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NM_153240.5(NPHP3):c.3756C>G (p.Ser1252Arg) AND NPHP3-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 7, 2024
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:
RCV004537410.1

Allele description [Variation Report for NM_153240.5(NPHP3):c.3756C>G (p.Ser1252Arg)]

NM_153240.5(NPHP3):c.3756C>G (p.Ser1252Arg)

Genes:
NPHP3-ACAD11:NPHP3-ACAD11 readthrough (NMD candidate) [Gene - HGNC]
NPHP3:nephrocystin 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q22.1
Genomic location:
Preferred name:
NM_153240.5(NPHP3):c.3756C>G (p.Ser1252Arg)
HGVS:
  • NC_000003.12:g.132682759G>C
  • NG_008130.2:g.44674C>G
  • NM_153240.5:c.3756C>GMANE SELECT
  • NP_694972.3:p.Ser1252Arg
  • NC_000003.11:g.132401603G>C
  • NG_008130.1:g.44674C>G
  • NM_153240.4:c.3756C>G
  • NR_037804.1:n.3762C>G
  • Q7Z494:p.Ser1252Arg
Protein change:
S1252R
Links:
UniProtKB: Q7Z494#VAR_022820; dbSNP: rs143451766
NCBI 1000 Genomes Browser:
rs143451766
Molecular consequence:
  • NM_153240.5:c.3756C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_037804.1:n.3762C>G - 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
SCV004115053PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Feb 7, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 PreventionGenetics, part of Exact Sciences, SCV004115053.2

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

Description

The NPHP3 c.3756C>G variant is predicted to result in the amino acid substitution p.Ser1252Arg. This variant was reported in one family with nephronophthisis 3 and a second variant in NPHP3 was not identified (Family F50, Olbrich et al 2003. PubMed ID: 12872122). This variant is reported in 0.12% of alleles in individuals of European (Non-Finnish) descent in gnomAD, including one homozygous individual, which may be too frequent to be a disease causing variant. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Jul 7, 2024