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NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr) AND Kidney disorder

Germline classification:
Likely benign (1 submission)
Last evaluated:
Dec 12, 2016
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:
RCV002294022.9

Allele description [Variation Report for NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr)]

NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr)

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.154G>A (p.Ala52Thr)
HGVS:
  • NC_000003.12:g.132722202C>T
  • NG_008130.2:g.5231G>A
  • NM_153240.5:c.154G>AMANE SELECT
  • NP_694972.3:p.Ala52Thr
  • NC_000003.11:g.132441046C>T
  • NG_008130.1:g.5231G>A
  • NM_153240.4:c.154G>A
  • NR_002811.2:n.453C>T
  • NR_037804.1:n.258G>A
  • NR_152743.1:n.453C>T
Protein change:
A52T
Links:
dbSNP: rs145643112
NCBI 1000 Genomes Browser:
rs145643112
Molecular consequence:
  • NM_153240.5:c.154G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_002811.2:n.453C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_037804.1:n.258G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_152743.1:n.453C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Kidney disorder
Synonyms:
Nephropathy; Kidney disease; Kidney Diseases
Identifiers:
MONDO: MONDO:0005240; MedGen: C0022658; Human Phenotype Ontology: HP:0000112

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002587214Genome Diagnostics Laboratory, The Hospital for Sick Children
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Dec 12, 2016) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 Genome Diagnostics Laboratory, The Hospital for Sick Children, SCV002587214.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024