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MutationTaster - study a chromosomal position

 MTQE documentation
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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: ENST00000374586
MT speed 0 s - this script 2.720108 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TMEM245polymorphism_automatic0.920821830566293simple_aaeaffectedH113Rsingle base exchangers1051474show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0791781694337072 (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) chr9:111881856T>CN/A show variant in all transcripts   IGV
HGNC symbol TMEM245
Ensembl transcript ID ENST00000374586
Genbank transcript ID NM_032012
UniProt peptide Q9H330
alteration type single base exchange
alteration region CDS
DNA changes c.338A>G
cDNA.370A>G
g.370A>G
AA changes H113R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 113
frameshift no
known variant Reference ID: rs1051474
databasehomozygous (C/C)heterozygousallele carriers
1000G142702844
ExAC90451426046
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3871
1.1041
(flanking)5.7091
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained3690.63mu: GCCTGCGCCGCGCGC CTGC|gccg
distance from splice site 242
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      113TRLGRHWLQRLHRAHTPIVLAALL
mutated  not conserved    113TRLGRHWLQRLRRAHTPIV
Ptroglodytes  all identical  ENSPTRG00000021237  113TRLGRHWLHRLHRAHTPIV
Mmulatta  all identical  ENSMMUG00000000695  113TRLGRHWLQRLHRAHTPIV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000055296  109TRLGRLWLRRLHRAHTPIV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0037536  92SWFHRLEVRDSNVLVSIC
Celegans  not conserved  M01F1.4  85ADTVQHWLRNLQKSNQTLAKSVI
Xtropicalis  not conserved  ENSXETG00000033754  134TGVGRRWLIRLQRQGSPIFLATF
protein features
start (aa)end (aa)featuredetails 
119139TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
148168TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
185205TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
210210CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
219239TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
241261TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
334334MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
354374TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
377397TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
460480TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
500500CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
511511CONFLICTN -> K (in Ref. 4; CAD38810).might get lost (downstream of altered splice site)
551551CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
575575CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
626646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
650670TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
732752TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
776796TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
785785CONFLICTL -> V (in Ref. 2; BAG61779).might get lost (downstream of altered splice site)
815835TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
855855CONFLICTN -> I (in Ref. 2; BAD18785).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2640 / 2640
position (AA) of stopcodon in wt / mu AA sequence 880 / 880
position of stopcodon in wt / mu cDNA 2672 / 2672
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 33 / 33
chromosome 9
strand -1
last intron/exon boundary 2627
theoretical NMD boundary in CDS 2544
length of CDS 2640
coding sequence (CDS) position 338
cDNA position
(for ins/del: last normal base / first normal base)		 370
gDNA position
(for ins/del: last normal base / first normal base)		 370
chromosomal position
(for ins/del: last normal base / first normal base)		 111881856
original gDNA sequence snippet CCACTGGCTGCAGCGCCTGCACCGCGCGCACACGCCCATCG
altered gDNA sequence snippet CCACTGGCTGCAGCGCCTGCGCCGCGCGCACACGCCCATCG
original cDNA sequence snippet CCACTGGCTGCAGCGCCTGCACCGCGCGCACACGCCCATCG
altered cDNA sequence snippet CCACTGGCTGCAGCGCCTGCGCCGCGCGCACACGCCCATCG
wildtype AA sequence MADGGGPKDA PSLRSSPGPA PRVPRAVGPS GGGGETPRTA ALALRFDKPI KQAFYNTGAV
LFVCLCCGAA VLVYFILEAF LRPLLWAVLC GTFLHPFKSS LTRLGRHWLQ RLHRAHTPIV
LAALLLPLCF VDYGVEALGE QALRRRRLLL LLGAGGPLLY GLYCLGSYLG VQVLLVHAAT
LICRGLDYFS SLWIWTLVVG YVLTVSFKWN ASTERYLRAV SIPVWIILLF HLASLAGSWR
IPVFLVIVFL MSVGTLYEKQ NGKESSGAEL PGQVISMAAS TLANLAISIT GYESSSEDQP
STQPAEAVDR GESAPTLSTS PSPSSPSPTS PSPTLGRRRP EIGTFLRKKK TSDIYFVSLV
WAIVVMQIWL NLWIVQLLPV PIAVWILKKL VIHFGVVDFL EKRYHVWWGI IESFLKERQG
ALAPWPIVGL GKFLLKVDSK LWHWLNKKMI IWLEKMLDKI ISIFIIFLLV IGTLLLALLL
TAKVHQESVH MIEVTSNLIN ETLANHPEWA NWLPEAQVVQ RALNSAANNV YQYGREWITH
KLHKILGDKV NNTAVIEKQV LELWDRLYHS WFVKNVTHSG RHKGQKLHVS RQNSWLGDIL
DWQDIVSFVH ENIETFLSIL ESLWIVMSRN VSLLFTTVTT LLTILFYSGT ALLNFVLSLI
IFLTTLFYLL SSSDEYYKPV KWVISLTPLS QPGPSSNIIG QSVEEAIRGV FDASLKMAGF
YGLYTWLTHT MFGINIVFIP SALAAILGAV PFLGTYWAAV PAVLDLWLTQ GLGCKAILLL
IFHLLPTYFV DTAIYSDISG GGHPYLTGLA VAGGAYYLGL EGAIIGPILL CILVVASNIY
SAMLVSPTNS VPTPNQTPWP AQPQRTFRDI SEDLKSSVG*
mutated AA sequence MADGGGPKDA PSLRSSPGPA PRVPRAVGPS GGGGETPRTA ALALRFDKPI KQAFYNTGAV
LFVCLCCGAA VLVYFILEAF LRPLLWAVLC GTFLHPFKSS LTRLGRHWLQ RLRRAHTPIV
LAALLLPLCF VDYGVEALGE QALRRRRLLL LLGAGGPLLY GLYCLGSYLG VQVLLVHAAT
LICRGLDYFS SLWIWTLVVG YVLTVSFKWN ASTERYLRAV SIPVWIILLF HLASLAGSWR
IPVFLVIVFL MSVGTLYEKQ NGKESSGAEL PGQVISMAAS TLANLAISIT GYESSSEDQP
STQPAEAVDR GESAPTLSTS PSPSSPSPTS PSPTLGRRRP EIGTFLRKKK TSDIYFVSLV
WAIVVMQIWL NLWIVQLLPV PIAVWILKKL VIHFGVVDFL EKRYHVWWGI IESFLKERQG
ALAPWPIVGL GKFLLKVDSK LWHWLNKKMI IWLEKMLDKI ISIFIIFLLV IGTLLLALLL
TAKVHQESVH MIEVTSNLIN ETLANHPEWA NWLPEAQVVQ RALNSAANNV YQYGREWITH
KLHKILGDKV NNTAVIEKQV LELWDRLYHS WFVKNVTHSG RHKGQKLHVS RQNSWLGDIL
DWQDIVSFVH ENIETFLSIL ESLWIVMSRN VSLLFTTVTT LLTILFYSGT ALLNFVLSLI
IFLTTLFYLL SSSDEYYKPV KWVISLTPLS QPGPSSNIIG QSVEEAIRGV FDASLKMAGF
YGLYTWLTHT MFGINIVFIP SALAAILGAV PFLGTYWAAV PAVLDLWLTQ GLGCKAILLL
IFHLLPTYFV DTAIYSDISG GGHPYLTGLA VAGGAYYLGL EGAIIGPILL CILVVASNIY
SAMLVSPTNS VPTPNQTPWP AQPQRTFRDI SEDLKSSVG*
speed 0.66 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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