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: ENST00000408999
Querying Taster for transcript #2: ENST00000354986
MT speed 2.3 s - this script 4.345425 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RGPD4	polymorphism_automatic	0.502336592006984	simple_aae		affected		V1428L	single base exchange	rs147825872		show file
RGPD4	polymorphism_automatic	0.502336592006984	simple_aae		affected		V1428L	single base exchange	rs147825872		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.497663407993016 (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)

chr2:108488742G>TN/A show variant in all transcripts IGV

HGNC symbol

RGPD4

Ensembl transcript ID

ENST00000408999

Genbank transcript ID

NM_182588

UniProt peptide

Q7Z3J3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.4282G>T
cDNA.4359G>T
g.45355G>T

AA changes

V1428L Score: 32 explain score(s)

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

1428

frameshift

known variant

Reference ID: rs147825872

database	homozygous (T/T)	heterozygous	allele carriers
1000G	212	765	977
ExAC	8225	16317	24542

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.324	1
	1.849	1
(flanking)	3.57	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
Donor increased	45348	wt: 0.55 / mu: 0.79	wt: GAAAGAGTATGGGTG mu: GAAAGAGTATGGTTG	AAGA\|gtat

distance from splice site

643

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1428

mutated

all conserved

1428

Ptroglodytes

all identical

ENSPTRG00000012330

1409

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000003226

2240

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0039302

1700

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1334	1470	DOMAIN	RanBD1 2.	lost
1703	1753	DOMAIN	GRIP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5277 / 5277

