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LOVD - Variant listings for SOX2

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+/+ 01 - Whole gene deletion 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 Case 1 SOX2 Anophthalmia Syndrome [12612584], [15812812], [16529618], United Kingdom (Great Britain):Edinburgh DNA FISH - 1 - female Sporadic Sporadic n/a t(3;11) n/a Bilateral anophthalmia, mild facial dysmorphism, delayed motor milestones, decreased muscle tone, brain anomalies (MRI) -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00013 Whole Gene - - - - - Deletion - FISH - - Patient has a 2.7Mb deletion (encompassing the whole SOX2 gene) and a t(3;7) translocation Case 1 Anophthalmia-esophageal-genital syndrome [16543359], United Kingdom (Great Britain):Edinburgh DNA FISH Case first described by Rogers (1988) Proceedings of the Greenwood Genetic Center, 7, 57 1 - female Sporadic Sporadic - - - Bilateral anophthalmia, oesophageal atresia, tracheo-oesophageal fistula -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00034 Whole Gene - - - - - Deletion - MLPA - - ~328Kb deletion detected by MLPA and confirmed by FISH Case 8 SOX2 Anophthalmia Syndrome [17522144], United Kingdom (Great Britain):Edinburgh DNA MLPA - 1 - male Sporadic Sporadic - - - Right anophthalmia, left cataract, seizures, brachycephaly, cryptorchidism, micropenis, delayed speech, delayed development -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00035 Whole Gene - - - - - Deletion - MLPA - - - Case 9 SOX2 Anophthalmia Syndrome [17522144], United Kingdom (Great Britain):Edinburgh DNA MLPA - 1 - male Sporadic Sporadic - - - Severe bilateral microphthalmia, feeding difficulties. Normal cranial MRI -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00036 Whole Gene - - - - - Deletion - MLPA - - ~550Kb deletion detected by MLPA and confirmed by FISH Case 10 SOX2 Anophthalmia Syndrome [17522144], United Kingdom (Great Britain):Edinburgh DNA MLPA - 1 - female Sporadic Sporadic - - - Bilateral microphthalmia with retinal detachments; perception of light maintained. Growth delay -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00037 Whole Gene - - - - - Deletion - MLPA - - - Case 11 SOX2 Anophthalmia Syndrome [17522144], United Kingdom (Great Britain):Edinburgh DNA MLPA - 1 - female Sporadic Sporadic - - - Left anophthalmia, right mild optic disc dysplasia (normal vision), delayed puberty, delayed motor speech and cognitive development Ureteric reflux (unclear if this is caused by SOX2 mutation - no obvious link to known expression pattern)
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00038 Whole Gene - - - - - Deletion - MLPA - - - Case 12 SOX2 Anophthalmia Syndrome [17522144] , United Kingdom (Great Britain):Edinburgh DNA MLPA - 1 - female Sporadic Sporadic - - - Right anophthalmia, left microphthalmia with sclerocornea. normal early development -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00073 Whole Gene - - - - - Deletion - CGH - - 731 kb deletion Patient 1 Anophthalmia [21919124], United Kingdom (Great Britain):Edinburgh DNA SEQ Motherís DNA normal; father unavailable 1 - female - Sporadic - - - Bilateral anophthalmia, developmental delay, hypogonadotropic hypogonadism, non-progressive pituitary tumour -
+/+ 01 - Whole gene deletion r.0 r.0 No transcription No translation SOX2_00084 Whole gene - - - - - Deletion - Other - - Deletion detcted by QMPSF Chassaing 2014 Patient 2 Anophthalmia/microphthalmia [24033328], United Kingdom (Great Britain):Edinburgh DNA Other Deletion detected by QMPSF. Absent in parents 1 - male Sporadic Sporadic - - - Pregnancy terminated at 30 weeks after detection of left anophthalmia. Right microphthalmia also found at autopsy. No cerebral abnormality. -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00109 Whole Gene - - - - - Deletion - CGH - - 2.3 Mb deletion Suzuki 2014 Case 7 Bilateral microphthalmia [24804704], United Kingdom (Great Britain):Edinburgh DNA CGH - 1 - female - - - - - Bilateral severe microphthalmia. Developmental delay, retarded postnatal growth, seizure. LH, FSH and GH deficiency. Ectopic posterior lobe by MRI -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00110 Whole Gene - - - - - Deletion - CGH - - 1.0 Mb deletion Suzuki 2014 Case 8 Bilateral anophthalmia [24804704], United Kingdom (Great Britain):Edinburgh DNA CGH - 1 - male - - - - - Developmental delay, retarded postnatal growth. LH, FSH and GH deficiency. Pituitary hypoplasia -
