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NM_000276.4(OCRL):c.739del (p.Trp247fs) AND Lowe syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 12, 2021
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:
RCV001420679.1

Allele description [Variation Report for NM_000276.4(OCRL):c.739del (p.Trp247fs)]

NM_000276.4(OCRL):c.739del (p.Trp247fs)

Gene:
OCRL:OCRL inositol polyphosphate-5-phosphatase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq26.1
Genomic location:
Preferred name:
NM_000276.4(OCRL):c.739del (p.Trp247fs)
HGVS:
  • NC_000023.11:g.129560566del
  • NG_008638.1:g.25292del
  • NM_000276.4:c.739delMANE SELECT
  • NM_001318784.2:c.742del
  • NM_001587.4:c.739del
  • NP_000267.2:p.Trp247fs
  • NP_001305713.1:p.Trp248fs
  • NP_001578.2:p.Trp247fs
  • NC_000023.10:g.128694543del
Protein change:
W247fs
Links:
dbSNP: rs2124404136
NCBI 1000 Genomes Browser:
rs2124404136
Molecular consequence:
  • NM_000276.4:c.739del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318784.2:c.742del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001587.4:c.739del - frameshift variant - [Sequence Ontology: SO:0001589]
Functional consequence:
effect on protein abundance [Variation Ontology: 0052]
Observations:
1

Condition(s)

Name:
Lowe syndrome (OCRL)
Synonyms:
Oculocerebrorenal Syndrome; Lowe oculocerebrorenal syndrome; Phosphatidylinositol 4,5-bisphosphate 5-phosphatase deficiency
Identifiers:
MONDO: MONDO:0010645; MedGen: C0028860; Orphanet: 534; OMIM: 309000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001596808Pediatrics Genetics, Post Graduate Institute of Medical Education and Research
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 12, 2021) 		inheritedclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
North Indianinheritedyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Pediatrics Genetics, Post Graduate Institute of Medical Education and Research, SCV001596808.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1North Indian1not providednot providedclinical testing PubMed (1)

Description

A hemizygous single base pair deletion in exon 9 of the OCRL gene (chrX:g.129560565del; Depth: 41x) that results in a frameshift and premature truncation of the protein 3 amino acids downstream to codon 247 (p.Trp247GlyfsTer3; ENST00000371113.9) was detected. This variant has not been reported in the 1000 genomes, gnomAD and our internal databases. The in silico prediction# of the variant is damaging by MutationTaster. The reference region is conserved across species.

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

Last Updated: Dec 24, 2023