NM_153240.5(NPHP3):c.2369T>C (p.Leu790Pro) AND NPHP3-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 8, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004528299.2

Allele description [Variation Report for NM_153240.5(NPHP3):c.2369T>C (p.Leu790Pro)]

NM_153240.5(NPHP3):c.2369T>C (p.Leu790Pro)

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.2369T>C (p.Leu790Pro)
HGVS:
  • NC_000003.12:g.132692760A>G
  • NG_008130.2:g.34673T>C
  • NM_153240.5:c.2369T>CMANE SELECT
  • NP_694972.3:p.Leu790Pro
  • NP_694972.3:p.Leu790Pro
  • NC_000003.11:g.132411604A>G
  • NG_008130.1:g.34673T>C
  • NM_153240.4:c.2369T>C
  • NR_037804.1:n.2375T>C
Protein change:
L790P
Links:
dbSNP: rs398124546
NCBI 1000 Genomes Browser:
rs398124546
Molecular consequence:
  • NM_153240.5:c.2369T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_037804.1:n.2375T>C - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004104122PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(May 8, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004104122.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The NPHP3 c.2369T>C variant is predicted to result in the amino acid substitution p.Leu790Pro. This variant has been reported in the compound heterozygous state in multiple individuals with nephronophthisis-related ciliopathies (Table 2, Halbritter et al. 2013. PubMed ID: 23559409; Table S2, Chen et al. 2021. PubMed ID: 34031707; Table 1, Sun et al. 2016. PubMed ID: 26184788). This variant has also been reported in the compound heterozygous state in multiple individuals with early onset end stage renal disease (Table 1, Tang et al. 2020. PubMed ID: 33323469). This variant is reported in 0.027% of alleles in individuals of East Asian descent in gnomAD. This variant is interpreted as likely pathogenic.

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

Last Updated: Nov 10, 2024