+/+ 01 - Whole gene deletion r.0 p.0 No transcription No translation SOX2_00111 Whole Gene - - - - - Deletion - CGH - - 2.5 Mb deletion Suzuki 2014 Case 9 Coloboma [24804704], United Kingdom (Great Britain):Edinburgh DNA CGH De novo deletion 1 - male Sporadic Sporadic - - - Right retinal fold, left optic disc coloboma. Developmental delay. LH and FSH deficiency. -
+/+ 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 - - - Chassaing 2014 Patient 1 Anophthalmia syndrome [24033328], United Kingdom (Great Britain):Edinburgh DNA CGH Deletion detected by QMPSF, confirmed by aCGH 1 - female - Sporadic - - - Bilateral anophthalmia, severe developmental delay, seizures, facial dysmorphism, small stature. Agenesis of the corpus callosum, optic nerve hypoplasia, and hypoplasia of the vermis by MRI -
+/+ 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 Chassaing 2014 Patient 5 Microphthalmia syndrome [24033328], United Kingdom (Great Britain):Edinburgh DNA CGH 4.3 Mb deletion detected by QMPSF, confirmed by aCGH. Absent in parents 1 - female Sporadic Sporadic - - - Intrauterine fetal death at 30 weeks gestation. Oesophageal atresia, hemi-uterus, ante-positioned anus, left microphthalmia with sclerocornea (normal right eye; normal cerebral structures; normal growth). -
+/+ 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 Dennert et al 2017 Patient 3 Developmental delay [27862890], United Kingdom (Great Britain):Edinburgh DNA CGH - 1 - female - - - - - Developmental delay, hypogonadotrophic hypogonadism, mild facial dysmorphism -
+/+ 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) Patient 1 Anophthalmia, Microphthalmia, Hypopituitarism [18285410], United Kingdom (Great Britain):Edinburgh DNA FISH - 1 - female Sporadic - - - - Right anophthalmia, left microphthalmia, mild pulmonary stenosis, pituitary anomalies, global developmental delay, brain anomalies by MRI -
+/+ 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 Dennert et al 2017 Patient 2 Intellectual disability [27862890], United Kingdom (Great Britain):Edinburgh DNA CGH De novo deletion 1 - female Sporadic Sporadic - - - - Moderate intellectual disability, dysmorphic features, oesophageal dysfunction
+/+ 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 Chassaing 2014 Patient 3 Anophthalmia syndrome [24033328], United Kingdom (Great Britain):Edinburgh DNA CGH Deletion detected by QMPSF, confirmed by aCGH 1 - male - Sporadic - - - Bilateral anophthalmia, developmental delay, small stature. Hypoplasia of the corpus callosum and periventricular heterotopia by MRI. -
+/+ 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 Chassaing 2014 Patient 4 Anophthalmia syndrome [24033328], United Kingdom (Great Britain):Edinburgh DNA CGH 80kb deletion detected by QMPSF, confirmed by aCGH. Absent in parents 1 - male Sporadic Sporadic - - - Bilateral anophthalmia, micropenis, severe developmental delay, short stature secondary to GH insufficiency. Normal MRI -
+/+ 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) Case 2850 Bilateral anophthalmia (24498598), United Kingdom (Great Britain):Edinburgh DNA CGH Deletion absent in unaffected parents 1 - female - Sporadic - - - Bilateral anophthalmia. Pineal cyst by MRI. Normal development -
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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.
Path.: Variant pathogenicity, in the format Reported/Concluded; '+' indicating the variant is pathogenic, '+?' probably pathogenic, '-' no known pathogenicity, '-?' probably no pathogenicity, '?' effect unknown. 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 Patient ID: Internal patient reference Disease: Disease phenotype, as reported in paper/by submitter, unless modified by the curator. Reference/Submitter: Links to PubMed ID (if available) and Submitter ID Template: Variant detected in DNA, RNA and/or Protein. Technique: Technique used to detect the variation. # Reported: Number of times this case has been reported Population: Patient population Gender: Patient gender Sequence Inheritance: Sequence Inheritance Phenotype Inheritance: Phenotype Inheritance Second PCR: Second PCR CIS: Other Mutation in Cis Conserved residue: Variation affects conserved base or amino acid Related Phenotype: Related Phenotype Unrelated Phenotype: Unrelated Phenotype