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

1759 / 1759

position of stopcodon in wt / mu cDNA

5354 / 5354

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

78 / 78

chromosome

strand

last intron/exon boundary

5344

theoretical NMD boundary in CDS

5216

length of CDS

5277

coding sequence (CDS) position

4282

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

4359

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

45355

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

108488742

original gDNA sequence snippet

AAGGGACAGAAAGAGTATGGGTGTGGACTGCATGTGATTTT

altered gDNA sequence snippet

AAGGGACAGAAAGAGTATGGTTGTGGACTGCATGTGATTTT

original cDNA sequence snippet

AAGGGACAGAAAGAGTATGGGTGTGGACTGCATGTGATTTT

altered cDNA sequence snippet

AAGGGACAGAAAGAGTATGGTTGTGGACTGCATGTGATTTT

wildtype AA sequence

MSCSKAYGER YVASVQGSAP SPRKKSTRGF YFAKLYYEAK EYDLAKKYIC TYINVREMDP
RAHRFLGLLY ELEENTEKAV ECYRRSVELN PTQKDLVLKI AELLCKNDVT DGRAKYWVER
AAKLFPGSPA IYKLKEQLLD CEGEDGWNKL FDLIQSELYV RPDDVHVNIR LVELYRSTKR
LKDAVARCHE AERNIALRSS LEWNSCVVQT LKEYLESLQC LESDKSDWRA TNTDLLLAYA
NLMLLTLSTR DVQESRELLE SFDSALQSAK SSLGGNDELS ATFLEMKGHF YMHAGSLLLK
MGQHGNNVQW RALSELAALC YLIAFQVPRP KIKLIKGEAG QNLLEMMACD RLSQSGHMLL
NLSRGKQDFL KVVVETFANK SGQSALYDAL FSSQSPKDTS FLGSDDIGNI DVQEPELEDL
ARYDVGAIRA HNGSLQHLTW LGLQWNSLPA LPGIRKWLKQ LFHHLPQETS RLETNAPESI
CILDLEVFLL GVVYTSHLQL KEKCNSHHSS YQPLCLPLPV CKQLCTERQK SWWDAVCTLI
HRKAVPGNSA KLRLLVQHEI NTLRAQEKHG LQPALLVHWA KCLQKMGSGL NSFYDQREYI
GRSVHYWKKV LPLLKIIKKK NSIPEPIDPL FKHFHSVDIQ ASEIVEYEED AHVTFAILDA
VNGNIEDAMT AFESIKSVVS YWNLALIFHR KAEDIANDAL SPEEQEECKN YLRKTRGYLI
KILDDSDSNL SVVKKLPVPL ESVKEMLKSV MQELENYSEG DPLYKNGSLR NADSEIKHST
PSPTKYSLSP SKSYKYSPKT PPRWAEDQNS LLKMIRQEVK AIKEEMQELK LNSSKSASHH
RWPTENYGPD SVPDGYQGSQ TFHGAPLTVA TTGPSVYYSQ SPAYNSQYLL RPAANVTPTK
GSSNTEFKST KEGFSIPVSA DGFKFGISEP GNQEKESEKP LENDTGFQAQ DISGQKNGRG
VIFGQTSSTF TFADVAKSTS GEGFQFGKKD PNFKGFSGAG EKLFSSQCGK MANKANTSGD
FEKDDDAYKT EDSDDIHFEP VVQMPEKVEL VIGEEGEKVL YSQGVKLFRF DAEVRQWKER
GLGNLKILKN EVNGKPRMLM RREQVLKVCA NHWITTTMNL KPLSGSDRAW MWSASDFSDG
DAKLERLAAK FKTPELAEEF KQKFEECQQL LLDIPLQTPH KLVDTGRAAK LIQRAEEMKS
GLKDFKTFLT NDQTKVTEEE NKGSGTGAAG ASDTTIKPNP ENTGPTLEWD NCDLREDALD
DSVSSSSVHA SPLASSPVRK NLFHFGESTT GSNFSFKSAL SPSKSPAKLN QSGTSVGTDE
ESDVTQEEER DGQYFEPVVP LPDLVEVSSG EENEKVVFSH RAELYRYDKD VGQWKERGIG
DIKILQNYDN KQVRIVMRRD QVLKLCANHT ITPDMSLQNM KGTERVWVWT ACDFADGERK
VEHLAVRFKL QDVADSFKKI FDEAKTAQEK DSLITPHVSR SSTPRESPCG KIAVAVLEET
TRERTDVIQG DDVADAASEV EVSSTSETTT KAVVSPPKFV FGSESVKRIF SSEKSKPFAF
GNSSATGSLF GFSFNASLKS NNSETSSVAQ SGSESKVEPK KCELSKNSDI EQSSDSKVKN
LSASFPMEES SINYTFKTPE KEPPLWHAEF TKEELVQKLS STTKSADHLN GLLREAEATS
AVLMEQIKLL KSEIRRLERN QEQEESAANV EHLKNVLLQF IFLKPGSERE RLLPVINTML
QLSPEEKGKL AAVAQGEE*

