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NM_153240.5(NPHP3):c.2851C>T (p.Arg951Ter) AND NPHP3-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 5, 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:
RCV004528417.2

Allele description [Variation Report for NM_153240.5(NPHP3):c.2851C>T (p.Arg951Ter)]

NM_153240.5(NPHP3):c.2851C>T (p.Arg951Ter)

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.2851C>T (p.Arg951Ter)
HGVS:
  • NC_000003.12:g.132689106G>A
  • NG_008130.2:g.38327C>T
  • NM_153240.5:c.2851C>TMANE SELECT
  • NP_694972.3:p.Arg951Ter
  • NC_000003.11:g.132407950G>A
  • NG_008130.1:g.38327C>T
  • NM_153240.4:c.2851C>T
  • NR_037804.1:n.2857C>T
Protein change:
R951*
Links:
dbSNP: rs148670389
NCBI 1000 Genomes Browser:
rs148670389
Molecular consequence:
  • NR_037804.1:n.2857C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_153240.5:c.2851C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004106016PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(Jan 5, 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, SCV004106016.3

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

Description

The NPHP3 c.2851C>T variant is predicted to result in premature protein termination (p.Arg951*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD. Nonsense variants in NPHP3 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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

Last Updated: Nov 3, 2024