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: ENST00000229416
MT speed 0 s - this script 2.952621 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GCLC	disease_causing_automatic	0.999999999983326	simple_aae			0	H370L	single base exchange	rs121907946		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999983326 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM992628)
known disease mutation: rs3958 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:53371799T>AN/A show variant in all transcripts IGV

HGNC symbol

GCLC

Ensembl transcript ID

ENST00000229416

Genbank transcript ID

NM_001498

UniProt peptide

P48506

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1109A>T
cDNA.1593A>T
g.109970A>T

AA changes

H370L Score: 99 explain score(s)

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

370

frameshift

known variant

Reference ID: rs121907946
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs3958 (pathogenic for Gamma-glutamylcysteine synthetase deficiency, hemolytic anemia due to) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992628)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992628)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992628)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.228	0.998
	4.913	1
(flanking)	5.946	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
Acc marginally increased	109971	wt: 0.3727 / mu: 0.3884 (marginal change - not scored)	wt: GATCATCTCCTGGCCCAGCATGTTGCTCATCTCTTTATTAG mu: GATCATCTCCTGGCCCAGCTTGTTGCTCATCTCTTTATTAG	gcat\|GTTG
Acc marginally increased	109961	wt: 0.4706 / mu: 0.5169 (marginal change - not scored)	wt: TGCAGGCATTGATCATCTCCTGGCCCAGCATGTTGCTCATC mu: TGCAGGCATTGATCATCTCCTGGCCCAGCTTGTTGCTCATC	tcct\|GGCC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

370

mutated

not conserved

370

Ptroglodytes

all identical

ENSPTRG00000018290

370

Mmulatta

all identical

ENSMMUG00000008684

370

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000032350

370

Ggallus

all identical

ENSGALG00000016313

321

Trubripes

all identical

ENSTRUG00000015144

372

Drerio

all identical

ENSDARG00000013095

371

Dmelanogaster

all identical

FBgn0040319

364

Celegans

all identical

F37B12.2

375

Xtropicalis

all identical

ENSXETG00000016009

371

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1914 / 1914

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

638 / 638

position of stopcodon in wt / mu cDNA

2398 / 2398

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

485 / 485

chromosome

strand

-1

last intron/exon boundary

2187

theoretical NMD boundary in CDS

1652

length of CDS

1914

coding sequence (CDS) position

1109

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

1593

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

109970

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

53371799

original gDNA sequence snippet

TGATCATCTCCTGGCCCAGCATGTTGCTCATCTCTTTATTA

altered gDNA sequence snippet

TGATCATCTCCTGGCCCAGCTTGTTGCTCATCTCTTTATTA

original cDNA sequence snippet

TGATCATCTCCTGGCCCAGCATGTTGCTCATCTCTTTATTA

altered cDNA sequence snippet

TGATCATCTCCTGGCCCAGCTTGTTGCTCATCTCTTTATTA

wildtype AA sequence

MGLLSQGSPL SWEETKRHAD HVRRHGILQF LHIYHAVKDR HKDVLKWGDE VEYMLVSFDH
ENKKVRLVLS GEKVLETLQE KGERTNPNHP TLWRPEYGSY MIEGTPGQPY GGTMSEFNTV
EANMRKRRKE ATSILEENQA LCTITSFPRL GCPGFTLPEV KPNPVEGGAS KSLFFPDEAI
NKHPRFSTLT RNIRHRRGEK VVINVPIFKD KNTPSPFIET FTEDDEASRA SKPDHIYMDA
MGFGMGNCCL QVTFQACSIS EARYLYDQLA TICPIVMALS AASPFYRGYV SDIDCRWGVI
SASVDDRTRE ERGLEPLKNN NYRISKSRYD SIDSYLSKCG EKYNDIDLTI DKEIYEQLLQ
EGIDHLLAQH VAHLFIRDPL TLFEEKIHLD DANESDHFEN IQSTNWQTMR FKPPPPNSDI
GWRVEFRPME VQLTDFENSA YVVFVVLLTR VILSYKLDFL IPLSKVDENM KVAQKRDAVL
QGMFYFRKDI CKGGNAVVDG CGKAQNSTEL AAEEYTLMSI DTIINGKEGV FPGLIPILNS
YLENMEVDVD TRCSILNYLK LIKKRASGEL MTVARWMREF IANHPDYKQD SVITDEMNYS
LILKCNQIAN ELCECPELLG SAFRKVKYSG SKTDSSN*

mutated AA sequence

MGLLSQGSPL SWEETKRHAD HVRRHGILQF LHIYHAVKDR HKDVLKWGDE VEYMLVSFDH
ENKKVRLVLS GEKVLETLQE KGERTNPNHP TLWRPEYGSY MIEGTPGQPY GGTMSEFNTV
EANMRKRRKE ATSILEENQA LCTITSFPRL GCPGFTLPEV KPNPVEGGAS KSLFFPDEAI
NKHPRFSTLT RNIRHRRGEK VVINVPIFKD KNTPSPFIET FTEDDEASRA SKPDHIYMDA
MGFGMGNCCL QVTFQACSIS EARYLYDQLA TICPIVMALS AASPFYRGYV SDIDCRWGVI
SASVDDRTRE ERGLEPLKNN NYRISKSRYD SIDSYLSKCG EKYNDIDLTI DKEIYEQLLQ
EGIDHLLAQL VAHLFIRDPL TLFEEKIHLD DANESDHFEN IQSTNWQTMR FKPPPPNSDI
GWRVEFRPME VQLTDFENSA YVVFVVLLTR VILSYKLDFL IPLSKVDENM KVAQKRDAVL
QGMFYFRKDI CKGGNAVVDG CGKAQNSTEL AAEEYTLMSI DTIINGKEGV FPGLIPILNS
YLENMEVDVD TRCSILNYLK LIKKRASGEL MTVARWMREF IANHPDYKQD SVITDEMNYS
LILKCNQIAN ELCECPELLG SAFRKVKYSG SKTDSSN*

speed

0.99 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

disease causing

Problems