mutated AA sequence

MSCSKAYGER YVASVQGSAP SPRKKSTRGF YFAKLYYEAK EYDLAKKYIC TYINVREMDP
RAHRFLGLLY ELEENTEKAV ECYRRSVELN PTQKDLVLKI AELLCKNDVT DGRAKYWVER
AAKLFPGSPA IYKLKEQLLD CEGEDGWNKL FDLIQSELYV RPDDVHVNIR LVELYRSTKR
LKDAVARCHE AERNIALRSS LEWNSCVVQT LKEYLESLQC LESDKSDWRA TNTDLLLAYA
NLMLLTLSTR DVQESRELLE SFDSALQSAK SSLGGNDELS ATFLEMKGHF YMHAGSLLLK
MGQHGNNVQW RALSELAALC YLIAFQVPRP KIKLIKGEAG QNLLEMMACD RLSQSGHMLL
NLSRGKQDFL KVVVETFANK SGQSALYDAL FSSQSPKDTS FLGSDDIGNI DVQEPELEDL
ARYDVGAIRA HNGSLQHLTW LGLQWNSLPA LPGIRKWLKQ LFHHLPQETS RLETNAPESI
CILDLEVFLL GVVYTSHLQL KEKCNSHHSS YQPLCLPLPV CKQLCTERQK SWWDAVCTLI
HRKAVPGNSA KLRLLVQHEI NTLRAQEKHG LQPALLVHWA KCLQKMGSGL NSFYDQREYI
GRSVHYWKKV LPLLKIIKKK NSIPEPIDPL FKHFHSVDIQ ASEIVEYEED AHVTFAILDA
VNGNIEDAMT AFESIKSVVS YWNLALIFHR KAEDIANDAL SPEEQEECKN YLRKTRGYLI
KILDDSDSNL SVVKKLPVPL ESVKEMLKSV MQELENYSEG DPLYKNGSLR NADSEIKHST
PSPTKYSLSP SKSYKYSPKT PPRWAEDQNS LLKMIRQEVK AIKEEMQELK LNSSKSASHH
RWPTENYGPD SVPDGYQGSQ TFHGAPLTVA TTGPSVYYSQ SPAYNSQYLL RPAANVTPTK
GSSNTEFKST KEGFSIPVSA DGFKFGISEP GNQEKESEKP LENDTGFQAQ DISGQKNGRG
VIFGQTSSTF TFADVAKSTS GEGFQFGKKD PNFKGFSGAG EKLFSSQCGK MANKANTSGD
FEKDDDAYKT EDSDDIHFEP VVQMPEKVEL VIGEEGEKVL YSQGVKLFRF DAEVRQWKER
GLGNLKILKN EVNGKPRMLM RREQVLKVCA NHWITTTMNL KPLSGSDRAW MWSASDFSDG
DAKLERLAAK FKTPELAEEF KQKFEECQQL LLDIPLQTPH KLVDTGRAAK LIQRAEEMKS
GLKDFKTFLT NDQTKVTEEE NKGSGTGAAG ASDTTIKPNP ENTGPTLEWD NCDLREDALD
DSVSSSSVHA SPLASSPVRK NLFHFGESTT GSNFSFKSAL SPSKSPAKLN QSGTSVGTDE
ESDVTQEEER DGQYFEPVVP LPDLVEVSSG EENEKVVFSH RAELYRYDKD VGQWKERGIG
DIKILQNYDN KQVRIVMRRD QVLKLCANHT ITPDMSLQNM KGTERVWLWT ACDFADGERK
VEHLAVRFKL QDVADSFKKI FDEAKTAQEK DSLITPHVSR SSTPRESPCG KIAVAVLEET
TRERTDVIQG DDVADAASEV EVSSTSETTT KAVVSPPKFV FGSESVKRIF SSEKSKPFAF
GNSSATGSLF GFSFNASLKS NNSETSSVAQ SGSESKVEPK KCELSKNSDI EQSSDSKVKN
LSASFPMEES SINYTFKTPE KEPPLWHAEF TKEELVQKLS STTKSADHLN GLLREAEATS
AVLMEQIKLL KSEIRRLERN QEQEESAANV EHLKNVLLQF IFLKPGSERE RLLPVINTML
QLSPEEKGKL AAVAQGEE*

speed

1.12 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: 0.497663407993016 (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)

chr2:108488742G>TN/A show variant in all transcripts IGV

HGNC symbol

RGPD4

Ensembl transcript ID

ENST00000354986

Genbank transcript ID

N/A

UniProt peptide

Q7Z3J3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.4282G>T
cDNA.4364G>T
g.45355G>T

AA changes

V1428L Score: 32 explain score(s)

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

1428

frameshift

known variant

Reference ID: rs147825872

database	homozygous (T/T)	heterozygous	allele carriers
1000G	212	765	977
ExAC	8225	16317	24542

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.324	1
	1.849	1
(flanking)	3.57	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
Donor increased	45348	wt: 0.55 / mu: 0.79	wt: GAAAGAGTATGGGTG mu: GAAAGAGTATGGTTG	AAGA\|gtat

distance from splice site

643

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1428

mutated

all conserved

1428

Ptroglodytes

all identical

ENSPTRG00000012330

1409

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000003226

2240

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0039302

1700

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1334	1470	DOMAIN	RanBD1 2.	lost
1703	1753	DOMAIN	GRIP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5301 / 5301

