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: ENST00000563385
Querying Taster for transcript #2: ENST00000421865
MT speed 0 s - this script 3.468348 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LAMA2	polymorphism_automatic	0.999999289550229	simple_aae		affected		A2587V	single base exchange	rs2229848		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 7.10449770538996e-07 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM023406)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:129807629C>TN/A show variant in all transcripts IGV

HGNC symbol

LAMA2

Ensembl transcript ID

ENST00000421865

Genbank transcript ID

NM_000426

UniProt peptide

P24043

alteration type

single base exchange

alteration region

CDS

DNA changes

c.7760C>T
cDNA.7809C>T
g.603288C>T

AA changes

A2587V Score: 64 explain score(s)

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

2587

frameshift

known variant

Reference ID: rs2229848

database	homozygous (T/T)	heterozygous	allele carriers
1000G	872	1180	2052
ExAC	27343	-21919	5424

known disease mutation at this position, please check HGMD for details (HGMD ID CM023406)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.202	1
	5.013	1
(flanking)	-0.851	0.369

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 increased	603299	wt: 0.23 / mu: 0.34	wt: CCTATTATGCAATACTCCTCAACAGGGGCCGTCTGGAAGTG mu: CCTATTATGTAATACTCCTCAACAGGGGCCGTCTGGAAGTG	ctca\|ACAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2587

mutated

not conserved

2587

Ptroglodytes

all identical

ENSPTRG00000018588

2586

Mmulatta

all identical

ENSMMUG00000022136

2551

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000019899

2583

Ggallus

all identical

ENSGALG00000014014

2552

Trubripes

all conserved

ENSTRUG00000017857

2562

EGD

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

all identical

T22A3.8

2713

Xtropicalis

all identical

ENSXETG00000014905

322

protein features

start (aa)	end (aa)	feature	details
2526	2710	DOMAIN	Laminin G-like 3.	lost
2624	2624	CONFLICT	H -> R (in Ref. 5; AAA63215).	might get lost (downstream of altered splice site)
2648	2648	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
2683	2683	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2710	2710	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2763	2934	DOMAIN	Laminin G-like 4.	might get lost (downstream of altered splice site)
2807	2807	CONFLICT	R -> A (in Ref. 1; CAA81394 and 2; AAB18388).	might get lost (downstream of altered splice site)
2868	2868	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
2893	2893	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
2909	2909	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2934	2934	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2939	3110	DOMAIN	Laminin G-like 5.	might get lost (downstream of altered splice site)
2969	2969	CONFLICT	R -> A (in Ref. 1; CAA81394 and 2; AAB18388).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

