Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 10 transcript(s)...
Querying Taster for transcript #1: ENST00000357568
Querying Taster for transcript #2: ENST00000349748
Querying Taster for transcript #3: ENST00000397163
Querying Taster for transcript #4: ENST00000397200
Querying Taster for transcript #5: ENST00000337571
Querying Taster for transcript #6: ENST00000569136
Querying Taster for transcript #7: ENST00000561817
Querying Taster for transcript #8: ENST00000397204
Querying Taster for transcript #9: ENST00000356316
Querying Taster for transcript #10: ENST00000318023
MT speed 0 s - this script 7.0461 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CAPN3disease_causing_automatic0.999999999399657simple_aaeaffected0R763Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999399657simple_aaeaffected0R769Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999399657simple_aaeaffected0R763Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999529268simple_aaeaffected0R257Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999638478simple_aaeaffected0R677Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999638478simple_aaeaffected0R676Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999976393simple_aaeaffected0R104Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999976393simple_aaeaffected0R104Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999976393simple_aaeaffected0R104Qsingle base exchangers80338802show file
CAPN3disease_causing_automatic0.999999999976393simple_aaeaffected0R104Qsingle base exchangers80338802show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999399657 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000357568
Genbank transcript ID NM_024344
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.2288G>A
cDNA.2509G>A
g.62824G>A
AA changes R763Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 763
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      763LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    763LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603LNSQLYDIITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNID
Trubripes  all identical  ENSTRUG00000006900  706LNNQLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNNRLLNALAHRYG
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
650821REGIONDomain IV.lost
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2448 / 2448
position (AA) of stopcodon in wt / mu AA sequence 816 / 816
position of stopcodon in wt / mu cDNA 2669 / 2669
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 222 / 222
chromosome 15
strand 1
last intron/exon boundary 2643
theoretical NMD boundary in CDS 2371
length of CDS 2448
coding sequence (CDS) position 2288
cDNA position
(for ins/del: last normal base / first normal base)		 2509
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVPIIFVS
DRANSNKELG VDQESEEGKG KTSPDKQKQS PQPQPGSSDQ ESEEQQQFRN IFKQIAGDDM
EICADELKKV LNTVVNKHKD LKTHGFTLES CRSMIALMDT DGSGKLNLQE FHHLWNKIKA
WQKIFKHYDT DQSGTINSYE MRNAVNDAGF HLNNQLYDII TMRYADKHMN IDFDSFICCF
VRLEGMFRAF HAFDKDGDGI IKLNVLEWLQ LTMYA*
mutated AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVPIIFVS
DRANSNKELG VDQESEEGKG KTSPDKQKQS PQPQPGSSDQ ESEEQQQFRN IFKQIAGDDM
EICADELKKV LNTVVNKHKD LKTHGFTLES CRSMIALMDT DGSGKLNLQE FHHLWNKIKA
WQKIFKHYDT DQSGTINSYE MRNAVNDAGF HLNNQLYDII TMQYADKHMN IDFDSFICCF
VRLEGMFRAF HAFDKDGDGI IKLNVLEWLQ LTMYA*
speed 0.51 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: simple_aae, prob: 0.999999999399657 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000397163
Genbank transcript ID NM_000070
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.2306G>A
cDNA.2525G>A
g.62824G>A
AA changes R769Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 769
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      769LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    769LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603LNSQLYDIITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNID
Trubripes  all identical  ENSTRUG00000006900  706LNNQLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673DIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LAHRYGSREGQIPFD
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
650821REGIONDomain IV.lost
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2466 / 2466
position (AA) of stopcodon in wt / mu AA sequence 822 / 822
position of stopcodon in wt / mu cDNA 2685 / 2685
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 220 / 220
chromosome 15
strand 1
last intron/exon boundary 2659
theoretical NMD boundary in CDS 2389
