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: ENST00000264828
MT speed 1.25 s - this script 4.682605 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL5A3	polymorphism_automatic	0.000161695274106033	simple_aae		affected		R1042P	single base exchange	rs2161468		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999838304725894 (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)

chr19:10088271C>GN/A show variant in all transcripts IGV

HGNC symbol

COL5A3

Ensembl transcript ID

ENST00000264828

Genbank transcript ID

NM_015719

UniProt peptide

P25940

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3125G>C
cDNA.3211G>C
g.32877G>C

AA changes

R1042P Score: 103 explain score(s)

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

1042

frameshift

known variant

Reference ID: rs2161468

database	homozygous (G/G)	heterozygous	allele carriers
1000G	309	1136	1445
ExAC	7976	16815	24791

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.149	0.996
	1.681	0.997
(flanking)	2.027	0.994

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	32878	sequence motif lost	-	wt: CCGG\|gtaa mu: CCCG.gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1042

mutated

not conserved

1042

Ptroglodytes

all conserved

ENSPTRG00000010454

1051

QGLPGPP

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000004098

1041

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000005692

1110

Drerio

not conserved

ENSDARG00000017360

801

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000011757

659

protein features

start (aa)	end (aa)	feature	details
392	1489	REGION	Triple-helical region.	lost
1430	1488	DOMAIN	Collagen-like 6.	might get lost (downstream of altered splice site)
1514	1744	DOMAIN	Fibrillar collagen NC1.	might get lost (downstream of altered splice site)
1544	1544	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1544	1544	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1567	1567	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1567	1567	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1576	1576	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1576	1576	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
1585	1585	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1651	1651	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1687	1687	CONFLICT	A -> T (in Ref. 1; AAF59902).	might get lost (downstream of altered splice site)
1696	1696	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1742	1742	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

5238 / 5238

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

1746 / 1746

position of stopcodon in wt / mu cDNA

5324 / 5324

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

87 / 87

chromosome

strand

-1

last intron/exon boundary

5178

theoretical NMD boundary in CDS

5041

length of CDS

5238

coding sequence (CDS) position

3125

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

3211

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

32877

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

10088271

original gDNA sequence snippet

TGCAGGCAAGAAGGGGTCCCGGGTAAGTGACTTGCCCATCC

altered gDNA sequence snippet

TGCAGGCAAGAAGGGGTCCCCGGTAAGTGACTTGCCCATCC

original cDNA sequence snippet

TGCAGGCAAGAAGGGGTCCCGGGGAGAACGTGGCCCCCCTG

altered cDNA sequence snippet

TGCAGGCAAGAAGGGGTCCCCGGGAGAACGTGGCCCCCCTG

wildtype AA sequence

MGNRRDLGQP RAGLCLLLAA LQLLPGTQAD PVDVLKALGV QGGQAGVPEG PGFCPQRTPE
GDRAFRIGQA STLGIPTWEL FPEGHFPENF SLLITLRGQP ANQSVLLSIY DERGARQLGL
ALGPALGLLG DPFRPLPQQV NLTDGRWHRV AVSIDGEMVT LVADCEAQPP VLGHGPRFIS
IAGLTVLGTQ DLGEKTFEGD IQELLISPDP QAAFQACERY LPDCDNLAPA ATVAPQGEPE
TPRPRRKGKG KGRKKGRGRK GKGRKKNKEI WTSSPPPDSA ENQTSTDIPK TETPAPNLPP
TPTPLVVTST VTTGLNATIL ERSLDPDSGT ELGTLETKAA REDEEGDDST MGPDFRAAEY
PSRTQFQIFP GAGEKGAKGE PAVIEKGQQF EGPPGAPGPQ GVVGPSGPPG PPGFPGDPGP
PGPAGLPGIP GIDGIRGPPG TVIMMPFQFA GGSFKGPPVS FQQAQAQAVL QQTQLSMKGP
PGPVGLTGRP GPVGLPGHPG LKGEEGAEGP QGPRGLQGPH GPPGRVGKMG RPGADGARGL
PGDTGPKGDR GFDGLPGLPG EKGQRGDFGH VGQPGPPGED GERGAEGPPG PTGQAGEPGP
RGLLGPRGSP GPTGRPGVTG IDGAPGAKGN VGPPGEPGPP GQQGNHGSQG LPGPQGLIGT
PGEKGPPGNP GIPGLPGSDG PLGHPGHEGP TGEKGAQGPP GSAGPPGYPG PRGVKGTSGN
RGLQGEKGEK GEDGFPGFKG DVGLKGDQGK PGAPGPRGED GPEGPKGQAG QAGEEGPPGS
AGEKGKLGVP GLPGYPGRPG PKGSIGFPGP LGPIGEKGKS GKTGQPGLEG ERGPPGSRGE
RGQPGATGQP GPKGDVGQDG APGIPGEKGL PGLQGPPGFP GPKGPPGHQG KDGRPGHPGQ
RGELGFQGQT GPPGPAGVLG PQGKTGEVGP LGERGPPGPP GPPGEQGLPG LEGREGAKGE
LGPPGPLGKE GPAGLRGFPG PKGGPGDPGP TGLKGDKGPP GPVGANGSPG ERGPLGPAGG
IGLPGQSGSE GPVGPAGKKG SRGERGPPGP TGKDGIPGPL GPLGPPGAAG PSGEEGDKGD
VGAPGHKGSK GDKGDAGPPG QPGIRGPAGH PGPPGADGAQ GRRGPPGLFG QKGDDGVRGF
VGVIGPPGLQ GLPGPPGEKG EVGDVGSMGP HGAPGPRGPQ GPTGSEGTPG LPGGVGQPGA
VGEKGERGDA GDPGPPGAPG IPGPKGDIGE KGDSGPSGAA GPPGKKGPPG EDGAKGSVGP
TGLPGDLGPP GDPGVSGIDG SPGEKGDPGD VGGPGPPGAS GEPGAPGPPG KRGPSGHMGR
EGREGEKGAK GEPGPDGPPG RTGPMGARGP PGRVGPEGLR GIPGPVGEPG LLGAPGQMGP
PGPLGPSGLP GLKGDTGPKG EKGHIGLIGL IGPPGEAGEK GDQGLPGVQG PPGPKGDPGP
PGPIGSLGHP GPPGVAGPLG QKGSKGSPGS MGPRGDTGPA GPPGPPGAPA ELHGLRRRRR
FVPVPLPVVE GGLEEVLASL TSLSLELEQL RRPPGTAERP GLVCHELHRN HPHLPDGEYW
IDPNQGCARD SFRVFCNFTA GGETCLYPDK KFEIVKLASW SKEKPGGWYS TFRRGKKFSY
VDADGSPVNV VQLNFLKLLS ATARQNFTYS CQNAAAWLDE ATGDYSHSAR FLGTNGEELS
FNQTTAATVS VPQDGCRLRK GQTKTLFEFS SSRAGFLPLW DVAATDFGQT NQKFGFELGP
VCFSS*

