SOX2-OT[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 145614	GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3	LOC115995524, LOC115995525 +2647 more	Copy number gain	See cases	GPathogenic
Select item 57983	GRCh38/hg38 3q24-29(chr3:147521892-198096565)x3	LOC123453201, LOC123453202 +1450 more	Copy number gain	See cases	GPathogenic
Select item 150609	GRCh38/hg38 3q25.1-29(chr3:152100512-198118383)x3	LOC129938169, LOC129938170 +1318 more	Copy number gain	See cases	GPathogenic
Select item 154213	GRCh38/hg38 3q25.31-29(chr3:156118441-198125115)x3	LOC108281160, LOC108281177 +1247 more	Copy number gain	See cases	GPathogenic
Select item 152257	GRCh38/hg38 3q25.31-29(chr3:156321878-198113452)x3	ABCC5, ABCC5-AS1 +1245 more	Copy number gain	See cases	GPathogenic
Select item 57984	GRCh38/hg38 3q25.31-29(chr3:157293378-198134727)x3	LOC132088897, LOC132088898 +1201 more	Copy number gain	See cases	GPathogenic
Select item 155627	GRCh38/hg38 3q26.1-29(chr3:166137209-198125115)x3	LOC129938260, LOC129938261 +1064 more	Copy number gain	See cases	GPathogenic
Select item 153893	GRCh38/hg38 3q26.1-28(chr3:167717962-188365272)x3	ABCC5, ABCC5-AS1 +627 more	Copy number gain	See cases	GLikely pathogenic
Select item 148012	GRCh38/hg38 3q26.2-29(chr3:168167568-198110178)x3	LOC129938077, LOC129938078 +1041 more	Copy number gain	See cases	GPathogenic
Select item 149685	GRCh38/hg38 3q26.32-29(chr3:176168525-198118383)x3	ZMAT3, ZNF639 +867 more	Copy number gain	See cases	GPathogenic
Select item 148947	GRCh38/hg38 3q26.32-29(chr3:176439911-198118383)x3	LOC129938282, LOC129938283 +866 more	Copy number gain	See cases	GPathogenic
Select item 224832	NC_000003.12:g.177772523_185716872dup	ALG3, AP2M1 +280 more	Duplication	Currarino triad	GLikely pathogenic
Select item 12819	NC_000003.12:g.(179547548_181649736)_(181808821_182152788)del	LINC01206, ACTL6A +44 more	Deletion	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 153734	GRCh38/hg38 3q26.33-28(chr3:181138664-192512023)x1	ABCC5, ABCC5-AS1 +399 more	Copy number loss	See cases	GPathogenic
Select item 148832	GRCh38/hg38 3q26.33(chr3:181221877-182452343)x1	LINC01206, LINC01994 +13 more	Copy number loss	See cases	GPathogenic
Select item 57865	GRCh38/hg38 3q26.33(chr3:181504586-182287821)x1	LINC01206, LOC108281177 +8 more	Copy number loss	See cases	GPathogenic
Select item 152968	GRCh38/hg38 3q26.33(chr3:181644991-181751723)x3	LOC108281177, LOC108281178 +2 more	Copy number gain	See cases	GBenign
Select item 147856	GRCh38/hg38 3q26.33(chr3:181689247-181794116)x1	LOC108281177, LOC108281178 +2 more	Copy number loss	See cases	GPathogenic
Select item 57866	GRCh38/hg38 3q26.33(chr3:181710887-181748657)x1	LOC108281177, LOC108281178 +2 more	Copy number loss	See cases	GPathogenic
Select item 151735	GRCh38/hg38 3q26.33(chr3:181712160-181713165)x3	LOC108281177, SOX2 +1 more	Copy number gain	See cases	GBenign
Select item 1294227	NM_003106.4(SOX2):c.-37C>T	LOC108281177, SOX2 +1 more	Single nucleotide variant (5 prime UTR variant)	not provided	GBenign
Select item 378636	NM_003106.4(SOX2):c.-31C>T	LOC108281177, SOX2 +1 more	Single nucleotide variant (5 prime UTR variant)	not specified	GBenign
Select item 986769	NM_003106.4(SOX2):c.-13_43del (p.Met1fs)	LOC108281177, SOX2 +1 more (M1fs)	Deletion (frameshift variant +1 more)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 682175	NM_003106.4(SOX2):c.-20G>T	LOC108281177, SOX2 +1 more	Single nucleotide variant (5 prime UTR variant)	not provided	GLikely benign
Select item 467820	NC_000003.12:g.(?_181712341)_(181874887_?)del	LOC108281177, LOC108281178 +3 more	Deletion	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 678529	NM_003106.4(SOX2):c.-11A>C	LOC108281177, SOX2 +1 more	Single nucleotide variant (5 prime UTR variant)	not provided	GLikely benign
