NM_004646.4(NPHS1):c.1339G>A (p.Glu447Lys) AND Finnish congenital nephrotic syndrome

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Dec 15, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000490526.2

Allele description [Variation Report for NM_004646.4(NPHS1):c.1339G>A (p.Glu447Lys)]

NM_004646.4(NPHS1):c.1339G>A (p.Glu447Lys)

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.1339G>A (p.Glu447Lys)
HGVS:
  • NC_000019.10:g.35848142C>T
  • NG_013356.2:g.26146G>A
  • NG_051206.1:g.1508C>T
  • NM_004646.4:c.1339G>AMANE SELECT
  • NP_004637.1:p.Glu447Lys
  • NP_004637.1:p.Glu447Lys
  • LRG_693t1:c.1339G>A
  • LRG_693:g.26146G>A
  • LRG_693p1:p.Glu447Lys
  • NC_000019.9:g.36339044C>T
  • NM_004646.3:c.1339G>A
  • O60500:p.Glu447Lys
Protein change:
E447K; GLU447LYS
Links:
UniProtKB: O60500#VAR_013042; OMIM: 602716.0007; dbSNP: rs28939695
NCBI 1000 Genomes Browser:
rs28939695
Molecular consequence:
  • NM_004646.4:c.1339G>A - 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; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009732; MedGen: C0403399; Orphanet: 839; OMIM: 256300

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000267423Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Centercriteria provided, single submitter
Uncertain significance
(Mar 18, 2016)
germlinereference population

PubMed (3)
[See all records that cite these PMIDs]

SCV000800799Counsylcriteria provided, single submitter
Likely benign
(Dec 15, 2017)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV001454156Natera, Inc.no assertion criteria providedBenign
(May 4, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
East Asiangermlineunknown7not providednot providednot providednot providedreference population

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

Functional analysis of NPHS1 mutations in Japanese patients.

Miyai T, Aya K, Takaiwa M, Yan K, Sado Y, Tanaka H, Morishima T.

Histol Histopathol. 2014 Feb;29(2):279-84. doi: 10.14670/HH-29.279. Epub 2013 Oct 21.

PubMed [citation]
PMID:
24142548
See all PubMed Citations (3)

Details of each submission

From Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center, SCV000267423.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1East Asian7not providednot providedreference population PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided7not providednot providednot provided

From Counsyl, SCV000800799.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001454156.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 4, 2021

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