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LOVD - Variant listings for SOX2

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01 - Whole gene deletion
  (Reported 12 times)		 r.0 p.0 No transcription No translation SOX2_00001 Whole Gene - - - - - Deletion - FISH - - Patient has a 600kb deletion (encompassing the whole SOX2 gene) and a t(3;11) translocation
01 - Whole gene deletion chr3:180,960,157-184,754,546 r.0 p.0 No transcription No translation SOX2_00083 Whole gene - - - - - Deletion - CGH - - -
01 - Whole gene deletion chr3:181,012,354-185,302,035 r.0 p.0 No transcription No translation SOX2_00087 Whole gene - - - - - Deletion - Other - - Deletion detected by QMPSF
01 - Whole gene deletion chr3:181,292,708_182,858,976 r.0 p.0 No transcription No translation SOX2_00124 Whole Gene - - - - - Deletion - CGH - - Patient has a 1.5-2Mb deletion
01 - Whole gene deletion chr3:181216930-189014508 r.0 p.0 No transcription No translation SOX2_00039 Whole Gene - - - - - Deletion - FISH - - Patient has a 7.8Mb deletion (detected by FISH, confirmed by CGH)
01 - Whole gene deletion chr3:181225746_181460587 r.0 p.0 No transcription No translation SOX2_00123 Whole Gene - - - - - Deletion - CGH - - Patient has a 235kb deletion
01 - Whole gene deletion chr3:182,775,402-183,101,622 r.0 p.0 No transcription No translation SOX2_00085 Whole gene - - - - - Deletion - Other - - Detected by QMPSF
01 - Whole gene deletion chr3:182,877,971-182,958,506 r.0 p.0 No transcription No translation SOX2_00086 Whole gene - - - - - Deletion - Other - - Detected by QMPSF
01 - Whole gene deletion chr3:182649000-184339000 r.0 p.0 No transcription No translation SOX2_00081 Whole Gene - - - - - Deletion - CGH - - 1.6 Mb deletion (encompassing the whole SOX2 gene)
01 - 3' gene deletion r.? p.? Effect on transcription unknown Effect on translation unknown SOX2_00033 Exon - - - - - Deletion Unknown MLPA - - 3' end of gene deleted; proximal breakpoint between bases 154-698
01 - c.16G>T - p.(Glu6*) Glu (gag) > Ter (uag) predicted Termination of translation predicted SOX2_00058 ORF exon 16 ATGATG G T AGACGG Substitution N-terminal domain Direct Sequencing - - -
01 - c.53C>A
  (Reported 2 times)		 - p.(Ser18*) Ser (ucg) > Ter (uag) predicted Nonsense PTC - truncated protein predicted SOX2_00027 Exon 53 AAACTT C A GGGGGG Substitution NTD Direct Sequencing - - -
01 - c.58_59dupGG - p.(Gly21Argfs*75) Predicted frame-shifting duplication of 2 bases Truncated protein predicted SOX2_00057 ORF exon 58 GGGGGG - GG CGGCGG Duplication N-terminal domain Direct Sequencing - - Replication slippage likely
01 - c.62dupG - p.(Gly22Argfs*74) Predicted frameshift leading to PTC Truncated protein has impaired nuclear localization and no DNA binding or transactivation activity SOX2_00017 Exon 62 GGGCGG - G CGGCGG Duplication NTD Direct Sequencing - - -
01 - c.67_69dupGGC - p.(Gly33_Asn34insGly) In-frame duplication of 3 bases Insertion of Glycine in a run of Glycines SOX2_00065 ORF exon 67 GGCGGC - GGC AACTCC Duplication N-terminal domain Direct Sequencing - - -
01 - c.67_89del23 - p.(Gly23Argfs*65) Frameshifting deletion predicted Truncated protein predicted SOX2_00007 Exon 67 GGCGGC GGCAACTCCACCGCGGCGGCGGC - CGGCGG Deletion NTD DHPLC - - Deleted sequence is in triplet repeat region - replication slippage likely
01 - c.70_86del17
  (Reported 3 times)		 - p.(Asn24Glyfs*66) Frame-shifting deletion predicted PTC predicted SOX2_00088 ORF exon 70 GGCGGC AACTCCACCGCGGCGGC - GGCCGG Deletion N-terminal Direct Sequencing - - -