Select item 859786	NM_003106.4(SOX2):c.3dup (p.Tyr2fs)	LOC108281177, SOX2 +1 more (Y2fs)	Duplication (frameshift variant +1 more)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 986774	NM_003106.4(SOX2):c.16G>T (p.Glu6Ter)	LOC108281177, SOX2 +1 more (E6*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 870447	NM_003106.4(SOX2):c.20C>T (p.Thr7Met)	LOC108281177, SOX2 +1 more (T7M)	Single nucleotide variant (missense variant)	not provided +1 more	GUncertain significance
Select item 2788953	NM_003106.4(SOX2):c.21G>C (p.Thr7=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 988074	NM_003106.4(SOX2):c.22G>T (p.Glu8Ter)	LOC108281177, SOX2 +1 more (E8*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GLikely pathogenic
Select item 2823248	NM_003106.4(SOX2):c.25del (p.Glu8_Leu9insTer)	LOC108281177, SOX2 +1 more	Deletion (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 707677	NM_003106.4(SOX2):c.33G>T (p.Pro11=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GLikely benign
Select item 2911393	NM_003106.4(SOX2):c.39C>A (p.Gly13=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GLikely benign
Select item 1327183	NM_003106.4(SOX2):c.42G>T (p.Pro14=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 467823	NM_003106.4(SOX2):c.45G>A (p.Gln15=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	not provided +1 more	GLikely benign
Select item 750266	NM_003106.4(SOX2):c.51T>C (p.Thr17=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1913933	NM_003106.4(SOX2):c.52_53delinsAA (p.Ser18Lys)	LOC108281177, SOX2 +1 more (S18K)	Indel (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome +1 more	GConflicting classifications of pathogenicity
Select item 855754	NM_003106.4(SOX2):c.53C>A (p.Ser18Ter)	LOC108281177, SOX2 +1 more (S18*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 279895	NM_003106.4(SOX2):c.59dup (p.Gly21fs)	LOC108281177, SOX2 +1 more (G21fs)	Duplication (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome +1 more	GPathogenic
Select item 29890	NM_003106.4(SOX2):c.58_59dup (p.Gly21fs)	LOC108281177, SOX2 +1 more (G21fs)	Duplication (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 986777	NM_003106.4(SOX2):c.59del (p.Gly20fs)	LOC108281177, SOX2 +1 more (G20fs)	Deletion (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 193252	NM_003106.4(SOX2):c.54G>C (p.Ser18=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	not provided	GConflicting classifications of pathogenicity
Select item 3253237	NM_003106.4(SOX2):c.56_57delinsTT (p.Gly19Val)	LOC108281177, SOX2 +1 more (G19V)	Indel (missense variant)	not provided	GUncertain significance
Select item 2405567	NM_003106.4(SOX2):c.56G>T (p.Gly19Val)	LOC108281177, SOX2 +1 more (G19V)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 986765	NM_003106.4(SOX2):c.58GGC[5] (p.Gly23dup)	LOC108281177, SOX2 +1 more	Microsatellite (inframe_insertion)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 581870	NM_003106.4(SOX2):c.67_89dup (p.Gly31fs)	LOC108281177, SOX2 +1 more (G31fs)	Duplication (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 3242251	NM_003106.4(SOX2):c.67_89del (p.Gly23fs)	LOC108281177, SOX2 +1 more (G23fs)	Deletion (frameshift variant)	not provided	GPathogenic
Select item 1992360	NM_003106.4(SOX2):c.70_89dup (p.Gly31fs)	LOC108281177, SOX2 +1 more (G31fs)	Duplication (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GLikely pathogenic
Select item 986778	NM_003106.4(SOX2):c.58_59delinsT (p.Gly20fs)	LOC108281177, SOX2 +1 more (G20fs)	Indel (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 94104	NM_003106.4(SOX2):c.70_89del (p.Asn24fs)	LOC108281177, SOX2 +1 more (N24fs)	Deletion (frameshift variant)	not provided +2 more	GPathogenic