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

1767 / 1767

position of stopcodon in wt / mu cDNA

5383 / 5383

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

83 / 83

chromosome

strand

last intron/exon boundary

5349

theoretical NMD boundary in CDS

5216

length of CDS

5301

coding sequence (CDS) position

4282

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

4364

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

45355

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

108488742

original gDNA sequence snippet

AAGGGACAGAAAGAGTATGGGTGTGGACTGCATGTGATTTT

altered gDNA sequence snippet

AAGGGACAGAAAGAGTATGGTTGTGGACTGCATGTGATTTT

original cDNA sequence snippet

AAGGGACAGAAAGAGTATGGGTGTGGACTGCATGTGATTTT

altered cDNA sequence snippet

AAGGGACAGAAAGAGTATGGTTGTGGACTGCATGTGATTTT

wildtype AA sequence

mutated AA sequence

MSCSKAYGER YVASVQGSAP SPRKKSTRGF YFAKLYYEAK EYDLAKKYIC TYINVREMDP
RAHRFLGLLY ELEENTEKAV ECYRRSVELN PTQKDLVLKI AELLCKNDVT DGRAKYWVER
AAKLFPGSPA IYKLKEQLLD CEGEDGWNKL FDLIQSELYV RPDDVHVNIR LVELYRSTKR
LKDAVARCHE AERNIALRSS LEWNSCVVQT LKEYLESLQC LESDKSDWRA TNTDLLLAYA
NLMLLTLSTR DVQESRELLE SFDSALQSAK SSLGGNDELS ATFLEMKGHF YMHAGSLLLK
MGQHGNNVQW RALSELAALC YLIAFQVPRP KIKLIKGEAG QNLLEMMACD RLSQSGHMLL
NLSRGKQDFL KVVVETFANK SGQSALYDAL FSSQSPKDTS FLGSDDIGNI DVQEPELEDL
ARYDVGAIRA HNGSLQHLTW LGLQWNSLPA LPGIRKWLKQ LFHHLPQETS RLETNAPESI
CILDLEVFLL GVVYTSHLQL KEKCNSHHSS YQPLCLPLPV CKQLCTERQK SWWDAVCTLI
HRKAVPGNSA KLRLLVQHEI NTLRAQEKHG LQPALLVHWA KCLQKMGSGL NSFYDQREYI
GRSVHYWKKV LPLLKIIKKK NSIPEPIDPL FKHFHSVDIQ ASEIVEYEED AHVTFAILDA
VNGNIEDAMT AFESIKSVVS YWNLALIFHR KAEDIANDAL SPEEQEECKN YLRKTRGYLI
KILDDSDSNL SVVKKLPVPL ESVKEMLKSV MQELENYSEG DPLYKNGSLR NADSEIKHST
PSPTKYSLSP SKSYKYSPKT PPRWAEDQNS LLKMIRQEVK AIKEEMQELK LNSSKSASHH
RWPTENYGPD SVPDGYQGSQ TFHGAPLTVA TTGPSVYYSQ SPAYNSQYLL RPAANVTPTK
GSSNTEFKST KEGFSIPVSA DGFKFGISEP GNQEKESEKP LENDTGFQAQ DISGQKNGRG
VIFGQTSSTF TFADVAKSTS GEGFQFGKKD PNFKGFSGAG EKLFSSQCGK MANKANTSGD
FEKDDDAYKT EDSDDIHFEP VVQMPEKVEL VIGEEGEKVL YSQGVKLFRF DAEVRQWKER
GLGNLKILKN EVNGKPRMLM RREQVLKVCA NHWITTTMNL KPLSGSDRAW MWSASDFSDG
DAKLERLAAK FKTPELAEEF KQKFEECQQL LLDIPLQTPH KLVDTGRAAK LIQRAEEMKS
GLKDFKTFLT NDQTKVTEEE NKGSGTGAAG ASDTTIKPNP ENTGPTLEWD NCDLREDALD
DSVSSSSVHA SPLASSPVRK NLFHFGESTT GSNFSFKSAL SPSKSPAKLN QSGTSVGTDE
ESDVTQEEER DGQYFEPVVP LPDLVEVSSG EENEKVVFSH RAELYRYDKD VGQWKERGIG
DIKILQNYDN KQVRIVMRRD QVLKLCANHT ITPDMSLQNM KGTERVWLWT ACDFADGERK
VEHLAVRFKL QDVADSFKKI FDEAKTAQEK DSLITPHVSR SSTPRESPCG KIAVAVLEET
TRERTDVIQG DDVADAASEV EVSSTSETTT KAVVSPPKFV FGSESVKRIF SSEKSKPFAF
GNSSATGSLF GFSFNASLKS NNSETSSVAQ SGSESKVEPK KCELSKNSDI EQSSDSKVKN
LSASFPMEES SINYTFKTPE KEPPLWHAEF TKEELVQKLS STTKSADHLN GLLREAEATS
AVLMEQIKLL KSEIRRLERN QEQEESAANV EHLKNVLLQF IFLKPGSERE RLLPVINTML
QLSPEEKGKL AAVAQAERGF VLNSTF*

speed

1.18 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems