MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000294854
Querying Taster for transcript #2: ENST00000542961
MT speed 0 s - this script 3.966939 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RGSL1	polymorphism_automatic	8.20454815197991e-14	simple_aae		affected		I683V	single base exchange	rs7535533		show file
RGSL1	polymorphism_automatic	8.20454815197991e-14	simple_aae		affected		I718V	single base exchange	rs7535533		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999918 (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)

chr1:182496829A>GN/A show variant in all transcripts IGV

HGNC symbol

RGSL1

Ensembl transcript ID

ENST00000294854

Genbank transcript ID

NM_001137669

UniProt peptide

A5PLK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2047A>G
cDNA.2067A>G
g.77574A>G

AA changes

I683V Score: 29 explain score(s)

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

683

frameshift

known variant

Reference ID: rs7535533

database	homozygous (G/G)	heterozygous	allele carriers
1000G	261	1041	1302
ExAC	1416	5035	6451

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.831	0
	0.14	0
(flanking)	-1.442	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	77573	wt: 0.54 / mu: 0.99	wt: ATCAGTATAGAGACC mu: ATCAGTGTAGAGACC	CAGT\|atag
Donor marginally increased	77571	wt: 0.9877 / mu: 0.9902 (marginal change - not scored)	wt: AGATCAGTATAGAGA mu: AGATCAGTGTAGAGA	ATCA\|gtat
Donor gained	77568	0.83	mu: AGAAGATCAGTGTAG	AAGA\|tcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

683

mutated

all conserved

683

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000006263

n/a

Fcatus

all identical

ENSFCAG00000018264

Mmusculus

all conserved

ENSMUSG00000042641

682

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
645	764	DOMAIN	RGS.	lost
683	683	CONFLICT	I -> V (in Ref. 6; BC121032/BC121033).	lost
823	823	CONFLICT	H -> L (in Ref. 6; BC121032).	might get lost (downstream of altered splice site)
960	982	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1044	1047	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3231 / 3231

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

1077 / 1077

position of stopcodon in wt / mu cDNA

3251 / 3251

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

21 / 21

chromosome

strand

last intron/exon boundary

3417

theoretical NMD boundary in CDS

3346

length of CDS

3231

coding sequence (CDS) position

2047

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

2067

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

77574

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

182496829

original gDNA sequence snippet

CAGCTGTACAGAAGATCAGTATAGAGACCAATGAAAAGATT

altered gDNA sequence snippet

CAGCTGTACAGAAGATCAGTGTAGAGACCAATGAAAAGATT

original cDNA sequence snippet

CAGCTGTACAGAAGATCAGTATAGAGACCAATGAAAAGATT

altered cDNA sequence snippet

CAGCTGTACAGAAGATCAGTGTAGAGACCAATGAAAAGATT

wildtype AA sequence

MSSAEIIGST NLIILLEDEV FADFFNTFLS LPVFGQTPFY TVENSQWSLW PEIPCNLIAK
YKGLLTWLEK CRLPFFCKTN LCFHYILCQE FISFIKSPEG GEELVDFWIL AENILSIDEM
DLEVRDYYLS LLLMLRATHL QEGSRVVTLC NMNIKSLLNL SIWHPNQSTT RREILSHMQK
VALFKLQSYW LPNFYTHTKM TMAKEEACHG LMQEYETRLY SVCYTHIGGL PLNMSIKKCH
HFQKRYSSRK AKRKMWQLVD PDSWSLEMDL KPDAIGMPLQ ETCPQEKVVI QMPSLKMASS
KETRISSLEK DMHYAKISSM ENKAKSHLHM EAPFETKVST HLRTVIPIVN HSSKMTIQKA
IKQSFSLGYI HLALCADACA GNPFRDHLKK LNLKVEIQLL DLWQDLQHFL SVLLNNKKNG
NAIFRHLLGD RICELYLNEQ IGPCLPLKSQ TIQGLKELLP SGDVIPWIPK AQKEICKMLS
PWYDEFLDEE DYWFLLFTTQ NRFISSRQHK REFIGKEENI LLYKRIQQSL ELSQALADMK
EMDYRQWRKI ATEDLKQGGS LQVELTSPVF LTDITKMSFE ELCYKNPKMA IQKISDDYKI
YCEKAPKIDF KMEIIKETKT VSRSNRKMSL LKRTLVRKPS MRPRNLTEVL LNTQHLEFFR
EFLKERKAKI PLQFLTAVQK ISIETNEKIC KSLIENVIKT FFQGQLSPEE MLQCDAPIIK
EIASMRHVTT STLLTLQGHV MKSIEEKWFK DYQDLFPPHH QEVEVQSEVQ ISSRKPSKIV
STYLQESQKK GWMRMISFIR SFCKYRRFML NPSKRQEFED YLHQEMQNSK ENFTTAHNTS
GRSAPPSTNV RSADQENGEI TLVKRRIFGH RIITVNFAIN DLYFFSEMEK FNDLVSSAHM
LQVNRAYNEN DVILMRSKMN IIQKLFLNSD IPPKLRVNVP EFQKDAILAA ITEGYLDRSV
FHGAIMSVFP VVMYFWKRFC FWKATRSYLQ YRGKKFKDRK SPPKSTDKYP FSSGGDNAIL
RFTLLRGIEW LQPQREAISS VQNSSSSKLT QPRLVVSAMQ LHPVQGQKLS YIKKEK*