Select item 521127	NM_003106.4(SOX2):c.70_86del (p.Asn24fs)	LOC108281177, SOX2 +1 more (N24fs)	Deletion (frameshift variant)	not provided +1 more	GPathogenic
Select item 167717	NM_003106.4(SOX2):c.64G>A (p.Gly22Ser)	LOC108281177, SOX2 +1 more	Single nucleotide variant	Anophthalmia/microphthalmia-esophageal atresia syndrome +1 more	GConflicting classifications of pathogenicity
Select item 2739833	NM_003106.4(SOX2):c.68G>T (p.Gly23Val)	LOC108281177, SOX2 +1 more (G23V)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 2809030	NM_003106.4(SOX2):c.69C>G (p.Gly23=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 597989	NM_003106.4(SOX2):c.76A>G (p.Thr26Ala)	SOX2-OT, LOC108281177 +1 more (T26A)	Single nucleotide variant (missense variant)	not provided +1 more	GUncertain significance
Select item 2436256	NM_003106.4(SOX2):c.81GGC[4] (p.Ala30_Gly31insAla)	LOC108281177, SOX2 +1 more	Microsatellite (inframe_insertion)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 976481	NM_003106.4(SOX2):c.87_96dup (p.Asn33fs)	LOC108281177, SOX2 +1 more (N33fs)	Duplication (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 2693648	NM_003106.4(SOX2):c.81G>C (p.Ala27=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 1966260	NM_003106.4(SOX2):c.85G>A (p.Ala29Thr)	LOC108281177, SOX2 +1 more (A29T)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 1710348	NM_003106.4(SOX2):c.103_110dup (p.Ser37fs)	LOC108281177, SOX2 +1 more (S37fs)	Duplication (frameshift variant)	Microphthalmia	GPathogenic
Select item 930243	NM_003106.4(SOX2):c.100C>T (p.Gln34Ter)	LOC108281177, SOX2 +1 more (Q34*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 1350991	NM_003106.4(SOX2):c.113C>T (p.Pro38Leu)	LOC108281177, SOX2 +1 more (P38L)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 449939	NM_003106.4(SOX2):c.127C>T (p.Arg43Trp)	LOC108281177, SOX2 +1 more (R43W)	Single nucleotide variant (missense variant)	not provided	GLikely pathogenic
Select item 3337615	NM_003106.4(SOX2):c.131C>T (p.Pro44Leu)	LOC108281177, SOX2 +1 more (P44L)	Single nucleotide variant (missense variant)	not provided	GLikely pathogenic
Select item 986763	NM_003106.4(SOX2):c.131C>G (p.Pro44Arg)	LOC108281177, SOX2 +1 more (P44R)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 2446148	NM_003106.4(SOX2):c.133A>C (p.Met45Leu)	LOC108281177, SOX2 +1 more (M45L)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 12822	NM_003106.4(SOX2):c.138T>G (p.Asn46Lys)	LOC108281177, SOX2 +1 more (N46K)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 2844603	NM_003106.4(SOX2):c.142_144del (p.Phe48del)	LOC108281177, SOX2 +1 more (F48del)	Deletion (inframe_deletion)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 3062095	NM_003106.4(SOX2):c.142T>G (p.Phe48Val)	LOC108281177, SOX2 +1 more (F48V)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GLikely pathogenic
Select item 947562	NM_003106.4(SOX2):c.143T>C (p.Phe48Ser)	LOC108281177, SOX2 +1 more (F48S)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GLikely pathogenic
Select item 39804	NM_003106.4(SOX2):c.143_144delinsAA (p.Phe48Ter)	LOC108281177, SOX2 +1 more (F48*)	Indel (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 1337934	NM_003106.4(SOX2):c.150G>A (p.Val50=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	not specified +1 more	GLikely benign
Select item 1710347	NM_003106.4(SOX2):c.154T>C (p.Ser52Pro)	LOC108281177, SOX2 +1 more (S52P)	Single nucleotide variant (missense variant)	Chorioretinal coloboma	GLikely pathogenic
Select item 467821	NM_003106.4(SOX2):c.157dup (p.Arg53fs)	LOC108281177, SOX2 +1 more (R53fs)	Duplication (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 1344918	NM_003106.4(SOX2):c.156C>A (p.Ser52=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	not provided	GBenign
