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

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 16, 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:
RCV001854072.2

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:
Nephronophthisis
Synonyms:
juvenile nephronophthisis
Identifiers:
MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002230435Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Aug 16, 2022)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia.

Bergmann C, Fliegauf M, Brüchle NO, Frank V, Olbrich H, Kirschner J, Schermer B, Schmedding I, Kispert A, Kränzlin B, Nürnberg G, Becker C, Grimm T, Girschick G, Lynch SA, Kelehan P, Senderek J, Neuhaus TJ, Stallmach T, Zentgraf H, Nürnberg P, Gretz N, et al.

Am J Hum Genet. 2008 Apr;82(4):959-70. doi: 10.1016/j.ajhg.2008.02.017. Epub 2008 Mar 27.

PubMed [citation]
PMID:
18371931
PMCID:
PMC2427297

Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy.

Halbritter J, Porath JD, Diaz KA, Braun DA, Kohl S, Chaki M, Allen SJ, Soliman NA, Hildebrandt F, Otto EA; GPN Study Group..

Hum Genet. 2013 Aug;132(8):865-84. doi: 10.1007/s00439-013-1297-0. Epub 2013 Apr 5.

PubMed [citation]
PMID:
23559409
PMCID:
PMC4643834
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002230435.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Glu212Glyfs*3) in the NPHP3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHP3 are known to be pathogenic (PMID: 18371931, 23559409). This variant is present in population databases (rs747052534, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 500889). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: May 12, 2024