9369 / 9369

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

3123 / 3123

position of stopcodon in wt / mu cDNA

9418 / 9418

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

50 / 50

chromosome

strand

last intron/exon boundary

9261

theoretical NMD boundary in CDS

9161

length of CDS

9369

coding sequence (CDS) position

7760

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

7809

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

603288

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

129807629

original gDNA sequence snippet

GCTGTTGCAGGCCTATTATGCAATACTCCTCAACAGGGGCC

altered gDNA sequence snippet

GCTGTTGCAGGCCTATTATGTAATACTCCTCAACAGGGGCC

original cDNA sequence snippet

GACTGGACAGGCCTATTATGCAATACTCCTCAACAGGGGCC

altered cDNA sequence snippet

GACTGGACAGGCCTATTATGTAATACTCCTCAACAGGGGCC

wildtype AA sequence

MPGAAGVLLL LLLSGGLGGV QAQRPQQQRQ SQAHQQRGLF PAVLNLASNA LITTNATCGE
KGPEMYCKLV EHVPGQPVRN PQCRICNQNS SNPNQRHPIT NAIDGKNTWW QSPSIKNGIE
YHYVTITLDL QQVFQIAYVI VKAANSPRPG NWILERSLDD VEYKPWQYHA VTDTECLTLY
NIYPRTGPPS YAKDDEVICT SFYSKIHPLE NGEIHISLIN GRPSADDPSP ELLEFTSARY
IRLRFQRIRT LNADLMMFAH KDPREIDPIV TRRYYYSVKD ISVGGMCICY GHARACPLDP
ATNKSRCECE HNTCGDSCDQ CCPGFHQKPW RAGTFLTKTE CEACNCHGKA EECYYDENVA
RRNLSLNIRG KYIGGGVCIN CTQNTAGINC ETCTDGFFRP KGVSPNYPRP CQPCHCDPIG
SLNEVCVKDE KHARRGLAPG SCHCKTGFGG VSCDRCARGY TGYPDCKACN CSGLGSKNED
PCFGPCICKE NVEGGDCSRC KSGFFNLQED NWKGCDECFC SGVSNRCQSS YWTYGKIQDM
SGWYLTDLPG RIRVAPQQDD LDSPQQISIS NAEARQALPH SYYWSAPAPY LGNKLPAVGG
QLTFTISYDL EEEEEDTERV LQLMIILEGN DLSISTAQDE VYLHPSEEHT NVLLLKEESF
TIHGTHFPVR RKEFMTVLAN LKRVLLQITY SFGMDAIFRL SSVNLESAVS YPTDGSIAAA
VEVCQCPPGY TGSSCESCWP RHRRVNGTIF GGICEPCQCF GHAESCDDVT GECLNCKDHT
GGPYCDKCLP GFYGEPTKGT SEDCQPCACP LNIPSNNFSP TCHLDRSLGL ICDGCPVGYT
GPRCERCAEG YFGQPSVPGG SCQPCQCNDN LDFSIPGSCD SLSGSCLICK PGTTGRYCEL
CADGYFGDAV DAKNCQPCRC NAGGSFSEVC HSQTGQCECR ANVQGQRCDK CKAGTFGLQS
ARGCVPCNCN SFGSKSFDCE ESGQCWCQPG VTGKKCDRCA HGYFNFQEGG CTACECSHLG
NNCDPKTGRC ICPPNTIGEK CSKCAPNTWG HSITTGCKAC NCSTVGSLDF QCNVNTGQCN
CHPKFSGAKC TECSRGHWNY PRCNLCDCFL PGTDATTCDS ETKKCSCSDQ TGQCTCKVNV
EGIHCDRCRP GKFGLDAKNP LGCSSCYCFG TTTQCSEAKG LIRTWVTLKA EQTILPLVDE