01 - c.70_89del20
  (Reported 15 times)		 - p.(Asn24Argfs*65) Frameshifting deletion predicted Frameshift PTC - truncated protein predicted SOX2_00011 Exon 70 GGCGGC AACTCCACCGCGGCGGCGGC - CGGCGG Deletion NTD Direct Sequencing - - Deleted sequence is in triplet repeat region - replication slippage likely
01 - c.86_95dup10 - p.(Asn33Glyfs*66) Frame-shifting duplication predicted PTC predicted SOX2_00089 ORF exon 86 CGGCGG CGGCCGGCGG CGGCCGGCGGCGGCCGGCGG CAACCA Duplication N-terminal Direct Sequencing - - -
01 - c.131C>G - p.(Pro44Arg) Pro (ccc) > Arg (cgc) predicted HMG missense mutation predicted SOX2_00066 ORF exon 131 AGCGGC C G CATGAA Substitution HMG Direct Sequencing - - -
01 - c.138T>G - p.(Asn46Lys) Asn (aau) > Lys (aag) predicted Predicted missense change in HMG box SOX2_00012 Exon 138 CATGAA T G GCCTTC Substitution HMG DHPLC StuI+ - Mutation inherited from normal mother (presumed gonosomal mosaic)
01 - c.138_140dupTGC - p.(Ala47dup) In-frame insertion predicted Duplication of Ala 47 predicted in HMG domain SOX2_00075 ORF exon 138 CATGAA TGC TGCTGC CTTCAT Duplication HMG Direct Sequencing - - -
01 - c.143_144delTCinsAA - p.(Phe48*) Phe (uuc) > Ter (uaa) predicted Premature termination of translation predicted within HMG domain. Truncated protein has impaired nuclear localisation and transcriptional control activity. SOX2_00071 ORF exon 143 ATGCCT TC AA ATGGTG Insertion/Deletion HMG Direct Sequencing - - -
01 - c.151T>C - p.(Trp51Arg) Trp (ugg) > Arg (cgg) predicted Missense change affecting highly conserved residue in HMG box SOX2_00090 ORF exon 151 ATGGTG T C GGTCCC Substitution HMG Direct Sequencing - - -
01 - c.158_174delinsATG - p.(Arg53Hisfs*37) Frame-shifting indel predicted PTC predicted SOX2_00091 ORF exon 158 GGTCCC GCGGGCAGCGGCGCAAG ATG ATGGCC Insertion/Deletion HMG Direct Sequencing - - -
01 - c.163C>T - p.(Gln55*) Gln (cag) > Ter (uag) predicted Nonsense PTC - truncated protein predicted SOX2_00014 Exon 163 CGCGGG C T AGCGGC Substitution HMG DHPLC - - -
01 - c.181C>T - p.(Gln61*) Nonsense mutation Gln (cag) > Ter (tag) predicted Truncated protein does not bind DNA or repress beta-catenin-mediated trasncription SOX2_00040 Exon 181 ATGGCC C T AGGAGA Substitution HMG Direct Sequencing BfaI+ - -
01 - c.188delA - p.(Asn63Thrfs*40) Predicted frameshift leading to PTC Truncated protein predicted SOX2_00028 Exon 188 AGGAGA A - CCCCAA Deletion HMG Direct Sequencing - - -
01 - c.200delA - p.(His67Profs*36) Frame-shifting deletion predicted PTC predicted SOX2_00092 ORF exon 200 AGATGC A - CAACTC Deletion HMG Direct Sequencing - - -
01 - c.221G>C
  (Reported 2 times)		 - p.(Arg74Pro) Arg (cgc) > Pro (ccc) predicted Missense change in HMG domain predicted SOX2_00015 Exon 221 GCAAGC G C CCTGGG Substitution HMG DHPLC - - -
01 - c.224T>A - p.(Leu75Gln) Leu (cug) > Gln (cag) predicted Missense protein has reduced DNA binding and transactivation activity SOX2_00026 Exon 224 AGCGCC T A GGGCGC Substitution HMG Direct Sequencing - 0/200 -
01 - c.235C>T - p.(Trp79Arg) ugg (Trp) > cgg (Arg) predicted Missense change predicted. Mutant protein has reduced in vitro transactivating activity SOX2_00103 ORF exon 235 GCCGAG T C GGAAAC Substitution HMG Direct Sequencing - - -
01 - c.236G>C - p.(Trp79Ser) Trp (ugg) > Ser (ucg) predicted Substitution of invariant Trp predicted SOX2_00094 ORF exon 236 CCGAGT G C GAAACT Substitution HMG Direct Sequencing - - -
01 - c.244_245delTT
