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NM_014625.4(NPHS2):c.138_142dup (p.Ser48fs) AND Nephrotic syndrome, type 2

Germline classification:
Likely pathogenic (3 submissions)
Last evaluated:
Apr 11, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000411511.4

Allele description [Variation Report for NM_014625.4(NPHS2):c.138_142dup (p.Ser48fs)]

NM_014625.4(NPHS2):c.138_142dup (p.Ser48fs)

Gene:
NPHS2:NPHS2 stomatin family member, podocin [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
1q25.2
Genomic location:
Preferred name:
NM_014625.4(NPHS2):c.138_142dup (p.Ser48fs)
HGVS:
  • NC_000001.11:g.179575723_179575727dup
  • NG_007535.1:g.5223_5227dup
  • NM_001297575.2:c.138_142dup
  • NM_014625.4:c.138_142dupMANE SELECT
  • NP_001284504.1:p.Ser48fs
  • NP_055440.1:p.Ser48fs
  • LRG_887:g.5223_5227dup
  • NC_000001.10:g.179544858_179544862dup
  • NM_014625.2:c.138_142dup5
  • NM_014625.2:c.138_142dupGGGCT
  • p.Ser48TrpfsX53
Protein change:
S48fs
Links:
dbSNP: rs1057516747
NCBI 1000 Genomes Browser:
rs1057516747
Molecular consequence:
  • NM_001297575.2:c.138_142dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_014625.4:c.138_142dup - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Nephrotic syndrome, type 2 (NPHS2)
Synonyms:
Nephrotic syndrome, steroid-resistant, autosomal recessive; Hereditary nephrotic syndrome
Identifiers:
MONDO: MONDO:0010974; MedGen: C1868672; Orphanet: 656; OMIM: 600995

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000486154Counsyl
criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))
Likely pathogenic
(Apr 6, 2016)
unknownclinical testing

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

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV001142713Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jun 26, 2019)
germlineclinical testing

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

SCV004049300Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Apr 11, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

NPHS2 mutations in steroid-resistant nephrotic syndrome: a mutation update and the associated phenotypic spectrum.

Bouchireb K, Boyer O, Gribouval O, Nevo F, Huynh-Cong E, Morinière V, Campait R, Ars E, Brackman D, Dantal J, Eckart P, Gigante M, Lipska BS, Liutkus A, Megarbane A, Mohsin N, Ozaltin F, Saleem MA, Schaefer F, Soulami K, Torra R, Garcelon N, et al.

Hum Mutat. 2014 Feb;35(2):178-86. doi: 10.1002/humu.22485. Epub 2013 Dec 9. Review.

PubMed [citation]
PMID:
24227627

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 Counsyl, SCV000486154.2

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

From Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota, SCV001142713.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Genome-Nilou Lab, SCV004049300.1

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

Last Updated: Mar 30, 2024