NM_003106.4(SOX2):c.181C>T (p.Gln61Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 15, 2016
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000265106.1

Allele description [Variation Report for NM_003106.4(SOX2):c.181C>T (p.Gln61Ter)]

NM_003106.4(SOX2):c.181C>T (p.Gln61Ter)

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.181C>T (p.Gln61Ter)

HGVS:

NC_000003.12:g.181712541C>T
NG_009080.1:g.5608C>T
NM_003106.4:c.181C>TMANE SELECT
NP_003097.1:p.Gln61Ter
LRG_719:g.5608C>T
NC_000003.11:g.181430329C>T
NM_003106.3:c.181C>T

Protein change:

Q61*

Links:

dbSNP: rs886041378

NCBI 1000 Genomes Browser:

rs886041378

Molecular consequence:

NM_003106.4:c.181C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000329898	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 15, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000329898

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 15, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000329898.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The Q61X pathogenic variant in the SOX2 gene has been reported previously in association with anophthalmia and pituitary anomalies including hypogonadotropic hypogonadism (Ragge et al., 2013; Kelberman et al., 2008). This variant is predicted to cause loss of normal protein function through protein truncation, and in vitro studies demonstrate that the Q61X variant results in complete loss of transciptional DNA binding and protein mislocalization (Kelberman et al., 2008). The Q61X variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret Q61X as a pathogenic variant.

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

Last Updated: Mar 26, 2023

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