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NM_014625.4(NPHS2):c.452del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 13, 2023
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:
RCV001859229.3

Allele description [Variation Report for NM_014625.4(NPHS2):c.452del]

NM_014625.4(NPHS2):c.452del

Gene:
NPHS2:NPHS2 stomatin family member, podocin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q25.2
Genomic location:
Preferred name:
NM_014625.4(NPHS2):c.452del
HGVS:
  • NC_000001.11:g.179559762del
  • NG_007535.1:g.21189del
  • NM_014625.4:c.452delMANE SELECT
  • LRG_887t1:c.452del
  • LRG_887:g.21189del
  • NC_000001.10:g.179528896del
  • NC_000001.10:g.179528897del
  • NM_014625.3:c.452delG
Links:
dbSNP: rs1250670041
NCBI 1000 Genomes Browser:
rs1250670041
Molecular consequence:
  • NM_014625.4:c.452del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002234325Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 13, 2023) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome.

Boute N, Gribouval O, Roselli S, Benessy F, Lee H, Fuchshuber A, Dahan K, Gubler MC, Niaudet P, Antignac C.

Nat Genet. 2000 Apr;24(4):349-54. Erratum in: Nat Genet 2000 May;25(1):125.

PubMed [citation]
PMID:
10742096

Early glomerular filtration defect and severe renal disease in podocin-deficient mice.

Roselli S, Heidet L, Sich M, Henger A, Kretzler M, Gubler MC, Antignac C.

Mol Cell Biol. 2004 Jan;24(2):550-60.

PubMed [citation]
PMID:
14701729
PMCID:
PMC343810
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV002234325.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Gly151Valfs*30) in the NPHS2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHS2 are known to be pathogenic (PMID: 10742096, 14701729, 15253708, 23595123). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with NPHS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 996286). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Mar 30, 2024