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NM_153240.5(NPHP3):c.2154C>T (p.Phe718=) AND Nephronophthisis

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 13, 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:
RCV001079754.7

Allele description [Variation Report for NM_153240.5(NPHP3):c.2154C>T (p.Phe718=)]

NM_153240.5(NPHP3):c.2154C>T (p.Phe718=)

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.2154C>T (p.Phe718=)
HGVS:
  • NC_000003.12:g.132696748G>A
  • NG_008130.2:g.30685C>T
  • NM_153240.5:c.2154C>TMANE SELECT
  • NP_694972.3:p.Phe718=
  • NC_000003.11:g.132415592G>A
  • NG_008130.1:g.30685C>T
  • NM_153240.4:c.2154C>T
  • NR_037804.1:n.2160C>T
Links:
dbSNP: rs558637226
NCBI 1000 Genomes Browser:
rs558637226
Molecular consequence:
  • NR_037804.1:n.2160C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_153240.5:c.2154C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Nephronophthisis
Synonyms:
juvenile nephronophthisis
Identifiers:
MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001009497Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jun 13, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Human urine-derived renal epithelial cells provide insights into kidney-specific alternate splicing variants.

Molinari E, Decker E, Mabillard H, Tellez J, Srivastava S, Raman S, Wood K, Kempf C, Alkanderi S, Ramsbottom SA, Miles CG, Johnson CA, Hildebrandt F, Bergmann C, Sayer JA.

Eur J Hum Genet. 2018 Dec;26(12):1791-1796. doi: 10.1038/s41431-018-0212-5. Epub 2018 Jul 12.

PubMed [citation]
PMID:
30002499
PMCID:
PMC6244279

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001009497.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 262696). This variant has been observed in individual(s) with clinical features of nephronophthisis (PMID: 30002499; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs558637226, gnomAD 0.005%). This sequence change affects codon 718 of the NPHP3 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the NPHP3 protein.

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

Last Updated: Jun 17, 2024