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NM_153240.5(NPHP3):c.406del (p.Thr136fs) AND Nephronophthisis

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 15, 2022
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:
RCV001228010.7

Allele description [Variation Report for NM_153240.5(NPHP3):c.406del (p.Thr136fs)]

NM_153240.5(NPHP3):c.406del (p.Thr136fs)

Genes:
NPHP3-ACAD11:NPHP3-ACAD11 readthrough (NMD candidate) [Gene - HGNC]
NPHP3:nephrocystin 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3q22.1
Genomic location:
Preferred name:
NM_153240.5(NPHP3):c.406del (p.Thr136fs)
HGVS:
  • NC_000003.12:g.132719823del
  • NG_008130.2:g.7615del
  • NM_153240.4:c.406delA
  • NM_153240.5:c.406delMANE SELECT
  • NP_694972.3:p.Thr136fs
  • NC_000003.11:g.132438662del
  • NC_000003.11:g.132438667del
  • NG_008130.1:g.7615del
  • NM_153240.4:c.406del
  • NR_037804.1:n.510del
Protein change:
T136fs
Links:
dbSNP: rs1379989124
NCBI 1000 Genomes Browser:
rs1379989124
Molecular consequence:
  • NM_153240.5:c.406del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_037804.1:n.510del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001400391Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Nov 15, 2022)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing.

Halbritter J, Diaz K, Chaki M, Porath JD, Tarrier B, Fu C, Innis JL, Allen SJ, Lyons RH, Stefanidis CJ, Omran H, Soliman NA, Otto EA.

J Med Genet. 2012 Dec;49(12):756-67. doi: 10.1136/jmedgenet-2012-100973.

PubMed [citation]
PMID:
23188109

Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia.

Bergmann C, Fliegauf M, Brüchle NO, Frank V, Olbrich H, Kirschner J, Schermer B, Schmedding I, Kispert A, Kränzlin B, Nürnberg G, Becker C, Grimm T, Girschick G, Lynch SA, Kelehan P, Senderek J, Neuhaus TJ, Stallmach T, Zentgraf H, Nürnberg P, Gretz N, et al.

Am J Hum Genet. 2008 Apr;82(4):959-70. doi: 10.1016/j.ajhg.2008.02.017. Epub 2008 Mar 27.

PubMed [citation]
PMID:
18371931
PMCID:
PMC2427297
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001400391.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 598394). This premature translational stop signal has been observed in individual(s) with nephronophthisis (PMID: 23188109). This variant is present in population databases (no rsID available, gnomAD 0.004%). This sequence change creates a premature translational stop signal (p.Thr136Argfs*13) in the NPHP3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHP3 are known to be pathogenic (PMID: 18371931, 23559409).

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

Last Updated: Jul 15, 2024