  (Reported 3 times)		 - p.(Leu82Valfs*13) Frame-shifting deletion predicted Truncated protein predicted SOX2_00076 ORF exon 244 AAACTT TT - GTCGGA Deletion HMG Direct Sequencing - - -
01 - c.245delT - p.(Leu82Cysfs*20) Frame-shifting deletion predicted PTC predicted SOX2_00095 ORF exon 245 AACTTT T - GTCGGA Deletion HMG Direct Sequencing - - -
01 - c.248C>A - p.(Ser83*) Set (ucg) > Ter (uag) predicted HMG nonsense mutation - truncated protein predicted SOX2_00003 Exon 248 TTTTGT C A GGAGAC Substitution HMG DHPLC - - -
01 - c.255_256delGGinsT - p.(Glu86Argfs*17) Frame-shifting indel predicted PTC predicted SOX2_00096 ORF exon 255 GGAGAC GG T AGAAGC Insertion/Deletion HMG Direct Sequencing - - -
01 - c.277G>T
  (Reported 3 times)		 - p.(Glu93*) Glu (gag) > Ter (uag) predicted HMG box nonsense mutation - truncated protein predicted SOX2_00002 Exon 272 ATCGAC G T AGGCTA Substitution HMG DHPLC MaeI+ - -
01 - c.285dupG - p.(Arg96Alafs*14) Frameshifting insertion predicted Frameshift creates PTC - truncated protein predicted SOX2_00032 Exon 285 GCTAAG - G CGGCTG Duplication HMG Direct Sequencing - - -
01 - c.290T>C - p.(Leu97Pro) Leu (cug) > Pro (ccg) missense change predicted Predicted amino acid substitution in HMG box SOX2_00008 Exon 290 AGCGGC T C GCGAGC Substitution HMG DHPLC - - -
01 - c.302A>G - p.(His101Arg) Missense change His (cac) > Arg (cgc) predicted Substitution of invariant amino acid in HMG domain predicted SOX2_00077 ORF exon 302 CGCTGC A G CATGAA Substitution HMG Direct Sequencing - - -
01 - c.310G>T
  (Reported 2 times)		 - p.(Glu104*) Glu (gag) > Ter (uag) predicted Truncated protein predicted SOX2_00048 ORF exon 310 ATGAAG G T AGCACC Substitution CTD Heteroduplex Analysis - 0/80 -
01 - c.329A>G - p.(Tyr110Cys) Tyr (uac) > Cys (ugc) predicted Missense mutation of invariant cysteine predicted. Mutatn protein has reduced DNA binding and transactivation activity SOX2_00102 ORF exon 329 ATAAAT A G CCGGCC Substitution - Direct Sequencing - 0/150 -
01 - c.355C>T - p.(Pro112Leu) Pro (ccc) > Leu (cuc) Amino acid substitution predicted SOX2_00122 ORF exon 335 ACCGGC C T CCGGCG Substitution - Other - - Whole exome sequencing
01 - c.368A>G
  (Reported 2 times)		 - p.(Asp123Gly) Asp (gau) > Gly (ggu) predicted Missense substitution of highly conserved aspartate residue predicted SOX2_00056 ORF exon 368 AGAAGG A G TAAGTA Substitution C-terminal domain Direct Sequencing - - -
01 - c.387C>G - p.(=) Gly (ggc) > Gly (ggg) predicted No effect predicted SOX2_00024 Exon 387 GCCCGG C G GGGCTG Substitution CTD Direct Sequencing - 0/100 Variant inherited from unaffected father
01 - c.387delC - p.(Leu131Cysfs*23 Predicted frameshift leading to PTC Truncated protein has impaired transactivation activity SOX2_00019 Exon 387 GCCCGG C - GGCTGC Deletion CTD Direct Sequencing - - -
01 - c.389G>C - p.(Gly130Ala) Missense change Gly (ggg) > Ala (gcg) predicted Nuclear localization, DNA binding and transactivation activity unaffected SOX2_00023 Exon 389 CCGGCG G C GCTGCT Substitution CTD Direct Sequencing BssHII+ 0/100 Variant inherited from unaffected father
01 - c.402delC - p.(Gly135Alafs*19) Frame-shifting deletion predicted Truncated protein predicted. Mutant protein has reduced in vitro transactivating activity SOX2_00108 ORF exon 402 GGCCCC C - GGCGGC Deletion CTD Direct Sequencing - - -
01 - c.453G>A - p.(=) Ala (gcg) > Ala (gca) predicted No change expected SOX2_00045 Exon 453 GGGCGC G A GGCGTG Substitution CTD Direct Sequencing - - Presumed neutral variant