ALQHTTTKGI VFQHPEIVAH MDLMREDLHL EPFYWKLPEQ FEGKKLMAYG GKLKYAIYFE
AREETGFSTY NPQVIIRGGT PTHARIIVRH MAAPLIGQLT RHEIEMTEKE WKYYGDDPRV
HRTVTREDFL DILYDIHYIL IKATYGNFMR QSRISEISME VAEQGRGTTM TPPADLIEKC
DCPLGYSGLS CEACLPGFYR LRSQPGGRTP GPTLGTCVPC QCNGHSSLCD PETSICQNCQ
HHTAGDFCER CALGYYGIVK GLPNDCQQCA CPLISSSNNF SPSCVAEGLD DYRCTACPRG
YEGQYCERCA PGYTGSPGNP GGSCQECECD PYGSLPVPCD PVTGFCTCRP GATGRKCDGC
KHWHAREGWE CVFCGDECTG LLLGDLARLE QMVMSINLTG PLPAPYKMLY GLENMTQELK
HLLSPQRAPE RLIQLAEGNL NTLVTEMNEL LTRATKVTAD GEQTGQDAER TNTRAKSLGE
FIKELARDAE AVNEKAIKLN ETLGTRDEAF ERNLEGLQKE IDQMIKELRR KNLETQKEIA
EDELVAAEAL LKKVKKLFGE SRGENEEMEK DLREKLADYK NKVDDAWDLL REATDKIREA
NRLFAVNQKN MTALEKKKEA VESGKRQIEN TLKEGNDILD EANRLADEIN SIIDYVEDIQ
TKLPPMSEEL NDKIDDLSQE IKDRKLAEKV SQAESHAAQL NDSSAVLDGI LDEAKNISFN
ATAAFKAYSN IKDYIDEAEK VAKEAKDLAH EATKLATGPR GLLKEDAKGC LQKSFRILNE
AKKLANDVKE NEDHLNGLKT RIENADARNG DLLRTLNDTL GKLSAIPNDT AAKLQAVKDK
ARQANDTAKD VLAQITELHQ NLDGLKKNYN KLADSVAKTN AVVKDPSKNK IIADADATVK
NLEQEADRLI DKLKPIKELE DNLKKNISEI KELINQARKQ ANSIKVSVSS GGDCIRTYKP
EIKKGSYNNI VVNVKTAVAD NLLFYLGSAK FIDFLAIEMR KGKVSFLWDV GSGVGRVEYP
DLTIDDSYWY RIVASRTGRN GTISVRALDG PKASIVPSTH HSTSPPGYTI LDVDANAMLF
VGGLTGKLKK ADAVRVITFT GCMGETYFDN KPIGLWNFRE KEGDCKGCTV SPQVEDSEGT
IQFDGEGYAL VSRPIRWYPN ISTVMFKFRT FSSSALLMYL ATRDLRDFMS VELTDGHIKV
SYDLGSGMAS VVSNQNHNDG KWKSFTLSRI QKQANISIVD IDTNQEENIA TSSSGNNFGL
DLKADDKIYF GGLPTLRNLS MKARPEVNLK KYSGCLKDIE ISRTPYNILS SPDYVGVTKG
CSLENVYTVS FPKPGFVELS PVPIDVGTEI NLSFSTKNES GIILLGSGGT PAPPRRKRRQ
TGQAYYAILL NRGRLEVHLS TGARTMRKIV IRPEPNLFHD GREHSVHVER TRGIFTVQVD
ENRRYMQNLT VEQPIEVKKL FVGGAPPEFQ PSPLRNIPPF EGCIWNLVIN SVPMDFARPV
SFKNADIGRC AHQKLREDED GAAPAEIVIQ PEPVPTPAFP TPTPVLTHGP CAAESEPALL
IGSKQFGLSR NSHIAIAFDD TKVKNRLTIE LEVRTEAESG LLFYMARINH ADFATVQLRN
GLPYFSYDLG SGDTHTMIPT KINDGQWHKI KIMRSKQEGI LYVDGASNRT ISPKKADILD
VVGMLYVGGL PINYTTRRIG PVTYSIDGCV RNLHMAEAPA DLEQPTSSFH VGTCFANAQR
GTYFDGTGFA KAVGGFKVGL DLLVEFEFRT TTTTGVLLGI SSQKMDGMGI EMIDEKLMFH
VDNGAGRFTA VYDAGVPGHL CDGQWHKVTA NKIKHRIELT VDGNQVEAQS PNPASTSADT
NDPVFVGGFP DDLKQFGLTT SIPFRGCIRS LKLTKGTGKP LEVNFAKALE LRGVQPVSCP
AN*

