Yum, tasty mutations...

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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000543878
Querying Taster for transcript #2: ENST00000379491
MT speed 0 s - this script 3.104117 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCM2disease_causing_automatic0.999999970191567simple_aaeaffected0R47Lsingle base exchangers104893959show file
SYCP2Ldisease_causing_automatic1without_aaeaffected0single base exchangers104893959show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999970191567 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM051508)
  • known disease mutation: rs6091 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:10877576C>AN/A show variant in all transcripts   IGV
HGNC symbol GCM2
Ensembl transcript ID ENST00000379491
Genbank transcript ID NM_004752
UniProt peptide O75603
alteration type single base exchange
alteration region CDS
DNA changes c.140G>T
cDNA.288G>T
g.4599G>T
AA changes R47L Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 47
frameshift no
known variant Reference ID: rs104893959
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs6091 (pathogenic for Hypoparathyroidism, familial isolated, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6571
3.0671
(flanking)2.891
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased4603wt: 0.29 / mu: 0.76wt: CCTGACGGCTATGTGCGCTTCATCTACAGCAGCGATGAGAA
mu: CCTGACGGCTATGTGCTCTTCATCTACAGCAGCGATGAGAA		 cttc|ATCT
Acc increased4609wt: 0.70 / mu: 0.88wt: GGCTATGTGCGCTTCATCTACAGCAGCGATGAGAAGAAGGC
mu: GGCTATGTGCTCTTCATCTACAGCAGCGATGAGAAGAAGGC		 ctac|AGCA
Acc increased4607wt: 0.85 / mu: 0.97wt: ACGGCTATGTGCGCTTCATCTACAGCAGCGATGAGAAGAAG
mu: ACGGCTATGTGCTCTTCATCTACAGCAGCGATGAGAAGAAG		 atct|ACAG
Acc gained46100.32mu: GCTATGTGCTCTTCATCTACAGCAGCGATGAGAAGAAGGCA taca|GCAG
Acc gained46040.51mu: CTGACGGCTATGTGCTCTTCATCTACAGCAGCGATGAGAAG ttca|TCTA
distance from splice site 50
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      47DQFREWPDGYVRFIYSSDEKKAQR
mutated  not conserved    47DQFREWPDGYVLFIYSSDEKKAQ
Ptroglodytes  all identical  ENSPTRG00000017724  47DQFREWPDGYVRFIYSSDEKKAQ
Mmulatta  all identical  ENSMMUG00000007719  47DQFREWPDGYVRFIYSSDEKKAQ
Fcatus  all identical  ENSFCAG00000001608  17DHFCEWPDGYVRFIYRSDEKKAQ
Mmusculus  all identical  ENSMUSG00000021362  47DHFREWPDGYVRFIYSSQEKKAQ
Ggallus  all identical  ENSGALG00000012768  31DAFQEWPDGYVRLIYSSEEKNAQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000045413  49DAFQEWTDGYVRYIYSSEDKNAQ
Dmelanogaster  all identical  FBgn0014179  60DDFNDWSNGHCRLIYSVQSDEAR
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000001068  50DSFQEWTDGYVRFIYNAEDKNAQ
protein features
start (aa)end (aa)featuredetails 
19174DNA_BINDGCM.lost
8181METALZinc 1 (By similarity).might get lost (downstream of altered splice site)
8787METALZinc 2 (By similarity).might get lost (downstream of altered splice site)
9191METALZinc 2 (By similarity).might get lost (downstream of altered splice site)
118118METALZinc 2 (By similarity).might get lost (downstream of altered splice site)
121121METALZinc 2 (By similarity).might get lost (downstream of altered splice site)
130130METALZinc 1 (By similarity).might get lost (downstream of altered splice site)
157157METALZinc 1 (By similarity).might get lost (downstream of altered splice site)
159159METALZinc 1 (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1521 / 1521
position (AA) of stopcodon in wt / mu AA sequence 507 / 507
position of stopcodon in wt / mu cDNA 1669 / 1669
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 149 / 149
chromosome 6
strand -1
last intron/exon boundary 731
theoretical NMD boundary in CDS 532
length of CDS 1521
coding sequence (CDS) position 140
cDNA position
