NM_003106.4(SOX2):c.163C>T (p.Gln55Ter) 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:: RCV000013668.23

Allele description [Variation Report for NM_003106.4(SOX2):c.163C>T (p.Gln55Ter)]

NM_003106.4(SOX2):c.163C>T (p.Gln55Ter)

Genes:

LOC108281177:SOX2 5' regulatory region [Gene]
SOX2-OT:SOX2 overlapping transcript [Gene - OMIM - HGNC]
SOX2:SRY-box transcription factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q26.33

Genomic location:

Preferred name:

NM_003106.4(SOX2):c.163C>T (p.Gln55Ter)

HGVS:

NC_000003.12:g.181712523C>T
NG_009080.1:g.5590C>T
NM_003106.4:c.163C>TMANE SELECT
NP_003097.1:p.Gln55Ter
LRG_719:g.5590C>T
NC_000003.11:g.181430311C>T

Protein change:

Q55*; GLN55TER

Links:

OMIM: 184429.0007; dbSNP: rs104893804

NCBI 1000 Genomes Browser:

rs104893804

Molecular consequence:

NM_003106.4:c.163C>T - nonsense - [Sequence Ontology: SO:0001587]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000033915	OMIM	no assertion criteria provided	Pathogenic (May 1, 2006)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 15346919, 16543359

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000033915

OMIM

no assertion criteria provided

Pathogenic
(May 1, 2006)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Association of oesophageal atresia, anophthalmia and renal duplex.

Petrackova I, Pozler O, Kokstein Z, Zizka J, Dedkova J, Rejtar P, Fiedler Z, Kuliacek P.

Eur J Pediatr. 2004 Jun;163(6):333-4. No abstract available.

PubMed [citation]

PMID:: 15346919

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, SCV000033915.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

In a male infant with bilateral clinical anophthalmia, esophageal atresia, duplication of the left kidney, and significant psychomotor delay (MCOPS3; 206900), originally reported by Petrackova et al. (2004), Williamson et al. (2006) identified heterozygosity for a 163C-T transition in the SOX2 gene, resulting in a gln55-to-ter (Q55X) substitution with production of a protein truncated within the HMG domain and therefore with no DNA-binding or transactivation activity. The mutation was not found in either parent.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 26, 2023

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