mutated AA sequence

MPGAAGVLLL LLLSGGLGGV QAQRPQQQRQ SQAHQQRGLF PAVLNLASNA LITTNATCGE
KGPEMYCKLV EHVPGQPVRN PQCRICNQNS SNPNQRHPIT NAIDGKNTWW QSPSIKNGIE
YHYVTITLDL QQVFQIAYVI VKAANSPRPG NWILERSLDD VEYKPWQYHA VTDTECLTLY
NIYPRTGPPS YAKDDEVICT SFYSKIHPLE NGEIHISLIN GRPSADDPSP ELLEFTSARY
IRLRFQRIRT LNADLMMFAH KDPREIDPIV TRRYYYSVKD ISVGGMCICY GHARACPLDP
ATNKSRCECE HNTCGDSCDQ CCPGFHQKPW RAGTFLTKTE CEACNCHGKA EECYYDENVA
RRNLSLNIRG KYIGGGVCIN CTQNTAGINC ETCTDGFFRP KGVSPNYPRP CQPCHCDPIG
SLNEVCVKDE KHARRGLAPG SCHCKTGFGG VSCDRCARGY TGYPDCKACN CSGLGSKNED
PCFGPCICKE NVEGGDCSRC KSGFFNLQED NWKGCDECFC SGVSNRCQSS YWTYGKIQDM
SGWYLTDLPG RIRVAPQQDD LDSPQQISIS NAEARQALPH SYYWSAPAPY LGNKLPAVGG
QLTFTISYDL EEEEEDTERV LQLMIILEGN DLSISTAQDE VYLHPSEEHT NVLLLKEESF
TIHGTHFPVR RKEFMTVLAN LKRVLLQITY SFGMDAIFRL SSVNLESAVS YPTDGSIAAA
VEVCQCPPGY TGSSCESCWP RHRRVNGTIF GGICEPCQCF GHAESCDDVT GECLNCKDHT
GGPYCDKCLP GFYGEPTKGT SEDCQPCACP LNIPSNNFSP TCHLDRSLGL ICDGCPVGYT
GPRCERCAEG YFGQPSVPGG SCQPCQCNDN LDFSIPGSCD SLSGSCLICK PGTTGRYCEL
CADGYFGDAV DAKNCQPCRC NAGGSFSEVC HSQTGQCECR ANVQGQRCDK CKAGTFGLQS
ARGCVPCNCN SFGSKSFDCE ESGQCWCQPG VTGKKCDRCA HGYFNFQEGG CTACECSHLG
NNCDPKTGRC ICPPNTIGEK CSKCAPNTWG HSITTGCKAC NCSTVGSLDF QCNVNTGQCN
CHPKFSGAKC TECSRGHWNY PRCNLCDCFL PGTDATTCDS ETKKCSCSDQ TGQCTCKVNV
EGIHCDRCRP GKFGLDAKNP LGCSSCYCFG TTTQCSEAKG LIRTWVTLKA EQTILPLVDE
ALQHTTTKGI VFQHPEIVAH MDLMREDLHL EPFYWKLPEQ FEGKKLMAYG GKLKYAIYFE
AREETGFSTY NPQVIIRGGT PTHARIIVRH MAAPLIGQLT RHEIEMTEKE WKYYGDDPRV
HRTVTREDFL DILYDIHYIL IKATYGNFMR QSRISEISME VAEQGRGTTM TPPADLIEKC
DCPLGYSGLS CEACLPGFYR LRSQPGGRTP GPTLGTCVPC QCNGHSSLCD PETSICQNCQ
HHTAGDFCER CALGYYGIVK GLPNDCQQCA CPLISSSNNF SPSCVAEGLD DYRCTACPRG
YEGQYCERCA PGYTGSPGNP GGSCQECECD PYGSLPVPCD PVTGFCTCRP GATGRKCDGC
KHWHAREGWE CVFCGDECTG LLLGDLARLE QMVMSINLTG PLPAPYKMLY GLENMTQELK
HLLSPQRAPE RLIQLAEGNL NTLVTEMNEL LTRATKVTAD GEQTGQDAER TNTRAKSLGE
FIKELARDAE AVNEKAIKLN ETLGTRDEAF ERNLEGLQKE IDQMIKELRR KNLETQKEIA
EDELVAAEAL LKKVKKLFGE SRGENEEMEK DLREKLADYK NKVDDAWDLL REATDKIREA
NRLFAVNQKN MTALEKKKEA VESGKRQIEN TLKEGNDILD EANRLADEIN SIIDYVEDIQ
TKLPPMSEEL NDKIDDLSQE IKDRKLAEKV SQAESHAAQL NDSSAVLDGI LDEAKNISFN
ATAAFKAYSN IKDYIDEAEK VAKEAKDLAH EATKLATGPR GLLKEDAKGC LQKSFRILNE
AKKLANDVKE NEDHLNGLKT RIENADARNG DLLRTLNDTL GKLSAIPNDT AAKLQAVKDK
ARQANDTAKD VLAQITELHQ NLDGLKKNYN KLADSVAKTN AVVKDPSKNK IIADADATVK
NLEQEADRLI DKLKPIKELE DNLKKNISEI KELINQARKQ ANSIKVSVSS GGDCIRTYKP
EIKKGSYNNI VVNVKTAVAD NLLFYLGSAK FIDFLAIEMR KGKVSFLWDV GSGVGRVEYP
DLTIDDSYWY RIVASRTGRN GTISVRALDG PKASIVPSTH HSTSPPGYTI LDVDANAMLF
VGGLTGKLKK ADAVRVITFT GCMGETYFDN KPIGLWNFRE KEGDCKGCTV SPQVEDSEGT
IQFDGEGYAL VSRPIRWYPN ISTVMFKFRT FSSSALLMYL ATRDLRDFMS VELTDGHIKV
SYDLGSGMAS VVSNQNHNDG KWKSFTLSRI QKQANISIVD IDTNQEENIA TSSSGNNFGL
DLKADDKIYF GGLPTLRNLS MKARPEVNLK KYSGCLKDIE ISRTPYNILS SPDYVGVTKG
CSLENVYTVS FPKPGFVELS PVPIDVGTEI NLSFSTKNES GIILLGSGGT PAPPRRKRRQ
TGQAYYVILL NRGRLEVHLS TGARTMRKIV IRPEPNLFHD GREHSVHVER TRGIFTVQVD
ENRRYMQNLT VEQPIEVKKL FVGGAPPEFQ PSPLRNIPPF EGCIWNLVIN SVPMDFARPV
SFKNADIGRC AHQKLREDED GAAPAEIVIQ PEPVPTPAFP TPTPVLTHGP CAAESEPALL
IGSKQFGLSR NSHIAIAFDD TKVKNRLTIE LEVRTEAESG LLFYMARINH ADFATVQLRN
GLPYFSYDLG SGDTHTMIPT KINDGQWHKI KIMRSKQEGI LYVDGASNRT ISPKKADILD
VVGMLYVGGL PINYTTRRIG PVTYSIDGCV RNLHMAEAPA DLEQPTSSFH VGTCFANAQR
GTYFDGTGFA KAVGGFKVGL DLLVEFEFRT TTTTGVLLGI SSQKMDGMGI EMIDEKLMFH
VDNGAGRFTA VYDAGVPGHL CDGQWHKVTA NKIKHRIELT VDGNQVEAQS PNPASTSADT
NDPVFVGGFP DDLKQFGLTT SIPFRGCIRS LKLTKGTGKP LEVNFAKALE LRGVQPVSCP
AN*

speed

1.37 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
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Problems

data problem

No NCBI gene ID found for this transcript

back to results table