mutated AA sequence

MGNRRDLGQP RAGLCLLLAA LQLLPGTQAD PVDVLKALGV QGGQAGVPEG PGFCPQRTPE
GDRAFRIGQA STLGIPTWEL FPEGHFPENF SLLITLRGQP ANQSVLLSIY DERGARQLGL
ALGPALGLLG DPFRPLPQQV NLTDGRWHRV AVSIDGEMVT LVADCEAQPP VLGHGPRFIS
IAGLTVLGTQ DLGEKTFEGD IQELLISPDP QAAFQACERY LPDCDNLAPA ATVAPQGEPE
TPRPRRKGKG KGRKKGRGRK GKGRKKNKEI WTSSPPPDSA ENQTSTDIPK TETPAPNLPP
TPTPLVVTST VTTGLNATIL ERSLDPDSGT ELGTLETKAA REDEEGDDST MGPDFRAAEY
PSRTQFQIFP GAGEKGAKGE PAVIEKGQQF EGPPGAPGPQ GVVGPSGPPG PPGFPGDPGP
PGPAGLPGIP GIDGIRGPPG TVIMMPFQFA GGSFKGPPVS FQQAQAQAVL QQTQLSMKGP
PGPVGLTGRP GPVGLPGHPG LKGEEGAEGP QGPRGLQGPH GPPGRVGKMG RPGADGARGL
PGDTGPKGDR GFDGLPGLPG EKGQRGDFGH VGQPGPPGED GERGAEGPPG PTGQAGEPGP
RGLLGPRGSP GPTGRPGVTG IDGAPGAKGN VGPPGEPGPP GQQGNHGSQG LPGPQGLIGT
PGEKGPPGNP GIPGLPGSDG PLGHPGHEGP TGEKGAQGPP GSAGPPGYPG PRGVKGTSGN
RGLQGEKGEK GEDGFPGFKG DVGLKGDQGK PGAPGPRGED GPEGPKGQAG QAGEEGPPGS
AGEKGKLGVP GLPGYPGRPG PKGSIGFPGP LGPIGEKGKS GKTGQPGLEG ERGPPGSRGE
RGQPGATGQP GPKGDVGQDG APGIPGEKGL PGLQGPPGFP GPKGPPGHQG KDGRPGHPGQ
RGELGFQGQT GPPGPAGVLG PQGKTGEVGP LGERGPPGPP GPPGEQGLPG LEGREGAKGE
LGPPGPLGKE GPAGLRGFPG PKGGPGDPGP TGLKGDKGPP GPVGANGSPG ERGPLGPAGG
IGLPGQSGSE GPVGPAGKKG SPGERGPPGP TGKDGIPGPL GPLGPPGAAG PSGEEGDKGD
VGAPGHKGSK GDKGDAGPPG QPGIRGPAGH PGPPGADGAQ GRRGPPGLFG QKGDDGVRGF
VGVIGPPGLQ GLPGPPGEKG EVGDVGSMGP HGAPGPRGPQ GPTGSEGTPG LPGGVGQPGA
VGEKGERGDA GDPGPPGAPG IPGPKGDIGE KGDSGPSGAA GPPGKKGPPG EDGAKGSVGP
TGLPGDLGPP GDPGVSGIDG SPGEKGDPGD VGGPGPPGAS GEPGAPGPPG KRGPSGHMGR
EGREGEKGAK GEPGPDGPPG RTGPMGARGP PGRVGPEGLR GIPGPVGEPG LLGAPGQMGP
PGPLGPSGLP GLKGDTGPKG EKGHIGLIGL IGPPGEAGEK GDQGLPGVQG PPGPKGDPGP
PGPIGSLGHP GPPGVAGPLG QKGSKGSPGS MGPRGDTGPA GPPGPPGAPA ELHGLRRRRR
FVPVPLPVVE GGLEEVLASL TSLSLELEQL RRPPGTAERP GLVCHELHRN HPHLPDGEYW
IDPNQGCARD SFRVFCNFTA GGETCLYPDK KFEIVKLASW SKEKPGGWYS TFRRGKKFSY
VDADGSPVNV VQLNFLKLLS ATARQNFTYS CQNAAAWLDE ATGDYSHSAR FLGTNGEELS
FNQTTAATVS VPQDGCRLRK GQTKTLFEFS SSRAGFLPLW DVAATDFGQT NQKFGFELGP
VCFSS*

speed

1.25 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