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NM_002547.3(OPHN1):c.1224C>A (p.Tyr408Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 6, 2022
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:
RCV003845720.1

Allele description [Variation Report for NM_002547.3(OPHN1):c.1224C>A (p.Tyr408Ter)]

NM_002547.3(OPHN1):c.1224C>A (p.Tyr408Ter)

Gene:
OPHN1:oligophrenin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq12
Genomic location:
Preferred name:
NM_002547.3(OPHN1):c.1224C>A (p.Tyr408Ter)
HGVS:
  • NC_000023.11:g.68192971G>T
  • NG_008960.1:g.245487C>A
  • NM_002547.3:c.1224C>AMANE SELECT
  • NP_002538.1:p.Tyr408Ter
  • NC_000023.10:g.67412813G>T
Protein change:
Y408*
Molecular consequence:
  • NM_002547.3:c.1224C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004643783Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 6, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in the oligophrenin-1 gene (OPHN1) cause X linked congenital cerebellar hypoplasia.

Philip N, Chabrol B, Lossi AM, Cardoso C, Guerrini R, Dobyns WB, Raybaud C, Villard L.

J Med Genet. 2003 Jun;40(6):441-6. No abstract available.

PubMed [citation]
PMID:
12807966
PMCID:
PMC1735502

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004643783.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with OPHN1-related conditions. This sequence change creates a premature translational stop signal (p.Tyr408*) in the OPHN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in OPHN1 are known to be pathogenic (PMID: 12807966).

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

Last Updated: Mar 5, 2024