length of CDS 2466
coding sequence (CDS) position 2306
cDNA position
(for ins/del: last normal base / first normal base)		 2525
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVKKKKTK
PIIFVSDRAN SNKELGVDQE SEEGKGKTSP DKQKQSPQPQ PGSSDQESEE QQQFRNIFKQ
IAGDDMEICA DELKKVLNTV VNKHKDLKTH GFTLESCRSM IALMDTDGSG KLNLQEFHHL
WNKIKAWQKI FKHYDTDQSG TINSYEMRNA VNDAGFHLNN QLYDIITMRY ADKHMNIDFD
SFICCFVRLE GMFRAFHAFD KDGDGIIKLN VLEWLQLTMY A*
mutated AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVKKKKTK
PIIFVSDRAN SNKELGVDQE SEEGKGKTSP DKQKQSPQPQ PGSSDQESEE QQQFRNIFKQ
IAGDDMEICA DELKKVLNTV VNKHKDLKTH GFTLESCRSM IALMDTDGSG KLNLQEFHHL
WNKIKAWQKI FKHYDTDQSG TINSYEMRNA VNDAGFHLNN QLYDIITMQY ADKHMNIDFD
SFICCFVRLE GMFRAFHAFD KDGDGIIKLN VLEWLQLTMY A*
speed 0.71 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: simple_aae, prob: 0.999999999399657 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000318023
Genbank transcript ID N/A
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.2288G>A
cDNA.2509G>A
g.62824G>A
AA changes R763Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 763
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      763LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    763LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603LNSQLYDIITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNID
Trubripes  all identical  ENSTRUG00000006900  706LNNQLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNNRLLNALAHRYG
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
650821REGIONDomain IV.lost
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2448 / 2448
position (AA) of stopcodon in wt / mu AA sequence 816 / 816
position of stopcodon in wt / mu cDNA 2669 / 2669
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 222 / 222
chromosome 15
strand 1
last intron/exon boundary 2643
theoretical NMD boundary in CDS 2371
length of CDS 2448
coding sequence (CDS) position 2288
cDNA position
(for ins/del: last normal base / first normal base)		 2509
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP HQMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVPIIFVS
DRANSNKELG VDQESEEGKG KTSPDKQKQS PQPQPGSSDQ ESEEQQQFRN IFKQIAGDDM
EICADELKKV LNTVVNKHKD LKTHGFTLES CRSMIALMDT DGSGKLNLQE FHHLWNKIKA
WQKIFKHYDT DQSGTINSYE MRNAVNDAGF HLNNQLYDII TMRYADKHMN IDFDSFICCF
VRLEGMFRAF HAFDKDGDGI IKLNVLEWLQ LTMYA*
mutated AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP HQMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVPIIFVS
DRANSNKELG VDQESEEGKG KTSPDKQKQS PQPQPGSSDQ ESEEQQQFRN IFKQIAGDDM
EICADELKKV LNTVVNKHKD LKTHGFTLES CRSMIALMDT DGSGKLNLQE FHHLWNKIKA
WQKIFKHYDT DQSGTINSYE MRNAVNDAGF HLNNQLYDII TMQYADKHMN IDFDSFICCF
VRLEGMFRAF HAFDKDGDGI IKLNVLEWLQ LTMYA*
speed 1.15 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: simple_aae, prob: 0.999999999529268 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000397200
Genbank transcript ID NM_173088
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.770G>A
cDNA.939G>A
g.62824G>A
AA changes R257Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 257
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      257LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    257LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603LNSQLYDIITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706LNNQLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNALAHRYGSREGQIPFD
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.lost
334334ACT_SITEBy similarity.might get lost (downstream of altered splice site)
358358ACT_SITEBy similarity.might get lost (downstream of altered splice site)
418586REGIONDomain III.might get lost (downstream of altered splice site)
587649REGIONLinker.might get lost (downstream of altered splice site)
649683DOMAINEF-hand 1.might get lost (downstream of altered splice site)
650821REGIONDomain IV.might get lost (downstream of altered splice site)
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 930 / 930
position (AA) of stopcodon in wt / mu AA sequence 310 / 310
position of stopcodon in wt / mu cDNA 1099 / 1099
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 170 / 170
chromosome 15
strand 1
last intron/exon boundary 1073
theoretical NMD boundary in CDS 853
length of CDS 930
coding sequence (CDS) position 770
cDNA position
(for ins/del: last normal base / first normal base)		 939
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MHGNKQHLQK DFFLYNASKA RSKTYINMRE VSQRFRLPPS EYVIVPSTYE PHQEGEFILR
VFSEKRNLSE EVENTISVDR PVKKKKTKPI IFVSDRANSN KELGVDQESE EGKGKTSPDK
QKQSPQPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