Select item 2577750	NM_003106.4(SOX2):c.160G>T (p.Gly54Trp)	LOC108281177, SOX2 +1 more (G54W)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 12820	NM_003106.4(SOX2):c.163C>T (p.Gln55Ter)	LOC108281177, SOX2 +1 more (Q55*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 986770	NM_003106.4(SOX2):c.166C>G (p.Arg56Gly)	LOC108281177, SOX2 +1 more (R56G)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 565623	NM_003106.4(SOX2):c.166C>T (p.Arg56Trp)	LOC108281177, SOX2 +1 more (R56W)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 1878615	NM_003106.4(SOX2):c.167G>C (p.Arg56Pro)	LOC108281177, SOX2 +1 more (R56P)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GUncertain significance
Select item 1184938	NM_003106.4(SOX2):c.170del (p.Arg57fs)	LOC108281177, SOX2 +1 more (R57fs)	Deletion (frameshift variant)	not provided	GPathogenic
Select item 1075154	NM_003106.4(SOX2):c.175del (p.Met59fs)	LOC108281177, SOX2 +1 more (M59fs)	Deletion (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 280092	NM_003106.4(SOX2):c.181C>T (p.Gln61Ter)	LOC108281177, SOX2 +1 more (Q61*)	Single nucleotide variant (nonsense)	not provided	GPathogenic
Select item 450122	NM_003106.4(SOX2):c.198dup (p.His67fs)	LOC108281177, SOX2 +1 more (H67fs)	Duplication (frameshift variant)	not provided	GPathogenic
Select item 2443521	NM_003106.4(SOX2):c.209A>G (p.Glu70Gly)	LOC108281177, SOX2 +1 more (E70G)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 3038104	NM_003106.4(SOX2):c.210G>A (p.Glu70=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	SOX2-related disorder	GLikely benign
Select item 12821	NM_003106.4(SOX2):c.221G>C (p.Arg74Pro)	LOC108281177, SOX2 +1 more (R74P)	Single nucleotide variant (missense variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 1683930	NM_003106.4(SOX2):c.227G>A (p.Gly76Asp)	LOC108281177, SOX2 +1 more (G76D)	Single nucleotide variant (missense variant)	not provided	GLikely pathogenic
Select item 705427	NM_003106.4(SOX2):c.231C>A (p.Ala77=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GBenign
Select item 2634342	NM_003106.4(SOX2):c.241C>T (p.Leu81Phe)	LOC108281177, SOX2 +1 more (L81F)	Single nucleotide variant (missense variant)	SOX2-related disorder	GUncertain significance
Select item 1709556	NM_003106.4(SOX2):c.241del (p.Leu81fs)	LOC108281177, SOX2 +1 more (L81fs)	Deletion (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GLikely pathogenic
Select item 467822	NM_003106.4(SOX2):c.244_245del (p.Leu82fs)	LOC108281177, SOX2 +1 more (L82fs)	Deletion (frameshift variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 516220	NM_003106.4(SOX2):c.243T>G (p.Leu81=)	LOC108281177, SOX2 +1 more	Single nucleotide variant (synonymous variant)	Anophthalmia/microphthalmia-esophageal atresia syndrome +2 more	GLikely benign
Select item 29891	NM_003106.4(SOX2):c.245T>A (p.Leu82Ter)	LOC108281177, SOX2 +1 more (L82*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 12816	NM_003106.4(SOX2):c.248C>A (p.Ser83Ter)	LOC108281177, SOX2 +1 more (S83*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 1300618	NM_003106.4(SOX2):c.254C>T (p.Thr85Met)	LOC108281177, SOX2 +1 more (T85M)	Single nucleotide variant (missense variant)	not provided	GLikely benign
Select item 1710324	NM_003106.4(SOX2):c.255_256delinsT (p.Glu86fs)	LOC108281177, SOX2 +1 more (E86fs)	Indel (frameshift variant)	Anophthalmia	GPathogenic
Select item 2762119	NM_003106.4(SOX2):c.256G>T (p.Glu86Ter)	LOC108281177, SOX2 +1 more (E86*)	Single nucleotide variant (nonsense)	Anophthalmia/microphthalmia-esophageal atresia syndrome	GPathogenic
Select item 3027253	NM_003106.4(SOX2):c.277G>C (p.Glu93Gln)	LOC108281177, SOX2 +1 more (E93Q)	Single nucleotide variant (missense variant)	not provided	GUncertain significance

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