Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999997722 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM051509)
  • known disease mutation: rs6092 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:10877529C>TN/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.187G>A
cDNA.335G>A
g.4646G>A
AA changes G63S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 63
frameshift no
known variant Reference ID: rs104893960
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs6092 (pathogenic for Hypoparathyroidism, familial isolated, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051509)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051509)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051509)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.1861
6.1861
(flanking)-0.3180.868
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased4638wt: 0.9531 / mu: 0.9546 (marginal change - not scored)wt: GCGTCACCTGAGCGG
mu: GCGTCACCTGAGCAG		 GTCA|cctg
Donor marginally increased4651wt: 0.8689 / mu: 0.9474 (marginal change - not scored)wt: GGCTGGGCCATGCGC
mu: AGCTGGGCCATGCGC		 CTGG|gcca
Donor gained46410.40mu: TCACCTGAGCAGCTG ACCT|gagc
Donor gained46460.71mu: TGAGCAGCTGGGCCA AGCA|gctg
distance from splice site 97
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      63SDEKKAQRHLSGWAMRNTNNHNGH
mutated  not conserved    63LSSWAMRNTNNHNG
Ptroglodytes  all identical  ENSPTRG00000017724  63LSGWAMRNTNNHNG
Mmulatta  all identical  ENSMMUG00000007719  63LSGWAMRNTNNHNG
Fcatus  all identical  ENSFCAG00000001608  33SDEKKAQRHLSGWAMRNTNNHNG
Mmusculus  all identical  ENSMUSG00000021362  63LSGWAMRNTNNHNG
Ggallus  all identical  ENSGALG00000012768  47SEEKNAQRHLSGWAMRNTNNHNC
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000045413  65SEDKNAQRHLSGWAMRNTNN
Dmelanogaster  all identical  FBgn0014179  76VQSDEARKHASGWAMRNTNNHNV
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000001068  66LSGWAMRNTNNHNC
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 187
cDNA position
(for ins/del: last normal base / first normal base)		 335
gDNA position
(for ins/del: last normal base / first normal base)		 4646
chromosomal position
(for ins/del: last normal base / first normal base)		 10877529
original gDNA sequence snippet AGGCACAGCGTCACCTGAGCGGCTGGGCCATGCGCAACACC
altered gDNA sequence snippet AGGCACAGCGTCACCTGAGCAGCTGGGCCATGCGCAACACC
original cDNA sequence snippet AGGCACAGCGTCACCTGAGCGGCTGGGCCATGCGCAACACC
altered cDNA sequence snippet AGGCACAGCGTCACCTGAGCAGCTGGGCCATGCGCAACACC
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 WPDGYVRFIY SSDEKKAQRH
LSSWAMRNTN 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 0.63 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