mutated AA sequence

MSSAEIIGST NLIILLEDEV FADFFNTFLS LPVFGQTPFY TVENSQWSLW PEIPCNLIAK
YKGLLTWLEK CRLPFFCKTN LCFHYILCQE FISFIKSPEG GEELVDFWIL AENILSIDEM
DLEVRDYYLS LLLMLRATHL QEGSRVVTLC NMNIKSLLNL SIWHPNQSTT RREILSHMQK
VALFKLQSYW LPNFYTHTKM TMAKEEACHG LMQEYETRLY SVCYTHIGGL PLNMSIKKCH
HFQKRYSSRK AKRKMWQLVD PDSWSLEMDL KPDAIGMPLQ ETCPQEKVVI QMPSLKMASS
KETRISSLEK DMHYAKISSM ENKAKSHLHM EAPFETKVST HLRTVIPIVN HSSKMTIQKA
IKQSFSLGYI HLALCADACA GNPFRDHLKK LNLKVEIQLL DLWQDLQHFL SVLLNNKKNG
NAIFRHLLGD RICELYLNEQ IGPCLPLKSQ TIQGLKELLP SGDVIPWIPK AQKEICKMLS
PWYDEFLDEE DYWFLLFTTQ NRFISSRQHK REFIGKEENI LLYKRIQQSL ELSQALADMK
EMDYRQWRKI ATEDLKQGGS LQVELTSPVF LTDITKMSFE ELCYKNPKMA IQKISDDYKI
YCEKAPKIDF KMEIIKETKT VSRSNRKMSL LKRTLVRKPS MRPRNLTEVL LNTQHLEFFR
EFLKERKAKI PLQFLTAVQK ISVETNEKIC KSLIENVIKT FFQGQLSPEE MLQCDAPIIK
EIASMRHVTT STLLTLQGHV MKSIEEKWFK DYQDLFPPHH QEVEVQSEVQ ISSRKPSKIV
STYLQESQKK GWMRMISFIR SFCKYRRFML NPSKRQEFED YLHQEMQNSK ENFTTAHNTS
GRSAPPSTNV RSADQENGEI TLVKRRIFGH RIITVNFAIN DLYFFSEMEK FNDLVSSAHM
LQVNRAYNEN DVILMRSKMN IIQKLFLNSD IPPKLRVNVP EFQKDAILAA ITEGYLDRSV
FHGAIMSVFP VVMYFWKRFC FWKATRSYLQ YRGKKFKDRK SPPKSTDKYP FSSGGDNAIL
RFTLLRGIEW LQPQREAISS VQNSSSSKLT QPRLVVSAMQ LHPVQGQKLS YIKKEK*

speed

0.98 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: 0.999999999999918 (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)

chr1:182496829A>GN/A show variant in all transcripts IGV

HGNC symbol

RGSL1

Ensembl transcript ID

ENST00000542961

Genbank transcript ID

N/A

UniProt peptide

A5PLK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2152A>G
cDNA.2172A>G
g.77574A>G

AA changes

I718V Score: 29 explain score(s)

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

718

frameshift

known variant

Reference ID: rs7535533

database	homozygous (G/G)	heterozygous	allele carriers
1000G	261	1041	1302
ExAC	1416	5035	6451

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.831	0
	0.14	0
(flanking)	-1.442	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	77573	wt: 0.54 / mu: 0.99	wt: ATCAGTATAGAGACC mu: ATCAGTGTAGAGACC	CAGT\|atag
Donor marginally increased	77571	wt: 0.9877 / mu: 0.9902 (marginal change - not scored)	wt: AGATCAGTATAGAGA mu: AGATCAGTGTAGAGA	ATCA\|gtat
Donor gained	77568	0.83	mu: AGAAGATCAGTGTAG	AAGA\|tcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

718

mutated

all conserved

718

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000006263

n/a

Fcatus

all identical

ENSFCAG00000018264

Mmusculus

all conserved

ENSMUSG00000042641

682

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
645	764	DOMAIN	RGS.	lost
823	823	CONFLICT	H -> L (in Ref. 6; BC121032).	might get lost (downstream of altered splice site)
960	982	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1044	1047	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2955 / 2955

