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NM_153240.5(NPHP3):c.3287T>C (p.Leu1096Pro) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Apr 16, 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:
RCV000681679.3

Allele description [Variation Report for NM_153240.5(NPHP3):c.3287T>C (p.Leu1096Pro)]

NM_153240.5(NPHP3):c.3287T>C (p.Leu1096Pro)

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.3287T>C (p.Leu1096Pro)
HGVS:
  • NC_000003.12:g.132686302A>G
  • NG_008130.2:g.41131T>C
  • NM_153240.5:c.3287T>CMANE SELECT
  • NP_694972.3:p.Leu1096Pro
  • NC_000003.11:g.132405146A>G
  • NG_008130.1:g.41131T>C
  • NR_037804.1:n.3293T>C
Protein change:
L1096P
Links:
dbSNP: rs777276873
NCBI 1000 Genomes Browser:
rs777276873
Molecular consequence:
  • NM_153240.5:c.3287T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_037804.1:n.3293T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000809126Gharavi Laboratory, Columbia University
no assertion criteria provided

(ACMG Guidelines, 2015)
Likely pathogenic
(Sep 16, 2018)
germlineresearch

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

SCV002003816GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Apr 16, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing, research

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 Gharavi Laboratory, Columbia University, SCV000809126.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV002003816.2

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31589614)

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

Last Updated: Mar 4, 2023