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NM_153240.5(NPHP3):c.3189A>G (p.Lys1063=) AND Nephronophthisis

Germline classification:
Benign (1 submission)
Last evaluated:
Jan 30, 2024
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:
RCV000549033.8

Allele description [Variation Report for NM_153240.5(NPHP3):c.3189A>G (p.Lys1063=)]

NM_153240.5(NPHP3):c.3189A>G (p.Lys1063=)

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.3189A>G (p.Lys1063=)
HGVS:
  • NC_000003.12:g.132687163T>C
  • NG_008130.2:g.40270A>G
  • NM_153240.5:c.3189A>GMANE SELECT
  • NP_694972.3:p.Lys1063=
  • NC_000003.11:g.132406007T>C
  • NG_008130.1:g.40270A>G
  • NM_153240.4:c.3189A>G
  • NR_037804.1:n.3195A>G
Links:
dbSNP: rs112386774
NCBI 1000 Genomes Browser:
rs112386774
Molecular consequence:
  • NR_037804.1:n.3195A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_153240.5:c.3189A>G - 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
SCV000636159Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jan 30, 2024)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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, SCV000636159.6

#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: Mar 10, 2024