mutated AA sequence MHGNKQHLQK DFFLYNASKA RSKTYINMRE VSQRFRLPPS EYVIVPSTYE PHQEGEFILR
VFSEKRNLSE EVENTISVDR PVKKKKTKPI IFVSDRANSN KELGVDQESE EGKGKTSPDK
QKQSPQPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMQYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
speed 1.05 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: simple_aae, prob: 0.999999999638478 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000349748
Genbank transcript ID NM_173087
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.2030G>A
cDNA.2251G>A
g.62824G>A
AA changes R677Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 677
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      677LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    677LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603LNSQLYDIITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706LNNQLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNNRLLNALAHRYGSREGQIPFD
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000012304  664LYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
649683DOMAINEF-hand 1.lost
650821REGIONDomain IV.lost
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2190 / 2190
position (AA) of stopcodon in wt / mu AA sequence 730 / 730
position of stopcodon in wt / mu cDNA 2411 / 2411
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 222 / 222
chromosome 15
strand 1
last intron/exon boundary 2385
theoretical NMD boundary in CDS 2113
length of CDS 2190
coding sequence (CDS) position 2030
cDNA position
(for ins/del: last normal base / first normal base)		 2251
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDTII PVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RRKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
mutated AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDTII PVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RRKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMQYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
speed 1.26 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: simple_aae, prob: 0.999999999638478 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000356316
Genbank transcript ID N/A
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.2027G>A
cDNA.2519G>A
g.62824G>A
AA changes R676Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 676
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      676LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    676LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769DIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603LNSQLYDIITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769DIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706LNNQLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873NRLLNALAHRYGSREGQIPFD
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
649683DOMAINEF-hand 1.lost
650821REGIONDomain IV.lost
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2187 / 2187
position (AA) of stopcodon in wt / mu AA sequence 729 / 729
position of stopcodon in wt / mu cDNA 2679 / 2679
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 493 / 493
chromosome 15
strand 1
last intron/exon boundary 2653
theoretical NMD boundary in CDS 2110
length of CDS 2187
coding sequence (CDS) position 2027
cDNA position
(for ins/del: last normal base / first normal base)		 2519
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MSWQISLKTQ TTQQKNEICE NPRFIIDGAN RTDICQGELG DCWFLAAIAC LTLNQHLLFR
VIPHDQSFIE NYAGIFHFQF WRYGEWVDVV IDDCLPTYNN QLVFTKSNHR NEFWSALLEK
AYAKLHGSYE ALKGGNTTEA MEDFTGGVAE FFEIRDAPSD MYKIMKKAIE RGSLMGCSID
DGTNMTYGTS PSGLNMGELI ARMVRNMDNS LLQDSDLDPR GSDERPTRTI IPVQYETRMA
CGLVRGHAYS VTGLDEVPFK GEKVKLVRLR NPWGQVEWNG SWSDRWKDWS FVDKDEKARL
QHQVTEDGEF WMSYEDFIYH FTKLEICNLT ADALQSDKLQ TWTVSVNEGR WVRGCSAGGC
RNFPDTFWTN PQYRLKLLEE DDDPDDSEVI CSFLVALMQK NRRKDRKLGA SLFTIGFAIY
EVPKEMHGNK QHLQKDFFLY NASKARSKTY INMREVSQRF RLPPSEYVIV PSTYEPHQEG
EFILRVFSEK RNLSEEVENT ISVDRPVPII FVSDRANSNK ELGVDQESEE GKGKTSPDKQ
KQSPQPQPGS SDQESEEQQQ FRNIFKQIAG DDMEICADEL KKVLNTVVNK HKDLKTHGFT
LESCRSMIAL MDTDGSGKLN LQEFHHLWNK IKAWQKIFKH YDTDQSGTIN SYEMRNAVND
AGFHLNNQLY DIITMRYADK HMNIDFDSFI CCFVRLEGMF RAFHAFDKDG DGIIKLNVLE
WLQLTMYA*
mutated AA sequence MSWQISLKTQ TTQQKNEICE NPRFIIDGAN RTDICQGELG DCWFLAAIAC LTLNQHLLFR
VIPHDQSFIE NYAGIFHFQF WRYGEWVDVV IDDCLPTYNN QLVFTKSNHR NEFWSALLEK
AYAKLHGSYE ALKGGNTTEA MEDFTGGVAE FFEIRDAPSD MYKIMKKAIE RGSLMGCSID
DGTNMTYGTS PSGLNMGELI ARMVRNMDNS LLQDSDLDPR GSDERPTRTI IPVQYETRMA
CGLVRGHAYS VTGLDEVPFK GEKVKLVRLR NPWGQVEWNG SWSDRWKDWS FVDKDEKARL
QHQVTEDGEF WMSYEDFIYH FTKLEICNLT ADALQSDKLQ TWTVSVNEGR WVRGCSAGGC
