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: ENST00000241125
MT speed 0 s - this script 2.775086 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GJA3	disease_causing_automatic	0.999999998685206	simple_aae		affected	0	R76H	single base exchange	rs121917827		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998685206 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042064)
known disease mutation: rs16981 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20717201C>TN/A show variant in all transcripts IGV

HGNC symbol

GJA3

Ensembl transcript ID

ENST00000241125

Genbank transcript ID

NM_021954

UniProt peptide

Q9Y6H8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.227G>A
cDNA.404G>A
g.17988G>A

AA changes

R76H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs121917827
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16981 (pathogenic for Zonular pulverulent cataract 3) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042064)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042064)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.427	1
	6.022	1
(flanking)	4.205	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	17994	wt: 0.9581 / mu: 0.9631 (marginal change - not scored)	wt: CATCTCCCACATCCGCTTCTGGGCGCTGCAGATCATCTTCG mu: CATCTCCCACATCCACTTCTGGGCGCTGCAGATCATCTTCG	tctg\|GGCG
Acc marginally increased	17983	wt: 0.8730 / mu: 0.8751 (marginal change - not scored)	wt: AGGGCCTTCCCCATCTCCCACATCCGCTTCTGGGCGCTGCA mu: AGGGCCTTCCCCATCTCCCACATCCACTTCTGGGCGCTGCA	ccac\|ATCC
Acc marginally increased	17988	wt: 0.7652 / mu: 0.8072 (marginal change - not scored)	wt: CTTCCCCATCTCCCACATCCGCTTCTGGGCGCTGCAGATCA mu: CTTCCCCATCTCCCACATCCACTTCTGGGCGCTGCAGATCA	tccg\|CTTC
Acc marginally increased	17991	wt: 0.6680 / mu: 0.7093 (marginal change - not scored)	wt: CCCCATCTCCCACATCCGCTTCTGGGCGCTGCAGATCATCT mu: CCCCATCTCCCACATCCACTTCTGGGCGCTGCAGATCATCT	gctt\|CTGG
Donor gained	17984	0.46	mu: CCCACATCCACTTCT	CACA\|tcca

distance from splice site

244

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005681

Mmulatta

all identical

ENSMMUG00000010524

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000048582

Ggallus

all identical

ENSGALG00000017137

Trubripes

all identical

ENSTRUG00000015739

Drerio

all identical

ENSDARG00000021889

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002644

protein features

start (aa)	end (aa)	feature	details
41	76	TOPO_DOM	Extracellular (Potential).	lost
77	97	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
98	152	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
153	173	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
174	201	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
202	222	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
223	435	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1308 / 1308

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

436 / 436

position of stopcodon in wt / mu cDNA

1485 / 1485

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

178 / 178

chromosome

strand

-1

last intron/exon boundary

161

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1308

coding sequence (CDS) position

227

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

404

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

17988

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

20717201

original gDNA sequence snippet

CTTCCCCATCTCCCACATCCGCTTCTGGGCGCTGCAGATCA

altered gDNA sequence snippet

CTTCCCCATCTCCCACATCCACTTCTGGGCGCTGCAGATCA

original cDNA sequence snippet

CTTCCCCATCTCCCACATCCGCTTCTGGGCGCTGCAGATCA

altered cDNA sequence snippet

CTTCCCCATCTCCCACATCCACTTCTGGGCGCTGCAGATCA

wildtype AA sequence

MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEDVWGDEQS DFTCNTQQPG
CENVCYDRAF PISHIRFWAL QIIFVSTPTL IYLGHVLHIV RMEEKKKERE EEEQLKRESP
SPKEPPQDNP SSRDDRGRVR MAGALLRTYV FNIIFKTLFE VGFIAGQYFL YGFELKPLYR
CDRWPCPNTV DCFISRPTEK TIFIIFMLAV ACASLLLNML EIYHLGWKKL KQGVTSRLGP
DASEAPLGTA DPPPLPPSSR PPAVAIGFPP YYAHTAAPLG QARAVGYPGA PPPAADFKLL
ALTEARGKGQ SAKLYNGHHH LLMTEQNWAN QAAERQPPAL KAYPAASTPA APSPVGSSSP
PLAHEAEAGA APLLLDGSGS SLEGSALAGT PEEEEQAVTT AAQMHQPPLP LGDPGRASKA
SRASSGRARP EDLAI*

mutated AA sequence

MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEDVWGDEQS DFTCNTQQPG
CENVCYDRAF PISHIHFWAL QIIFVSTPTL IYLGHVLHIV RMEEKKKERE EEEQLKRESP
SPKEPPQDNP SSRDDRGRVR MAGALLRTYV FNIIFKTLFE VGFIAGQYFL YGFELKPLYR
CDRWPCPNTV DCFISRPTEK TIFIIFMLAV ACASLLLNML EIYHLGWKKL KQGVTSRLGP
DASEAPLGTA DPPPLPPSSR PPAVAIGFPP YYAHTAAPLG QARAVGYPGA PPPAADFKLL
ALTEARGKGQ SAKLYNGHHH LLMTEQNWAN QAAERQPPAL KAYPAASTPA APSPVGSSSP
PLAHEAEAGA APLLLDGSGS SLEGSALAGT PEEEEQAVTT AAQMHQPPLP LGDPGRASKA
SRASSGRARP EDLAI*

speed

0.72 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