U.S. flag

An official website of the United States government

NC_000003.12:g.(179547548_181649736)_(181808821_182152788)del AND Anophthalmia/microphthalmia-esophageal atresia syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 1, 2006
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000013667.26

Allele description [Variation Report for NC_000003.12:g.(179547548_181649736)_(181808821_182152788)del]

NC_000003.12:g.(179547548_181649736)_(181808821_182152788)del

Genes:
  • LOC129937985:ATAC-STARR-seq lymphoblastoid active region 20871 [Gene]
  • LOC129937986:ATAC-STARR-seq lymphoblastoid active region 20872 [Gene]
  • LOC129937987:ATAC-STARR-seq lymphoblastoid active region 20873 [Gene]
  • LOC129937990:ATAC-STARR-seq lymphoblastoid active region 20874 [Gene]
  • LOC129937991:ATAC-STARR-seq lymphoblastoid active region 20875 [Gene]
  • LOC129937993:ATAC-STARR-seq lymphoblastoid active region 20876 [Gene]
  • LOC129937994:ATAC-STARR-seq lymphoblastoid active region 20877 [Gene]
  • LOC129937996:ATAC-STARR-seq lymphoblastoid active region 20879 [Gene]
  • LOC129937982:ATAC-STARR-seq lymphoblastoid silent region 14920 [Gene]
  • LOC129937983:ATAC-STARR-seq lymphoblastoid silent region 14921 [Gene]
  • LOC129937984:ATAC-STARR-seq lymphoblastoid silent region 14922 [Gene]
  • LOC129937988:ATAC-STARR-seq lymphoblastoid silent region 14924 [Gene]
  • LOC129937989:ATAC-STARR-seq lymphoblastoid silent region 14925 [Gene]
  • LOC129937992:ATAC-STARR-seq lymphoblastoid silent region 14926 [Gene]
  • LOC129937995:ATAC-STARR-seq lymphoblastoid silent region 14927 [Gene]
  • LOC129937997:ATAC-STARR-seq lymphoblastoid silent region 14928 [Gene]
  • LOC126806882:BRD4-independent group 4 enhancer GRCh37_chr3:181077271-181078470 [Gene]
  • CCDC39-AS1:CCDC39 antisense RNA 1 [Gene - HGNC]
  • LOC126806881:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:181010183-181011382 [Gene]
  • DNAJC19:DnaJ heat shock protein family (Hsp40) member C19 [Gene - OMIM - HGNC]
  • FXR1:FMR1 autosomal homolog 1 [Gene - OMIM - HGNC]
  • LOC126806883:MED14-independent group 3 enhancer GRCh37_chr3:181252985-181254184 [Gene]
  • NDUFB5:NADH:ubiquinone oxidoreductase subunit B5 [Gene - OMIM - HGNC]
  • PEX5L-AS2:PEX5L antisense RNA 2 [Gene - HGNC]
  • LOC108281177:SOX2 5' regulatory region [Gene]
  • SOX2-OT:SOX2 overlapping transcript [Gene - OMIM - HGNC]
  • LOC108281178:SRR2 enhancer downstream of SOX2 [Gene]
  • SOX2:SRY-box transcription factor 2 [Gene - OMIM - HGNC]
  • LOC114004376:Sharpr-MPRA regulatory region 15084 [Gene]
  • LOC123256953:Sharpr-MPRA regulatory region 7561 [Gene]
  • LOC123256954:Sharpr-MPRA regulatory region 7910 [Gene]
  • LOC123256955:Sharpr-MPRA regulatory region 859 [Gene]
  • TTC14-DT:TTC14 divergent transcript [Gene - HGNC]
  • LOC110120606:VISTA enhancer hs192 [Gene]
  • LOC110120632:VISTA enhancer hs258 [Gene]
  • LOC110120734:VISTA enhancer hs655 [Gene]
  • ACTL6A:actin like 6A [Gene - OMIM - HGNC]
  • CCDC39:coiled-coil domain containing 39 [Gene - OMIM - HGNC]
  • LINC01206:long intergenic non-protein coding RNA 1206 [Gene - HGNC]
  • LINC02053:long intergenic non-protein coding RNA 2053 [Gene - HGNC]
  • MRPL47:mitochondrial ribosomal protein L47 [Gene - OMIM - HGNC]
  • PEX5L:peroxisomal biogenesis factor 5 like [Gene - OMIM - HGNC]
  • TTC14:tetratricopeptide repeat domain 14 [Gene - HGNC]
  • USP13:ubiquitin specific peptidase 13 [Gene - OMIM - HGNC]
  • LOC101928882:uncharacterized LOC101928882 [Gene]
  • LOC102724604:uncharacterized LOC102724604 [Gene]
Variant type:
Deletion
Cytogenetic location:
3q26.33
Genomic location:
Chr3: 179547548 - 182152788 (on Assembly GRCh38)
Preferred name:
NC_000003.12:g.(179547548_181649736)_(181808821_182152788)del
Other names:
SOX2, DEL
HGVS:
NC_000003.12:g.(179547548_181649736)_(181808821_182152788)del
Note:
NCBI staff provided an HGVS expression for allelic variant 184429.0006 based only on the deletion of SOX2, which was described as "2.7 Mb, extending from RP11-145M9 (AC007620) to RP11-296J4 (AC109131)" in the paper by Williamson et al., 2006 (PubMed 16543359). The translocation accompanying this deletion is not captured in the HGVS.
Nucleotide change:
DEL
Links:
OMIM: 184429.0006

Condition(s)

Name:
Anophthalmia/microphthalmia-esophageal atresia syndrome (MCOPS3)
Synonyms:
Microphthalmia syndromic 3; Microphthalmia and esophageal atresia syndrome; Anophthalmia clinical with associated anomalies; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008799; MedGen: C1859773; Orphanet: 77298; OMIM: 206900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000033914OMIM
no assertion criteria provided
Pathogenic
(May 1, 2006) 		germlineliterature only

PubMed (1)
[See all records that cite this PMID]

Rogers, R. C. Unknown cases: S.C.B. (GGC-10079) 11 month old white male. Proc. Greenwood Genet. Center 7: 57-only, 1988.

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations in SOX2 cause anophthalmia-esophageal-genital (AEG) syndrome.

Williamson KA, Hever AM, Rainger J, Rogers RC, Magee A, Fiedler Z, Keng WT, Sharkey FH, McGill N, Hill CJ, Schneider A, Messina M, Turnpenny PD, Fantes JA, van Heyningen V, FitzPatrick DR.

Hum Mol Genet. 2006 May 1;15(9):1413-22. Epub 2006 Mar 16. Erratum in: Hum Mol Genet. 2006 Jun 15;15(12):2030.

PubMed [citation]
PMID:
16543359

Details of each submission

From OMIM, SCV000033914.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a patient with bilateral clinical anophthalmia, esophageal atresia, and glanular hypospadias (MCOPS3; 206900), originally reported by Rogers (1988), Williamson et al. (2006) identified heterozygosity for a 2.7-Mb deletion encompassing the SOX2 gene, extending from RP11-145M9 to RP11-296J4 and associated with a cryptic translocation t(3,7)(q28;p21.3). The deletion and translocation breakpoints on chromosome 3q are more than 8.6 Mb apart, and both chromosomal rearrangements occurred de novo.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 14, 2023