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LOVD - Variant listings for OTX2

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00 - 47 kb deletion of OTX2 promoter region - - - - OTX2_00039 - - - - - - Deletion - CGH - - Deletion of OTX2 promoter region
01 c.252delC c.81delC - p.(Ser28Profs*23) Predicted frameshift leading to PTC - NMD likely Translation unlikely OTX2_00003 Exon 81 GCACCC C - TCCGTG Deletion N-terminal domain Direct Sequencing - 0/188 Mutant allele inherited from unaffected mosaic mother
01 - c.85G>A - p.(Val29Met) Val (gug) > Met (aug) predicted Predicted missense substitution of conserved N-terminal residue OTX2_00022 Exon 85 CCCTCC G A TGGGCT Substitution N-terminal domain Amplicon Melting Analysis - - Same variant in unaffected father
01 c.264C>G c.93C>G - p.(Tyr31*) Tyr (uac) > Stop (uag) predicted. NMD likely NMD predicted - protein synthesis unlikely OTX2_00018 Exon 93 GGGCTA C G CCGGCC Substitution N-terminal domain Amplicon Melting Analysis - - -
01 c.268+12C>T c.97+12C>T - p.= Probable neutral intronic substitution No effect predicted OTX2_00009 Intron 97 TGAGCC C T TGCTGC Substitution - Direct Sequencing - C=0.981/T=0.019 SNP frequency assessed in 188 control chromosomes
01 c.269-70C>A c.98-70C>A - p.= No effect on transcription expected No change expected OTX2_00010 Intron 98 - C A - Substitution - Direct Sequencing - - -
02 - c.106delC - p.(Arg36Glyfs*15) Frame-shifting deletion leading to PTC Truncated protein predicted OTX2_00041 Exon 106 ACCCCC C - GGAAAC Deletion N-terminal domain Direct Sequencing - - -
02 - c.106dupC - p.(Arg36Profs*52) Frame-shifting insertion predicted to create PTC Truncated protein predicted OTX2_00019 Exon 106 CCCCCC - C GGAAAC Duplication N-terminal domain Amplicon Melting Analysis - - Probable replication slippage
02 c.288delCC c.117_118delCC - p.(Arg40Glyfs*47) Predicted frameshifting deletion leading to PTC in last coding exon Truncated protein predicted OTX2_00005 Exon 117 ACAGCG CC - GGGAGA Deletion Homeodomain Direct Sequencing - 0/188 -
02 - c.136dupA - p.(Thr46Asnfs*42) Frame-shifting duplication creates PTC in last exon (exon 3) Truncated protein predicted OTX2_00032 Exon 136 CGTTCA - A CTCGGG Duplication Homeodomain Direct Sequencing - 0/192 -
02 - c.203G>C - p.(Arg68Pro) Arg (cga) > Pro (cca) predicted. Missense change in homeodomain affects activation of the IRBP promoter but not the POU1F1 promoter. OTX2_00037 Exon 203 TCATGC G C AGAGGA Substitution Homeodomain Direct Sequencing - - -
02 - c.214_217delGCACinsCA - p.(Ala72Hisfs*15) Predicted frame-shifting deletion leading to PTC PTC is in last exon - truncated protein predicted. Mutant protein has severely decreased transactivation activity OTX2_00026 Exon 214 GAGGTG GCAG CA TGAAAA Insertion/Deletion - Direct Sequencing - 0/100 This variant has arisen de novo. Patient also has an apparently neutral missense change
02 - c.221_236del16 - p.(Lys74Serfs*30) Frame-shifting deletion leading to PTC PTC is in last exon - truncated protein predicted. Mutant protein has impaired transactivation activity OTX2_00024 Exon 221 CACTGA AAATCAACTTGCCCGA - GTCGAG Deletion Homeodomain Direct Sequencing - 0/100 Patient also has an apparently neutral missense change
02 - c.234delC - p.(Glu79Serfs*30) Frame-shifting deletion predicted PTC predicted OTX2_00044 Exon 234 CTTGCC C - GAGTCG Deletion Homeodomain Direct Sequencing - - -
02 - c.247_249dupCAG - p.(Gln83dup) Duplication of glutamine codon (cag) predicted Duplication of glutamine predicted OTX2_00058 Exon 247 GTGCAG - CAG /GTAGGG Duplication Homeodomain Direct Sequencing - - Variant associated with highly variable phenotype