RNFPDTFWTN PQYRLKLLEE DDDPDDSEVI CSFLVALMQK NRRKDRKLGA SLFTIGFAIY
EVPKEMHGNK QHLQKDFFLY NASKARSKTY INMREVSQRF RLPPSEYVIV PSTYEPHQEG
EFILRVFSEK RNLSEEVENT ISVDRPVPII FVSDRANSNK ELGVDQESEE GKGKTSPDKQ
KQSPQPQPGS SDQESEEQQQ FRNIFKQIAG DDMEICADEL KKVLNTVVNK HKDLKTHGFT
LESCRSMIAL MDTDGSGKLN LQEFHHLWNK IKAWQKIFKH YDTDQSGTIN SYEMRNAVND
AGFHLNNQLY DIITMQYADK HMNIDFDSFI CCFVRLEGMF RAFHAFDKDG DGIIKLNVLE
WLQLTMYA*
speed 0.73 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: simple_aae, prob: 0.999999999976393 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000337571
Genbank transcript ID NM_173089
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.311G>A
cDNA.569G>A
g.62824G>A
AA changes R104Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 104
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      104LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    104LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603ITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706QLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNNRLLNALAHRYGSREGQIPFD
Celegans  all identical  C06G4.2  112LIGGIFDNVVNRKGKKEQD
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.lost
129129MUTAGENC->S: Loss of activity. No effect on CMYA5-binding.might get lost (downstream of altered splice site)
129129ACT_SITEBy similarity.might get lost (downstream of altered splice site)
334334ACT_SITEBy similarity.might get lost (downstream of altered splice site)
358358ACT_SITEBy similarity.might get lost (downstream of altered splice site)
418586REGIONDomain III.might get lost (downstream of altered splice site)
587649REGIONLinker.might get lost (downstream of altered splice site)
649683DOMAINEF-hand 1.might get lost (downstream of altered splice site)
650821REGIONDomain IV.might get lost (downstream of altered splice site)
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 471 / 471
position (AA) of stopcodon in wt / mu AA sequence 157 / 157
position of stopcodon in wt / mu cDNA 729 / 729
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 259 / 259
chromosome 15
strand 1
last intron/exon boundary 703
theoretical NMD boundary in CDS 394
length of CDS 471
coding sequence (CDS) position 311
cDNA position
(for ins/del: last normal base / first normal base)		 569
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMRYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEWL QLTMYA*
mutated AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMQYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEWL QLTMYA*
speed 0.68 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: simple_aae, prob: 0.999999999976393 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000569136
Genbank transcript ID N/A
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.311G>A
cDNA.700G>A
g.62824G>A
AA changes R104Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 104
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      104LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    104LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603ITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706QLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNNRLLNALAHRYGSREGQIPFD
Celegans  all identical  C06G4.2  112LIGGIFDNVVNRKGKKEQD
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.lost
129129MUTAGENC->S: Loss of activity. No effect on CMYA5-binding.might get lost (downstream of altered splice site)
129129ACT_SITEBy similarity.might get lost (downstream of altered splice site)
334334ACT_SITEBy similarity.might get lost (downstream of altered splice site)
358358ACT_SITEBy similarity.might get lost (downstream of altered splice site)
418586REGIONDomain III.might get lost (downstream of altered splice site)
587649REGIONLinker.might get lost (downstream of altered splice site)
649683DOMAINEF-hand 1.might get lost (downstream of altered splice site)
650821REGIONDomain IV.might get lost (downstream of altered splice site)
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 471 / 471
position (AA) of stopcodon in wt / mu AA sequence 157 / 157
position of stopcodon in wt / mu cDNA 860 / 860
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 390 / 390
chromosome 15
strand 1
last intron/exon boundary 834
theoretical NMD boundary in CDS 394
length of CDS 471
coding sequence (CDS) position 311
cDNA position
(for ins/del: last normal base / first normal base)		 700
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMRYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEWL QLTMYA*