(for ins/del: last normal base / first normal base)		 288
gDNA position
(for ins/del: last normal base / first normal base)		 4599
chromosomal position
(for ins/del: last normal base / first normal base)		 10877576
original gDNA sequence snippet GTGGCCTGACGGCTATGTGCGCTTCATCTACAGCAGCGATG
altered gDNA sequence snippet GTGGCCTGACGGCTATGTGCTCTTCATCTACAGCAGCGATG
original cDNA sequence snippet GTGGCCTGACGGCTATGTGCGCTTCATCTACAGCAGCGATG
altered cDNA sequence snippet GTGGCCTGACGGCTATGTGCTCTTCATCTACAGCAGCGATG
wildtype AA sequence MPAAAVQEAV GVCSYGMQLS WDINDPQMPQ ELALFDQFRE WPDGYVRFIY SSDEKKAQRH
LSGWAMRNTN NHNGHILKKS CLGVVVCTQA CTLPDGSRLQ LRPAICDKAR LKQQKKACPN
CHSALELIPC RGHSGYPVTN FWRLDGNAIF FQAKGVHDHP RPESKSETEA RRSAIKRQMA
SFYQPQKKRI RESEAEENQD SSGHFSNIPP LENPEDFDIV TETSFPIPGQ PCPSFPKSDV
YKATCDLATF QGDKMPPFQK YSSPRIYLPR PPCSYELANP GYTNSSPYPT LYKDSTSIPN
DTDWVHLNTL QCNVNSYSSY ERSFDFTNKQ HGWKPALGKP SLVERTNHGQ FQAMATRPYY
NPELPCRYLT TPPPGAPALQ TVITTTTKVS YQAYQPPAMK YSDSVREVKS LSSCNYAPED
TGMSVYPEPW GPPVTVTRAA SPSGPPPMKI AGDCRAIRPT VAIPHEPVSS RTDEAETWDV
CLSGLGSAVS YSDRVGPFFT YNNEDF*
mutated AA sequence MPAAAVQEAV GVCSYGMQLS WDINDPQMPQ ELALFDQFRE WPDGYVLFIY SSDEKKAQRH
LSGWAMRNTN NHNGHILKKS CLGVVVCTQA CTLPDGSRLQ LRPAICDKAR LKQQKKACPN
CHSALELIPC RGHSGYPVTN FWRLDGNAIF FQAKGVHDHP RPESKSETEA RRSAIKRQMA
SFYQPQKKRI RESEAEENQD SSGHFSNIPP LENPEDFDIV TETSFPIPGQ PCPSFPKSDV
YKATCDLATF QGDKMPPFQK YSSPRIYLPR PPCSYELANP GYTNSSPYPT LYKDSTSIPN
DTDWVHLNTL QCNVNSYSSY ERSFDFTNKQ HGWKPALGKP SLVERTNHGQ FQAMATRPYY
NPELPCRYLT TPPPGAPALQ TVITTTTKVS YQAYQPPAMK YSDSVREVKS LSSCNYAPED
TGMSVYPEPW GPPVTVTRAA SPSGPPPMKI AGDCRAIRPT VAIPHEPVSS RTDEAETWDV
CLSGLGSAVS YSDRVGPFFT YNNEDF*
speed 1.02 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM051508)
  • known disease mutation: rs6091 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:10877576C>AN/A show variant in all transcripts   IGV
HGNC symbol SYCP2L
Ensembl transcript ID ENST00000543878
Genbank transcript ID N/A
UniProt peptide Q5T4T6
alteration type single base exchange
alteration region intron
DNA changes g.129550C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104893959
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs6091 (pathogenic for Hypoparathyroidism, familial isolated, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6571
3.0671
(flanking)2.891
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -155) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased129545wt: 0.89 / mu: 0.98wt: GTAGATGAAGCGCAC
mu: GTAGATGAAGAGCAC		 AGAT|gaag
distance from splice site 14170
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
214214CONFLICTM -> V (in Ref. 1; CAL25570).might get lost (downstream of altered splice site)
276276CONFLICTR -> I (in Ref. 4; AAH12225).might get lost (downstream of altered splice site)
314314CONFLICTK -> E (in Ref. 1; CAL25570).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 701 / 701
chromosome 6
strand 1
last intron/exon boundary 1536
theoretical NMD boundary in CDS 785
length of CDS 867
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 129550
chromosomal position
(for ins/del: last normal base / first normal base)		 10877576
original gDNA sequence snippet CATCGCTGCTGTAGATGAAGCGCACATAGCCGTCAGGCCAC
altered gDNA sequence snippet CATCGCTGCTGTAGATGAAGAGCACATAGCCGTCAGGCCAC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MLDSFLLSLG FLVTEKTVNH LLQQEGLKTF NCILHAVPRE ERKKFPLSEG MCHLMKDLAR
TLLTVGDYDQ QVAISEALCR LTIKKSRDEL VHKWFDDEVI AEAFKEIKDR EFETDSRRFL
NHLNNRLGDQ RRVYSFPCIA AFADEHEMRK PADEKLEKFW IDFNLGSQSV TFYIDNAENT
LWDSVTLPKE AVMNFSITET EKIKIFIIYL KKPMIISYKE VMKIEIHFDL QFNISQVSIQ
ALGEDKQMLP DQTKISSELF SKSDKEDRES PSGLERETEV SLQKTSLL*
mutated AA sequence N/A
speed 0.09 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

Problems