02 - c.249G>C r.(spl)? p.(Gln83His)/p.? Gln (cag) > His (cac) predicted. Last base of exon substituted - may affect splicing Outcome unknown without RNA analysis OTX2_00060 Exon 249 GGTGCA G C /GTAGGG Substitution Homeodomain Direct Sequencing - - -
02 - c.249G>T r.(spl)? p.(Gln83His)/p.? Gln (cag) > His (cau) predicted. Last base of exon substituted - may affect splicing Outcome unknown without RNA analysis OTX2_00045 Exon 249 GGTGCA G T /GTAGGG Substitution Homeodomain Direct Sequencing - - -
03 - c.254G>T - p.(Trp85Leu) Trp (ugg) > Leu (uug) predicted. Missense mutation in homeodomain. OTX2_00064 Exon 254 GTAT G T GTTTAA Substitution HD Other - - Exome sequencing
03 c.436C>G c.265C>G - p.(Arg89Gly) Arg (cga) > Gly (gga) predicted Predicted missense change in homeodomain. Mutant protein has reduced DNA binding activity OTX2_00002 Exon 265 AAGAAT C G GAAGAG Substitution Homeodomain - TaqI(-) 0/188 -
03 c.436C>G c.265C>T
  (Reported 3 times)
- p.(Arg89*) Arg (cga) > Ter (tga) predicted Predicted nonsense change in homeodomain OTX2_00036 Exon 265 AAGAAT C T GAAGAG Substitution Homeodomain Direct Sequencing TaqI(-) - -
03 - c.266G>C - p.(Arg89Pro) Arg (cga) > Pro (cca) predicted Missense mutation in HD predicted. Mutant protein shows greatly reduced DNA binding and reporter activation OTX2_00061 Exon 288 AGAATC G C AAGAGC Substitution HD Direct Sequencing - - Mutation not present in 150 controls or variation databases
03 - c.270A>T - p.(Arg90Ser) Arg (aga) > Ser (agu) predicted Missense change in homeodomain predicted. Mutant protein has greatly reduced DNA binding and trans-activation activities OTX2_00031 Exon 270 TCGAAG A T GCTAAG Substitution Homeodomain Direct Sequencing - - -
03 - c.276_294del19 - p.(Lys92Asnfs*11) Frame-shifting deletion predicted Truncated protein predicted OTX2_00046 Exon 276 AGCTAA GTGCCGCCAACAACAGCAA - CAACAG Deletion C-terminal domain Direct Sequencing - - -
03 - c.289C>T - p.(Gln97*) Gln (cag) > Ter (uag) predicted. Protein truncation predicted immediately after homeodomain OTX2_00020 Exon 289 CAACAA C T AGCAAT Substitution C-terminal domain Amplicon Melting Analysis - - -
03 - c.292delC - p.(Gln98Asnfs*11) Frame-shifting deletion leading to PTC Truncated protein predicted OTX2_00040 Exon 292 CAACAG C - AACAAC Deletion C-terminal domain Direct Sequencing - - -
03 c.466C>T c.295C>T - p.(Gln99*) Predicted nonsense mutation: Gln (caa) > Ter (uaa) Truncated protein predicted OTX2_00006 Exon 295 CAGCAA C T AACAGC Substitution C-terminal domain Direct Sequencing - 0/188 Variant inherited from normal father
03 - c.313C>T
  (Reported 2 times)
- p.(Gln105*) Gln (caa) > Ter (uaa) predicted Truncated protein predicted OTX2_00033 Exon 313 GGAGGT C T AAAACA Substitution C-terminal domain Direct Sequencing - 0/384 -
03 - c.373_374delAG - p.(Gly126Trpfs*11) Frame-shifting deletion predicted to create PTC Truncated protein predicted OTX2_00021 Exon 373 TCAGAG AG - TGGAAC Deletion C-terminal domain Amplicon Melting Analysis - - Replication slippage likely
03 c.568C>A c.397C>A - p.(Pro133Thr) Missense change predicted: Pro (ccc) > Thr (acc) Mutation affects last residue of highly conserved SGQFTP motif. No effect on DNA binding, nuclear localisation or transcriptional activity OTX2_00007 Exon 397 TTCACT C A CCCCCT Substitution SGQFTP motif Direct Sequencing - 0/328 -