01 - c.463C>T - p.(Gln155*) Gln (cag) > Ter (uag) predicted Nonsense PTC - truncated protein predicted SOX2_00010 Exon 463 GTGAAC C T AGCGCA Substitution CTD SSCP MaeI+ 0/142 -
01 - c.479delA - p.(Tyr160Serfs*4) Frameshifting deletion predicted Truncated protein has impaired transactivation activity SOX2_00022 Exon 479 ACAGTT A - CGCGCA Deletion CTD Direct Sequencing - - -
01 - c.479dupA
  (Reported 2 times)		 - p.(Tyr160*) Insertion creates immediate PTC Truncated protein has impaired transactivation activity SOX2_00020 Exon 479 CAGTTA - A CGCGCA Duplication CTD Direct Sequencing HpaI+ - -
01 - c.479_480dupAC - p.(Ala161Thrfs*4) Frame-shifting insertion predicted Truncated protein predicted SOX2_00079 ORF exon 479 ACAGTT AC ACAC GCGCAC Substitution C-terminal Direct Sequencing - - -
01 - c.480C>G
  (Reported 3 times)		 - p.(Tyr160*) Tyr (uac) > Ter (uag) predicted Nonsense PTC - truncated protein predicted SOX2_00030 Exon 480 CAGTTA C G GCGCAC Substitution CTD Direct Sequencing - - -
01 - c.481G>T - p.(Ala161Ser) Ala (gcg) > Ser (ucg) predicted Missense change predicted (Ala is conserved at this position in all vertebrates) SOX2_00115 ORF exon 481 AGTTAC G T CGCACA Substitution - Direct Sequencing - - -
01 - c.486_487dupCA - p.(Met163Thrfs*2) Predicted frameshifting insertion, followed immediately by termination codon. Termination of translation predicted SOX2_00062 ORF exon 486 CGCGCA - CA TGAACG Duplication C-terminal domain Direct Sequencing - - -
01 - c.513C>G - p.(Tyr171*) Nonsense mutation predicted PTC predicted SOX2_00099 ORF exon 513 CAGCTA C G AGCATG Substitution CTD Direct Sequencing - - -
01 - c.529C>T
  (Reported 3 times)		 - p.(Gln177*) Gln (cag) > Ter (uag) predicted Truncated protein predicted SOX2_00004 Exon 529 CAGGAC C T AGCTGG Substitution CTD DHPLC AvaI-, BfaI+ - -
01 - c.540C>G - p.(Tyr190*) Nonsense mutation Tyr (uac) > Ter (uag) predicted Truncated protein predicted SOX2_00063 ORF exon 540 GGGCTA C G CCGCAG Substitution C-terminal domain Direct Sequencing - - -
01 - c.542delC - p(Pro181Argfs*22) Frame-shifting deletion predicted Truncated protein predicted SOX2_00072 ORF exon 542 GCTACC C - GCAGCA Deletion - Direct Sequencing - - -
01 - c.551delC - p.(Pro184Argfs*19) Frameshifting deletion leads to premature stop codon Truncated protein predicted SOX2_00049 ORF exon 551 AGCACC C - GGGCCT Deletion CTD Heteroduplex Analysis - 0/80 Mutation inherted from normal mother
01 - c.561T>C - p.(=) Asn (aau) > Asn (aac) predicted No effect predicted SOX2_00044 Exon 561 CCTCAA T C GCGCAC Substitution CTD Direct Sequencing - - Presumed neutral variant
01 - c.571G>A - p.(Ala191Thr) Missense change predicted: Ala (gca) > Thr (aca) Nuclear localization, DNA binding and transactivation activity unaffected SOX2_00025 Exon 571 CACGGC G A CAGCGC Substitution CTD Direct Sequencing HhaI- 0/100 Variant inherited from unaffected father
01 - c.599delA - p.(Tyr200Serfs*3) Frame-shifting deletion predicted PTC predicted SOX2_00100 ORF exon 599 ACCGCT A - CGACGT Deletion CTD Direct Sequencing - - -
01 - c.628delA - p.(Met210*) Frameshifting deletion creates immediate PTC Truncated protein predicted SOX2_00009 Exon 628 AACTCC A - TGACCA Deletion CTD DHPLC NlaIII- - -
01 - c.695C>A - p.(Thr232Asn) Thr (acc) > Asn (aac) predicted Missense change predicted SOX2_00047 ORF exon 695 AGGGCA C A CCCTGG Substitution CTD Direct Sequencing - 0/103 -
01 - c.834C>T - p.(=) Leu (cuc) > Leu (cuu) predicted No change expected SOX2_00046 Exon 834 GTATCT C T CCCGGC Substitution NTD Direct Sequencing - - -
