NM_153240.5(NPHP3):c.155C>T (p.Ala52Val) AND NPHP3-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 4, 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:: RCV004741182.1

Allele description [Variation Report for NM_153240.5(NPHP3):c.155C>T (p.Ala52Val)]

NM_153240.5(NPHP3):c.155C>T (p.Ala52Val)

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.155C>T (p.Ala52Val)

HGVS:

NC_000003.12:g.132722201G>A
NG_008130.2:g.5232C>T
NM_153240.5:c.155C>TMANE SELECT
NP_694972.3:p.Ala52Val
NC_000003.11:g.132441045G>A
NM_153240.4:c.155C>T
NR_002811.2:n.452G>A
NR_037804.1:n.259C>T
NR_152743.1:n.452G>A

Protein change:

A52V

Links:

dbSNP: rs747055547

NCBI 1000 Genomes Browser:

rs747055547

Molecular consequence:

NM_153240.5:c.155C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_002811.2:n.452G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_037804.1:n.259C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_152743.1:n.452G>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
SCV005347993	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Uncertain significance (Sep 4, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005347993

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Uncertain significance
(Sep 4, 2024)

germline

clinical testing

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005347993.1

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

Description

The NPHP3 c.155C>T variant is predicted to result in the amino acid substitution p.Ala52Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0% of alleles in individuals of African descent in gnomAD. 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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