03 c.571C>G c.400C>G - p.(Pro134Ala) Pro (ccc) > Ala (gcc) predicted Missense change predicted. No effect on DNA binding, nuclear localisation or transcriptional activity OTX2_00008 Exon 400 ACTCCC C G CCTCTA Substitution C-terminal domain Direct Sequencing - 0/328 Variant absent from affected mother
03 - c.401C>G - p.(Pro134Arg) Pro (ccc) > Arg (cgc) predicted Mutant protein shows impaired transactivation activity OTX2_00042 Exon 401 CTCCCC C G CTCTAG Substitution C-terminal domain Direct Sequencing - - -
03 - c.402delC - p.(Ser135Leufs*43) Frame-shifting deletion leading to PTC Truncated protein predicted OTX2_00062 Exon 402 TCCCCC C - TCTAGC Deletion - Direct Sequencing - - -
03 c.573dupC c.402dupC - p.(Ser135Leufs*2) Frameshifting insertion leads to premature stop codon Truncated protein localizes to nucleus but has impaired inactivation of HESX1 and POU1F1 promoters OTX2_00012 Exon 402 CCCCCC - C TCTAGC Duplication C-terminal domain Direct Sequencing - - De novo mutation in patient
03 c.575_576dupCT c.404_405dupCT - p.(Ser136Leufs*43) Frameshifting insertion creates PTC in C-terminal domain Truncated protein predicted OTX2_00015 Exon 404 CCCTCT - CT AGCACC Duplication C-terminal domain Direct Sequencing - - -
03 - c.413C>G - p.(Ser138*) Ser (uca) > Ter (uga) predicted Truncated protein predicted OTX2_00023 Exon 413 GCACCT C G AGTCCC Substitution C-terminal domain Direct Sequencing - 0/181 -
03 - c.456_457delGAinsAT - p.(Trp152*) Trp (ugg) > Ter (uga) predicted Truncated protein predicted OTX2_00034 Exon 456 TATCTG GA AT GCCCAG Insertion/Deletion SIWSPA Direct Sequencing - 0/384 -
03 c.635insGC c.463_464dupGC - p.(Ser156Leufs*23) Predicted frameshifting insertion leading to PTC Truncated protein predicted OTX2_00001 Exon 463 CCCAGC - GC TTCCAT Duplication C-terminal domain Direct Sequencing - 0/188 -
03 - c.501C>G - p.(=) Ser (tcc) > Ser (tcg) predicted No effect predicted OTX2_00056 Exon 501 CACCTC C G TCTTCC Substitution - Direct Sequencing - - c.525C>G in NM_021728.2
03 - c.532A>T - p.(Thr178Ser) Thr (acc) > Ser (ucc) predicted Missense change in C-terminal domain. No effect on transactivation activity. OTX2_00025 Exon 532 CCCATG A T CCTATA Substitution C-terminal domain Direct Sequencing - 0/100 Patient also has a pathological deletion
03 c.708T>A c.537T>A - p.(Tyr179*) Tyr (uau) > Ter (uaa) predicted Truncated protein predicted OTX2_00004 Exon 537 GACCTA T A ACTCAG Substitution C-terminal domain Direct Sequencing - 0/188 Mutation inherited from mosaic mother
03 - c.553_556dupTATA - p.(Ser186Ilefs*2) Frame-shifting duplication creates PTC Truncated protein predicted OTX2_00035 Exon 553 GTTATA - TATA GTCAAG Duplication C-terminal domain Direct Sequencing - 0/384 -
03 - c.562G>T
  (Reported 2 times)
- p.(Gly188*) Gly (gga) > Ter (tga) predicted Truncated protein predicted. Mutant protein has reduced transactivation activity OTX2_00028 Exon 562 AGTCAA G T GATATG Substitution C-terminal domain Direct Sequencing - 0/100 -
03 - c.651delC - p.(Thr218Hisfs*76) - Synthesis of truncated protein predicted OTX2_00059 Exon 651 AGGGGC C - ACACTC Deletion - Direct Sequencing - - Variant not found in population databases
03 c.845A>G c.674A>G
  (Reported 2 times)
- p.(Asn225Ser) Missense change Asn (aau) > Ser (agu) predicted in transcription activation domain Mutant protein binds DNA normally but has dominant negative activity in reporter activation tests OTX2_00013 Exon 674 GTACCA A G TGCAGT Substitution C-terminal domain Direct Sequencing - 0/50 -