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

985 / 985

position of stopcodon in wt / mu cDNA

2975 / 2975

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

21 / 21

chromosome

strand

last intron/exon boundary

3131

theoretical NMD boundary in CDS

3060

length of CDS

2955

coding sequence (CDS) position

2152

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

2172

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

77574

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

182496829

original gDNA sequence snippet

CAGCTGTACAGAAGATCAGTATAGAGACCAATGAAAAGATT

altered gDNA sequence snippet

CAGCTGTACAGAAGATCAGTGTAGAGACCAATGAAAAGATT

original cDNA sequence snippet

CAGCTGTACAGAAGATCAGTATAGAGACCAATGAAAAGATT

altered cDNA sequence snippet

CAGCTGTACAGAAGATCAGTGTAGAGACCAATGAAAAGATT

wildtype AA sequence

MSSAEIIGST NLIILLEDEV FADFFNTFLS LPVFGQTPFY TVENSQWSLW PEIPCNLIAK
YKGLLTWLEK CRLPFFCKTN LCFHYILCQE FISFIKSPEG AKMMRWKKAD QWLLQKCIGG
VRGMWRFYSY LTGSAGEELV DFWILAENIL SIDEMDLEVR DYYLSLLLML RATHLQEGSR
VVTLCNMNIK SLLNLSIWHP NQSTTRREIL SHMQKVALFK LQSYWLPNFY THTKMTMAKE
EACHGLMQEY ETRLYSVCYT HIGGLPLNMS IKKCHHFQKR YSSRKAKRKM WQLVDPDSWS
LEMDLKPDAI GMPLQETCPQ EKVVIQMPSL KMASSKETRI SSLEKDMHYA KISSMENKAK
SHLHMEAPFE TKVSTHLRTV IPIVNHSSKM TIQKAIKQSF SLGYIHLALC ADACAGNPFR
DHLKKLNLKV EIQLLDLWQD LQHFLSVLLN NKKNGNAIFR HLLGDRICEL YLNEQIGPCL
PLKSQTIQGL KELLPSGDVI PWIPKAQKEI CKMLSPWYDE FLDEEDYWFL LFTTQNRFIS
SRQHKREFIG KEENILLYKR IQQSLELSQA LADMKEMDYR QWRKIATEDL KQGGSLQVEL
TSPVFLTDIT KMSFEELCYK NPKMAIQKIS DDYKIYCEKA PKIDFKMEII KETKTVSRSN
RKMSLLKRTL VRKPSMRPRN LTEVLLNTQH LEFFREFLKE RKAKIPLQFL TAVQKISIET
NEKICKSLIE NVIKTFFQGQ LSPEEMLQCD APIIKEIASM RHVTTSTLLT LQGHVMKSIE
EKWFKDYQDL FPPHHQEVEV QSEVQISSRK PSKIVSTYLQ ESQKKGWMRM ISFIRSFCKY
RRFMLNPSKR QEFEDYLHQE MQNSKENFTT AHNTSGRSAP PSTNVRSADQ ENGEITLVKR
RIFGHRIITV NFAINDLYFF SEMEKFNDLV SSAHMLQVNR AYNENDVILM RSKMNIIQKL
FLNSDIPPKL RVLFLEGNPL LLTV*

mutated AA sequence

MSSAEIIGST NLIILLEDEV FADFFNTFLS LPVFGQTPFY TVENSQWSLW PEIPCNLIAK
YKGLLTWLEK CRLPFFCKTN LCFHYILCQE FISFIKSPEG AKMMRWKKAD QWLLQKCIGG
VRGMWRFYSY LTGSAGEELV DFWILAENIL SIDEMDLEVR DYYLSLLLML RATHLQEGSR
VVTLCNMNIK SLLNLSIWHP NQSTTRREIL SHMQKVALFK LQSYWLPNFY THTKMTMAKE
EACHGLMQEY ETRLYSVCYT HIGGLPLNMS IKKCHHFQKR YSSRKAKRKM WQLVDPDSWS
LEMDLKPDAI GMPLQETCPQ EKVVIQMPSL KMASSKETRI SSLEKDMHYA KISSMENKAK
SHLHMEAPFE TKVSTHLRTV IPIVNHSSKM TIQKAIKQSF SLGYIHLALC ADACAGNPFR
DHLKKLNLKV EIQLLDLWQD LQHFLSVLLN NKKNGNAIFR HLLGDRICEL YLNEQIGPCL
PLKSQTIQGL KELLPSGDVI PWIPKAQKEI CKMLSPWYDE FLDEEDYWFL LFTTQNRFIS
SRQHKREFIG KEENILLYKR IQQSLELSQA LADMKEMDYR QWRKIATEDL KQGGSLQVEL
TSPVFLTDIT KMSFEELCYK NPKMAIQKIS DDYKIYCEKA PKIDFKMEII KETKTVSRSN
RKMSLLKRTL VRKPSMRPRN LTEVLLNTQH LEFFREFLKE RKAKIPLQFL TAVQKISVET
NEKICKSLIE NVIKTFFQGQ LSPEEMLQCD APIIKEIASM RHVTTSTLLT LQGHVMKSIE
EKWFKDYQDL FPPHHQEVEV QSEVQISSRK PSKIVSTYLQ ESQKKGWMRM ISFIRSFCKY
RRFMLNPSKR QEFEDYLHQE MQNSKENFTT AHNTSGRSAP PSTNVRSADQ ENGEITLVKR
RIFGHRIITV NFAINDLYFF SEMEKFNDLV SSAHMLQVNR AYNENDVILM RSKMNIIQKL
FLNSDIPPKL RVLFLEGNPL LLTV*

speed

0.98 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems