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NM_002547.3(OPHN1):c.2062G>T (p.Ala688Ser) AND History of neurodevelopmental disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 28, 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:
RCV000719205.1

Allele description

NM_002547.3(OPHN1):c.2062G>T (p.Ala688Ser)

Gene:
OPHN1:oligophrenin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq12
Genomic location:
Preferred name:
NM_002547.3(OPHN1):c.2062G>T (p.Ala688Ser)
HGVS:
  • NC_000023.11:g.68063950C>A
  • NG_008960.1:g.374508G>T
  • NM_002547.3:c.2062G>TMANE SELECT
  • NP_002538.1:p.Ala688Ser
  • NC_000023.10:g.67283792C>A
  • NM_002547.2:c.2062G>T
Protein change:
A688S
Links:
dbSNP: rs199985543
NCBI 1000 Genomes Browser:
rs199985543
Molecular consequence:
  • NM_002547.3:c.2062G>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
History of neurodevelopmental disorder
Identifiers:
MedGen: C2711754

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000850071Ambry Genetics
criteria provided, single submitter

(Ambry Autosomal Dominant and X-Linked criteria (10/2015))		Uncertain significance
(Jun 28, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Ambry Genetics, SCV000850071.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The p.A688S variant (also known as c.2062G>T), located in coding exon 20 of the OPHN1 gene, results from a G to T substitution at nucleotide position 2062. The alanine at codon 688 is replaced by serine, an amino acid with similar properties. This variant was previously reported in the SNPDatabase as rs199985543. Based on data from the NHLBI Exome Sequencing Project (ESP), the T allele has an overall frequency of approximately 0.04% (1/2443) total male alleles studied and 0.05% (1/1872) European American male alleles. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Aug 23, 2022