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NM_153240.5(NPHP3):c.634dup (p.Glu212fs) AND NPHP3-related disorder

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003336089.1

Allele description [Variation Report for NM_153240.5(NPHP3):c.634dup (p.Glu212fs)]

NM_153240.5(NPHP3):c.634dup (p.Glu212fs)

Genes:
NPHP3-ACAD11:NPHP3-ACAD11 readthrough (NMD candidate) [Gene - HGNC]
NPHP3:nephrocystin 3 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
3q22.1
Genomic location:
Preferred name:
NM_153240.5(NPHP3):c.634dup (p.Glu212fs)
HGVS:
  • NC_000003.12:g.132719033dup
  • NG_008130.2:g.8403dup
  • NM_153240.5:c.634dupMANE SELECT
  • NP_694972.3:p.Glu212fs
  • NC_000003.11:g.132437873_132437874insC
  • NC_000003.11:g.132437877dup
  • NG_008130.1:g.8403dup
  • NM_153240.4:c.634dup
  • NR_037804.1:n.738dup
Protein change:
E212fs
Links:
dbSNP: rs747052534
NCBI 1000 Genomes Browser:
rs747052534
Molecular consequence:
  • NM_153240.5:c.634dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_037804.1:n.738dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
NPHP3-related disorder
Synonyms:
NPHP3-related disorders; NPHP3-related condition
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004046109Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot 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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV004046109.1

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

Description

This frameshifting variant in exon 3 of 27 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has not been previously reported or functionally characterized in the literature to our knowledge. Loss-of-function variants have been reported in individuals with NPHP3-related disorders (PMID: 32596782). The c.634dup (p.Glu212GlyfsTer3) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.001% (2/251454) and thus is presumed to be rare. Based on the available evidence, the c.634dup (p.Glu212GlyfsTer3) variant is classified as Likely Pathogenic.

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

Last Updated: May 12, 2024