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NM_153240.5(NPHP3):c.2154C>T (p.Phe718=) AND Nephronophthisis 3

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 2, 2021
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:
RCV001775105.1

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]
Observations:
1

Condition(s)

Name:
Nephronophthisis 3 (NPHP3)
Synonyms:
Adolescent nephronophthisis
Identifiers:
MONDO: MONDO:0011456; MedGen: C1858392; Orphanet: 655; OMIM: 604387

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV0020123283billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 2, 2021)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot provided1not providedclinical 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 3billion, SCV002012328.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Functional studies provide supportting evidence of the variant having a damaging effect on the gene or gene product (PMID: 30002499, PS3_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.00001061, PM2). The variant was observed in trans with a pathogenic variant (NM_153240.4:c.2694-2_2694-1del) as compound heterozygous (3billion dataset, PM3). In addition, It has been reported to co-segregate with the disease in at least one similarly affected relative/individual in the same family or similarly affected unrelated family (PMID: 30002499). The variant has been reported as pathogenic (ClinVar ID: VCV000262696.4).Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

Last Updated: Jul 15, 2024