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NM_004646.4(NPHS1):c.794G>C (p.Cys265Ser) AND Finnish congenital nephrotic syndrome

Germline classification:
Uncertain significance (1 submission)
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:
RCV001823539.3

Allele description [Variation Report for NM_004646.4(NPHS1):c.794G>C (p.Cys265Ser)]

NM_004646.4(NPHS1):c.794G>C (p.Cys265Ser)

Gene:
NPHS1:NPHS1 adhesion molecule, nephrin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.12
Genomic location:
Preferred name:
NM_004646.4(NPHS1):c.794G>C (p.Cys265Ser)
HGVS:
  • NC_000019.10:g.35849282C>G
  • NG_013356.2:g.25006G>C
  • NG_051206.1:g.2648C>G
  • NM_004646.4:c.794G>CMANE SELECT
  • NP_004637.1:p.Cys265Ser
  • LRG_693t1:c.[794G>C]
  • LRG_693:g.25006G>C
  • NC_000019.9:g.36340184C>G
  • NM_004646.3:c.[794G>C]
Protein change:
C265S
Links:
dbSNP: rs748287435
NCBI 1000 Genomes Browser:
rs748287435
Molecular consequence:
  • NM_004646.4:c.794G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Finnish congenital nephrotic syndrome (NPHS1)
Synonyms:
NEPHROTIC SYNDROME, TYPE 1; Nephrosis 1, congenital, Finnish type; Congenital nephrotic syndrome 1
Identifiers:
MONDO: MONDO:0009732; MedGen: C0403399; Orphanet: 839; OMIM: 256300

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002073047Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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 Neuberg Centre For Genomic Medicine, NCGM, SCV002073047.1

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

Description

The missense variant p.C265S in NPHS1 (NM_004646.4) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.C265S variant is observed in 7/30,606 (0.0229%) alleles from individuals of South Asian background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.C265S missense variant is predicted to be damaging by both SIFT and PolyPhen2. The cysteine residue at codon 265 of NPHS1 is conserved in all mammalian species. The nucleotide c.794 in NPHS1 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

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

Last Updated: Sep 29, 2024