous	allele carriers
1000G	113	800	913
ExAC	2877	20109	22986

regulatory features

Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
SP1, Transcription Factor, SP1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.279	1
	3.702	1
(flanking)	0.655	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

864

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

146 / 146

chromosome

strand

last intron/exon boundary

1926

theoretical NMD boundary in CDS

1730

length of CDS

1803

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)

13093

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

116950734

original gDNA sequence snippet

CAACATTCATTCCCAGGGTCGCTGTAATTGGTTCAACTCCA

altered gDNA sequence snippet

CAACATTCATTCCCAGGGTCACTGTAATTGGTTCAACTCCA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEDSTSPKQE KENQEELGET RRPWEGKTAA SPQYSEPESS EPLEAKQGPE TGRQSRSSRP
WSPQSRAKTP LGGPAGPETS SPAPVSPREP SSSPSPLAPA RQDLAAPPQS DRTTSVIPEA
GTPYPDPLEQ SSDKRESTPH HTSQSEGNTF QQSQQPKPHL CGRRDVSYNN AKQKELRFDV
FQEEDSNSDY DLQQPAPGGS EVAPSMLEIT IQNAKAYLLK TSSNSGFNLY DHLSNMLTKI
LNERPENAVD IFENISQDVK MAHFSKKFDA LQNENELLPT YEIAEKQKAL FLQGHLEGVD
QELEDEIAEN ALPNVMESAF YFEQAGVGLG TDETYRIFLA LKQLTDTHPI QRCRFWGKIL
GLEMNYIVAE VEFREGEDEE EVEEEDVAEE RDNGESEAHE DEEDELPKSF YKAPQAIPKE
ESRTGANKYV YFVCNEPGRP WVKLPPVIPA QIVIARKIKK FFTGRLDAPI ISYPPFPGNE
SNYLRAQIAR ISAGTHVSPL GFYQFGEEEG EEEEEAEGGR NSFEENPDFE GIQVIDLVES
LSNWVHHVQH ILSQRFRIYP PGQHGYPQIS FHNMLLQSFN PTFGLEHMPS PMAKSLKIST
*

mutated AA sequence

N/A

speed

0.39 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems