mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999627342 (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)

chr6:112493872A>GN/A show variant in all transcripts IGV

HGNC symbol

LAMA4

Ensembl transcript ID

ENST00000230538

Genbank transcript ID

NM_001105206

UniProt peptide

Q16363

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1492T>C
cDNA.1890T>C
g.82270T>C

AA changes

Y498H Score: 83 explain score(s)

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

498

frameshift

known variant

Reference ID: rs1050348

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1462	874	2336
ExAC	27246	-21725	5521

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.539	0.008
	0.826	0.295
(flanking)	1.557	0.428

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 increased	82277	wt: 0.3268 / mu: 0.3435 (marginal change - not scored)	wt: CCAGGCCCTTAACTATGTCAGGGATGCCGAAGACATGAACA mu: CCAGGCCCTTAACCATGTCAGGGATGCCGAAGACATGAACA	tcag\|GGAT
Acc marginally increased	82272	wt: 0.3618 / mu: 0.3787 (marginal change - not scored)	wt: CTTGACCAGGCCCTTAACTATGTCAGGGATGCCGAAGACAT mu: CTTGACCAGGCCCTTAACCATGTCAGGGATGCCGAAGACAT	ctat\|GTCA
Donor marginally increased	82272	wt: 0.9755 / mu: 0.9856 (marginal change - not scored)	wt: AACTATGTCAGGGAT mu: AACCATGTCAGGGAT	CTAT\|gtca
Donor marginally increased	82267	wt: 0.9215 / mu: 0.9454 (marginal change - not scored)	wt: CCCTTAACTATGTCA mu: CCCTTAACCATGTCA	CTTA\|acta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

498

mutated

all conserved

498

Ptroglodytes

all conserved

ENSPTRG00000018514

498

Mmulatta

no alignment

ENSMMUG00000013782

n/a

Fcatus

not conserved

ENSFCAG00000006308

433

Mmusculus

all conserved

ENSMUSG00000019846

491

Ggallus

all identical

ENSGALG00000015001

437

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000020785

555

Dmelanogaster

no alignment

FBgn0015774

n/a

Celegans

no alignment

F41C6.1

n/a

Xtropicalis

not conserved

ENSXETG00000007336

436

protein features

start (aa)	end (aa)	feature	details
256	832	REGION	Domain II and I.	lost
473	528	COILED	Potential.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5472 / 5472

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

1824 / 1824

position of stopcodon in wt / mu cDNA

5870 / 5870

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

399 / 399

chromosome

strand

-1

last intron/exon boundary

5725

theoretical NMD boundary in CDS

5276

length of CDS

5472

coding sequence (CDS) position

1492

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

1890

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

82270

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

112493872

original gDNA sequence snippet

CACTTGACCAGGCCCTTAACTATGTCAGGGATGCCGAAGAC

altered gDNA sequence snippet

CACTTGACCAGGCCCTTAACCATGTCAGGGATGCCGAAGAC

original cDNA sequence snippet

CACTTGACCAGGCCCTTAACTATGTCAGGGATGCCGAAGAC

altered cDNA sequence snippet

CACTTGACCAGGCCCTTAACCATGTCAGGGATGCCGAAGAC

wildtype AA sequence

MALSSAWRSV LPLWLLWSAA CSRAASGDDN AFPFDIEGSS AVGRQDPPET SEPRVALGRL
PPAAEKCNAG FFHTLSGECV PCDCNGNSNE CLDGSGYCVH CQRNTTGEHC EKCLDGYIGD
SIRGAPQFCQ PCPCPLPHLA NFAESCYRKN GAVRCICNEN YAGPNCERCA PGYYGNPLLI
GSTCKKCDCS GNSDPNLIFE DCDEVTGQCR NCLRNTTGFK CERCAPGYYG DARIAKNCAV
CNCGGGPCDS VTGECLEEGF EPPTGMDCPT ISCDKCVWDL TDALRLAALS IEEGKSGVLS
VSSGAAAHRH VNEINATIYL LKTKLSEREN QYALRKIQIN NAENTMKSLL SDVEELVEKE
NQASRKGQLV QKESMDTINH ASQLVEQAHD MRDKIQEINN KMLYYGEEHE LSPKEISEKL
VLAQKMLEEI RSRQPFFTQR ELVDEEADEA YELLSQAESW QRLHNETRTL FPVVLEQLDD
YNAKLSDLQE ALDQALNYVR DAEDMNRATA ARQRDHEKQQ ERVREQMEVV NMSLSTSADS
LTTPRLTLSE LDDIIKNASG IYAEIDGAKS ELQVKLSNLS NLSHDLVQEA IDHAQDLQQE
ANELSRKLHS SDMNGLVQKA LDASNVYENI VNYVSEANET AEFALNTTDR IYDAVSGIDT
QIIYHKDESE NLLNQARELQ AKAESSSDEA VADTSRRVGG ALARKSALKT RLSDAVKQLQ
AAERGDAQQR LGQSRLITEE ANRTTMEVQQ ATAPMANNLT NWSQNLQHFD SSAYNTAVNS
ARDAVRNLTE VVPQLLDQLR TVEQKRPASN VSASIQRIRE LIAQTRSVAS KIQVSMMFDG
QSAVEVHSRT SMDDLKAFTS LSLYMKPPVK RPELTETADQ FILYLGSKNA KKEYMGLAIK
NDNLVYVYNL GTKDVEIPLD SKPVSSWPAY FSIVKIERVG KHGKVFLTVP SLSSTAEEKF
IKKGEFSGDD SLLDLDPEDT VFYVGGVPSN FKLPTSLNLP GFVGCLELAT LNNDVISLYN
FKHIYNMDPS TSVPCARDKL AFTQSRAASY FFDGSGYAVV RDITRRGKFG QVTRFDIEVR
TPADNGLILL MVNGSMFFRL EMRNGYLHVF YDFGFSGGPV HLEDTLKKAQ INDAKYHEIS
IIYHNDKKMI LVVDRRHVKS MDNEKMKIPF TDIYIGGAPP EILQSRALRA HLPLDINFRG
CMKGFQFQKK DFNLLEQTET LGVGYGCPED SLISRRAYFN GQSFIASIQK ISFFDGFEGG
FNFRTLQPNG LLFYYASGSD VFSISLDNGT VIMDVKGIKV QSVDKQYNDG LSHFVISSVS
PTRYELIVDK SRVGSKNPTK GKIEQTQASE KKFYFGGSPI SAQYANFTGC ISNAYFTRVD
RDVEVEDFQR YTEKVHTSLY ECPIESSPLF LLHKKGKNLS KPKASQNKKG GKSKDAPSWD
PVALKLPERN TPRNSHCHLS NSPRAIEHAY QYGGTANSRQ EFEHLKGDFG AKSQFSIRLR
TRSSHGMIFY VSDQEENDFM TLFLAHGRLV YMFNVGHKKL KIRSQEKYND GLWHDVIFIR
ERSSGRLVID GLRVLEESLP PTEATWKIKG PIYLGGVAPG KAVKNVQINS IYSFSGCLSN
LQLNGASITS ASQTFSVTPC FEGPMETGTY FSTEGGYVVL DESFNIGLKF EIAFEVRPRS
SSGTLVHGHS VNGEYLNVHM KNGQVIVKVN NGIRDFSTSV TPKQSLCDGR WHRITVIRDS
NVVQLDVDSE VNHVVGPLNP KPIDHREPVF VGGVPESLLT PRLAPSKPFT GCIRHFVIDG
HPVSFSKAAL VSGAVSINSC PAA*

mutated AA sequence

MALSSAWRSV LPLWLLWSAA CSRAASGDDN AFPFDIEGSS AVGRQDPPET SEPRVALGRL
PPAAEKCNAG FFHTLSGECV PCDCNGNSNE CLDGSGYCVH CQRNTTGEHC EKCLDGYIGD
SIRGAPQFCQ PCPCPLPHLA NFAESCYRKN GAVRCICNEN YAGPNCERCA PGYYGNPLLI
GSTCKKCDCS GNSDPNLIFE DCDEVTGQCR NCLRNTTGFK CERCAPGYYG DARIAKNCAV
CNCGGGPCDS VTGECLEEGF EPPTGMDCPT ISCDKCVWDL TDALRLAALS IEEGKSGVLS
VSSGAAAHRH VNEINATIYL LKTKLSEREN QYALRKIQIN NAENTMKSLL SDVEELVEKE
NQASRKGQLV QKESMDTINH ASQLVEQAHD MRDKIQEINN KMLYYGEEHE LSPKEISEKL
VLAQKMLEEI RSRQPFFTQR ELVDEEADEA YELLSQAESW QRLHNETRTL FPVVLEQLDD
YNAKLSDLQE ALDQALNHVR DAEDMNRATA ARQRDHEKQQ ERVREQMEVV NMSLSTSADS
LTTPRLTLSE LDDIIKNASG IYAEIDGAKS ELQVKLSNLS NLSHDLVQEA IDHAQDLQQE
ANELSRKLHS SDMNGLVQKA LDASNVYENI VNYVSEANET AEFALNTTDR IYDAVSGIDT
QIIYHKDESE NLLNQARELQ AKAESSSDEA VADTSRRVGG ALARKSALKT RLSDAVKQLQ
AAERGDAQQR LGQSRLITEE ANRTTMEVQQ ATAPMANNLT NWSQNLQHFD SSAYNTAVNS
ARDAVRNLTE VVPQLLDQLR TVEQKRPASN VSASIQRIRE LIAQTRSVAS KIQVSMMFDG
QSAVEVHSRT SMDDLKAFTS LSLYMKPPVK RPELTETADQ FILYLGSKNA KKEYMGLAIK
NDNLVYVYNL GTKDVEIPLD SKPVSSWPAY FSIVKIERVG KHGKVFLTVP SLSSTAEEKF
IKKGEFSGDD SLLDLDPEDT VFYVGGVPSN FKLPTSLNLP GFVGCLELAT LNNDVISLYN
FKHIYNMDPS TSVPCARDKL AFTQSRAASY FFDGSGYAVV RDITRRGKFG QVTRFDIEVR
TPADNGLILL MVNGSMFFRL EMRNGYLHVF YDFGFSGGPV HLEDTLKKAQ INDAKYHEIS
IIYHNDKKMI LVVDRRHVKS MDNEKMKIPF TDIYIGGAPP EILQSRALRA HLPLDINFRG
CMKGFQFQKK DFNLLEQTET LGVGYGCPED SLISRRAYFN GQSFIASIQK ISFFDGFEGG
FNFRTLQPNG LLFYYASGSD VFSISLDNGT VIMDVKGIKV QSVDKQYNDG LSHFVISSVS
PTRYELIVDK SRVGSKNPTK GKIEQTQASE KKFYFGGSPI SAQYANFTGC ISNAYFTRVD
RDVEVEDFQR YTEKVHTSLY ECPIESSPLF LLHKKGKNLS KPKASQNKKG GKSKDAPSWD
PVALKLPERN TPRNSHCHLS NSPRAIEHAY QYGGTANSRQ EFEHLKGDFG AKSQFSIRLR
TRSSHGMIFY VSDQEENDFM TLFLAHGRLV YMFNVGHKKL KIRSQEKYND GLWHDVIFIR
ERSSGRLVID GLRVLEESLP PTEATWKIKG PIYLGGVAPG KAVKNVQINS IYSFSGCLSN
LQLNGASITS ASQTFSVTPC FEGPMETGTY FSTEGGYVVL DESFNIGLKF EIAFEVRPRS
SSGTLVHGHS VNGEYLNVHM KNGQVIVKVN NGIRDFSTSV TPKQSLCDGR WHRITVIRDS
NVVQLDVDSE VNHVVGPLNP KPIDHREPVF VGGVPESLLT PRLAPSKPFT GCIRHFVIDG
HPVSFSKAAL VSGAVSINSC PAA*

speed

0.82 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