03 - c.734C>T - p.(Ala245Val) Ala (gcu) > Val (guu) predicted Apparently neutral change. Mutant protein has normal transactivation activity OTX2_00027 Exon 734 ATGGAG C T TTCAAG Substitution C-terminal domain Direct Sequencing - 0/100 Neutral variant inherited from normal father
03 - c.737C>A - p.(Ser246*) Ser (uca) > Ter (uaa) predicted Truncated protein predicted OTX2_00057 Exon 737 GAGCTT C A AAGCTT Substitution - Direct Sequencing - - Whole-genome sequencung
03 c.1051G>A c.*10G>A - p.= Substitution of 10th base of 3'UTR - no effect predicted No effect predicted OTX2_00011 3' UTR 880 CCTGTA G A AACCTC Substitution 3'UTR Direct Sequencing - - -
All - Whole gene deletion (120 kb) r.0 p.0 - - OTX2_00063 - - - - - - Deletion - CGH - - Heterozygous deletion of OTX2 gene
All - Whole gene deletion (400 kb) r.0 p.0 - - OTX2_00054 - - - - - - Deletion - CGH - - Deletion of OTX2 gene
All - Whole gene deletion + insertion g.5600653158867091delins931 r.0 p.0 - - OTX2_00030 - - - - - - Insertion/Deletion - MLPA - - 1.9Mb deletion + 931b insertion
All - Whole gene deletion 14q22.2q23.1(54,287,767-56,543,234)x1 r.0 p.0 No transcription No translation OTX2_00049 - - - - - - Deletion - CGH - - Proband also has a paternal deletion of 4q43
All - Whole gene deletion 14q23.1q23.1(56,326,564-56,433,789)x1 r.0 p.0 - - OTX2_00050 - - - - - - Deletion - CGH - - Patient also has a deletion of 11p15
All - Whole gene deletion chr14(52,820,533-60,588,720)x1 r.0 p.0 - - OTX2_00051 - - - - - - Deletion - CGH - - -
All - Whole gene deletion g.52830547- 59031284 r.0 p.0 - - OTX2_00043 - - - - - - Deletion - CGH - - Whole gene deletion (6.2 Mb)
All - Whole gene deletion g.53758044-56834649 r.0 p.0 - - OTX2_00016 - - - - - - Deletion - FISH - - Whole gene deletion (3Mb)
All - Whole gene deletion g.56094000-62594000 r.0 p.0 - - OTX2_00048 - - - - - - Deletion - CGH - - Whole gene deletion (6.5 Mb)
All - Whole gene deletion g.56224000-56679000 r.0 p.0 - - OTX2_00047 - - - - - - Deletion - CGH - - Whole gene deletion (455 kb)
All - Whole gene deletion g.56268037-57541514 r.0 p.0 - - OTX2_00017 - - - - - - Deletion - MLPA - - Whole gene deletion (1.28Mb)
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Legend: [ OTX2 full legend ]
Sequence variations are described basically as recommended by the Ad-Hoc Committee for Mutation Nomenclature (AHCMN), with the recently suggested additions (den Dunnen JT and Antonarakis SE [2000], Hum.Mut. 15:7-12); for a summary see Nomenclature. Coding DNA Reference Sequence, with the first base of the Met-codon counted as position 1.
Exon: Exon numbering. Legacy DNA ID: Legacy DNA ID DNA change: Variation at DNA-level (see Full Legend for examples) RNA change: Variation at RNA-level (see Full Legend for examples) Protein change: Variation at protein level (see Full Legend for examples) RNA information: Additional information about RNA change Protein information: Additional information about protein change OTX2 DB-ID: Database IDentifier; When available, links to OMIM ID's are provided. Location: Variant location at DNA level. Base number: Location of DNA change 5' Sequence Context: 6 bases immediately 5' of the change Original Sequence: Original (normal) sequence Variant Sequence: Variant (new/mutated) sequence 3' Sequence Context: 6 bases immediately 3' of the change Type: Type of variant at DNA level. Domain: NTD, N-terminal domain; HD, homeodomain; CTD, C-terminal domain Detection Method: Mutation detection technique RE Site: Variant creates (+) or destroys (-) a restriction enzyme recognition site. Frequency: Frequency of variant Remarks: Other remarks about the sequence change