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NM_153240.5(NPHP3):c.2805C>T (p.Gly935=) AND NPHP3-related disorder

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003336373.1

Allele description [Variation Report for NM_153240.5(NPHP3):c.2805C>T (p.Gly935=)]

NM_153240.5(NPHP3):c.2805C>T (p.Gly935=)

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.2805C>T (p.Gly935=)
HGVS:
  • NC_000003.12:g.132689152G>A
  • NG_008130.2:g.38281C>T
  • NM_153240.5:c.2805C>TMANE SELECT
  • NP_694972.3:p.Gly935=
  • NC_000003.11:g.132407996G>A
  • NG_008130.1:g.38281C>T
  • NM_153240.4:c.2805C>T
  • NR_037804.1:n.2811C>T
Links:
dbSNP: rs1281725083
NCBI 1000 Genomes Browser:
rs1281725083
Molecular consequence:
  • NR_037804.1:n.2811C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_153240.5:c.2805C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Functional consequence:
effect on RNA splicing [Variation Ontology: 0362]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004046219Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot 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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV004046219.1

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

Description

This synonymous variant affects exon 20 of 27 and is predicted to activate a cryptic splice donor site mid exon 20. This variant has been previously reported as a homozygous change in six affected individuals from five families (PMID: 34212438). The c.2805C>T (p.Gly935=) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.001% (2/251374) and thus is presumed to be rare. Based on the available evidence, the c.2805C>T (p.Gly935=) variant is classified as Likely Pathogenic.

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

Last Updated: Sep 29, 2024