01 - c.837delC - p.(Gly280Alafs*91) Frame-shifting deletion predicted Out-of-frame extension into 3'UTR predicted SOX2_00070 ORF exon 837 TCTCCC C - GGCGCC Deletion NTD Direct Sequencing - - -
01 - c.841_651del11insA - p.(Ala281Argfs*87) Frame-shifting deletion predicted Translation into 3'UTR predicted SOX2_00080 ORF exon 841 CCCGGC GCCGAGGTGCC A GGAACC Insertion/Deletion C-terminal Direct Sequencing - - -
01 - c.859G>C - p.(Ala287Pro) Ala (gcc) > Pro (ccc) predicted Missense change in C-terminal domain SOX2_00067 ORF exon 859 GAACCC G C CCGCCC Substitution C-terminal domain Direct Sequencing - - -
01 - c.905delC - p.(Pro302Argfs*69) Frame-shifting deletion predicted Translation into 3'UTR predicted SOX2_00101 ORF exon 905 GCGGCC C - GGTGCC Deletion - Direct Sequencing - 0/6500 -
01 - c.940delC - p.(Leu314Serfs*57) Frame-shifting deletion at C-terminal end of ORF Translational run-on into 3'UTR predicted SOX2_00064 ORF exon 940 TGCCCC C - TCTCAC Deletion C-terminal domain Direct Sequencing - - Deletion of a C from a run of C's - replication slippage likely
01 - c.943_944delTC - p.(Ser315Thrfs*112) Frameshifting deletion predicted Translation into 3'UTR predicted SOX2_00006 Exon 943 CCCCTC TC - ACACAT Deletion CTD DHPLC - - Deletion of TC from TCTC motif
01 - c.*22G>A
  (Reported 2 times)		 - - Presumed neutral substitution at base 22 of 3'UTR No effect predicted SOX2_00042 3' UTR 976 CTGGAG G A GGGGAG Substitution - DHPLC - 5/88 3'UTR polymorphism
01 - c.*26dupG - p.(=) Single nucleotide insertion in 3'UTR predicted No effect predicted SOX2_00116 3' UTR - GGGGGG - G AGAAAT Duplication - Direct Sequencing - - -
01 - c.*469C>A
  (Reported 2 times)		 - - 3'UTR change - no effect predicted No effect predicted SOX2_00051 3' UTR 1850 AAGCAA C A TTTTGT Substitution 3'UTR Heteroduplex Analysis - - Probable 3'UTR polymorphism
01 - c.*557G>A - - 3'UTR change - no effect predicted based on current evidence No effect predicted SOX2_00050 3' UTR 1938 AGGAGA G A GCTTCT Substitution 3'UTR Heteroduplex Analysis - 0/80 Mutation unlikely to be causative based on current knowledge
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Legend: [ SOX2 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 number (always '01' for SOX2) Legacy DNA ID: This column is not used in the SOX2 database DNA change: Variation at DNA level (see full legend for details and examples). RNA change: Variation at RNA level (see Full Legend for examples) Protein change: Variation at protein level (see Full Legend for details and examples) RNA information: Additional information about RNA change Protein information: Additional information about protein change SOX2 DB-ID: Database IDentifier; unique identifier for each sequence variant Location: Variant location within the gene Base number: Position of change within cDNA 5' Sequence Context: Six bases immediately 5' of the change Original Sequence: The original (wild type) sequence Variant Sequence: The new (mutant or variant) sequence 3' Sequence Context: Six bases immediately 3' of the change Type: Type of variant at DNA level Domain: SOX2 protein domain: NTD (N-terminal domain), HMG (HMG box) or CTD (C-terminal domain) Detection Method: Technique used to detect the mutation RE Site: Variant creates (+) or destroys (-) a restriction enzyme recognition site Frequency: Frequency of polymorphism/variant Remarks: Any other comments

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