NM_153240.5(NPHP3):c.116G>T (p.Arg39Leu) AND NPHP3-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 14, 2023
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:: RCV004531075.1

Allele description [Variation Report for NM_153240.5(NPHP3):c.116G>T (p.Arg39Leu)]

NM_153240.5(NPHP3):c.116G>T (p.Arg39Leu)

Genes:

LOC129937586:ATAC-STARR-seq lymphoblastoid silent region 14743 [Gene]
NPHP3-AS1:NPHP3 antisense RNA 1 [Gene - HGNC]
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.116G>T (p.Arg39Leu)

HGVS:

NC_000003.12:g.132722240C>A
NG_008130.2:g.5193G>T
NM_153240.5:c.116G>TMANE SELECT
NP_694972.3:p.Arg39Leu
NC_000003.11:g.132441084C>A
NG_008130.1:g.5193G>T
NM_153240.4:c.116G>T
NR_002811.2:n.491C>A
NR_037804.1:n.220G>T
NR_152743.1:n.491C>A

Protein change:

R39L

Links:

dbSNP: rs753467164

NCBI 1000 Genomes Browser:

rs753467164

Molecular consequence:

NM_153240.5:c.116G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_002811.2:n.491C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_037804.1:n.220G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_152743.1:n.491C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: NPHP3-related disorder
Synonyms:: NPHP3-related disorders; NPHP3-related condition
Identifiers:: MedGen: CN379163

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004114253	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 14, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004114253

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 14, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV004114253.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The NPHP3 c.116G>T variant is predicted to result in the amino acid substitution p.Arg39Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.021% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-132441084-C-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2025

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