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NM_014625.4(NPHS2):c.855_856del (p.Arg286fs) AND NPHS2-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 20, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003398864.6

Allele description [Variation Report for NM_014625.4(NPHS2):c.855_856del (p.Arg286fs)]

NM_014625.4(NPHS2):c.855_856del (p.Arg286fs)

Genes:
NPHS2:NPHS2 stomatin family member, podocin [Gene - OMIM - HGNC]
AXDND1:axonemal dynein light chain domain containing 1 [Gene - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q25.2
Genomic location:
Preferred name:
NM_014625.4(NPHS2):c.855_856del (p.Arg286fs)
HGVS:
  • NC_000001.11:g.179552621_179552622del
  • NG_007535.1:g.28329_28330del
  • NG_033075.1:g.191902_191903del
  • NM_001297575.2:c.651_652del
  • NM_014625.4:c.855_856delMANE SELECT
  • NM_144696.6:c.3032-1891_3032-1890delMANE SELECT
  • NP_001284504.1:p.Arg218fs
  • NP_055440.1:p.Arg286Thrfs
  • NP_055440.1:p.Arg286fs
  • NP_055440.1:p.Arg286fs
  • LRG_887t1:c.855_856del
  • LRG_887:g.28329_28330del
  • LRG_887p1:p.Arg286fs
  • NC_000001.10:g.179521755_179521756del
  • NC_000001.10:g.179521756_179521757del
  • NM_014625.2:c.855_856del
  • NM_014625.2:c.855_856delAA
  • NM_014625.3:c.854_855delAA
  • NM_014625.3:c.855_856del
  • NM_014625.3:c.855_856delAA
  • p.Q285fs
Protein change:
R218fs
Links:
OMIM: 604766.0005; dbSNP: rs749740335
NCBI 1000 Genomes Browser:
rs749740335
Molecular consequence:
  • NM_001297575.2:c.651_652del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_014625.4:c.855_856del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_144696.6:c.3032-1891_3032-1890del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
NPHS2-related disorder
Synonyms:
NPHS2-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004104805PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jun 20, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004104805.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The NPHS2 c.855_856delAA variant is predicted to result in a frameshift and premature protein termination (p.Arg286Thrfs*17). Also known as Q285fsX302 or R285fx302X, this variant has been reported to be pathogenic for steroid-resistant nephrotic syndrome (SRNS) (Boute et al. 2000. PubMed ID: 10742096; Machuca et al. 2009. PubMed ID: 19145239; Santín et al. 2011. PubMed ID: 20947785). This variant is reported in 0.016% of alleles in individuals of European (non-Finnish) descent in gnomAD. Frameshift variants in NPHS2 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Jan 13, 2025