mutated AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMQYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEWL QLTMYA*
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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999976393 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000561817
Genbank transcript ID N/A
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.311G>A
cDNA.550G>A
g.62824G>A
AA changes R104Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 104
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      104LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    104LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603ITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706QLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNNRLLNALAHRYGSREGQIPFD
Celegans  all identical  C06G4.2  112LIGGIFDNVVNRKGKKEQD
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.lost
129129MUTAGENC->S: Loss of activity. No effect on CMYA5-binding.might get lost (downstream of altered splice site)
129129ACT_SITEBy similarity.might get lost (downstream of altered splice site)
334334ACT_SITEBy similarity.might get lost (downstream of altered splice site)
358358ACT_SITEBy similarity.might get lost (downstream of altered splice site)
418586REGIONDomain III.might get lost (downstream of altered splice site)
587649REGIONLinker.might get lost (downstream of altered splice site)
649683DOMAINEF-hand 1.might get lost (downstream of altered splice site)
650821REGIONDomain IV.might get lost (downstream of altered splice site)
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 576 / 576
position (AA) of stopcodon in wt / mu AA sequence 192 / 192
position of stopcodon in wt / mu cDNA 815 / 815
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 240 / 240
chromosome 15
strand 1
last intron/exon boundary 684
theoretical NMD boundary in CDS 394
length of CDS 576
coding sequence (CDS) position 311
cDNA position
(for ins/del: last normal base / first normal base)		 550
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMRYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEAV CRSTCRWHSA PPCARALHHL HAVPPWARNQ
TSTGFYCCGV N*
mutated AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMQYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEAV CRSTCRWHSA PPCARALHHL HAVPPWARNQ
TSTGFYCCGV N*
speed 0.87 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: simple_aae, prob: 0.999999999976393 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000397204
Genbank transcript ID N/A
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.311G>A
cDNA.535G>A
g.62824G>A
AA changes R104Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 104
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      104LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    104LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603ITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706QLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNNRLLNALAHRYGSREGQIPFD
Celegans  all identical  C06G4.2  112LIGGIFDNVVNRKGKKEQD
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.lost
129129MUTAGENC->S: Loss of activity. No effect on CMYA5-binding.might get lost (downstream of altered splice site)
129129ACT_SITEBy similarity.might get lost (downstream of altered splice site)
334334ACT_SITEBy similarity.might get lost (downstream of altered splice site)
358358ACT_SITEBy similarity.might get lost (downstream of altered splice site)
418586REGIONDomain III.might get lost (downstream of altered splice site)
587649REGIONLinker.might get lost (downstream of altered splice site)
649683DOMAINEF-hand 1.might get lost (downstream of altered splice site)
650821REGIONDomain IV.might get lost (downstream of altered splice site)
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 471 / 471
position (AA) of stopcodon in wt / mu AA sequence 157 / 157
position of stopcodon in wt / mu cDNA 695 / 695
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 225 / 225
chromosome 15
strand 1
last intron/exon boundary 669
theoretical NMD boundary in CDS 394
length of CDS 471
coding sequence (CDS) position 311
cDNA position
(for ins/del: last normal base / first normal base)		 535
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMRYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEWL QLTMYA*
mutated AA sequence MEICADELKK VLNTVVNKHK DLKTHGFTLE SCRSMIALMD TDGSGKLNLQ EFHHLWNKIK
AWQKIFKHYD TDQSGTINSY EMRNAVNDAG FHLNNQLYDI ITMQYADKHM NIDFDSFICC
FVRLEGMFRA FHAFDKDGDG IIKLNVLEWL QLTMYA*
speed 0.94 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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Problems