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NM_004646.4(NPHS1):c.1440+2T>C AND Finnish congenital nephrotic syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 19, 2018
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:
RCV000779257.4

Allele description [Variation Report for NM_004646.4(NPHS1):c.1440+2T>C]

NM_004646.4(NPHS1):c.1440+2T>C

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.1440+2T>C
HGVS:
  • NC_000019.10:g.35848039A>G
  • NG_013356.2:g.26249T>C
  • NG_051206.1:g.1405A>G
  • NG_161439.1:g.30A>G
  • NM_004646.4:c.1440+2T>CMANE SELECT
  • LRG_693t1:c.1440+2T>C
  • LRG_693:g.26249T>C
  • NC_000019.9:g.36338941A>G
  • NM_004646.3:c.1440+2T>C
Links:
dbSNP: rs1568455470
NCBI 1000 Genomes Browser:
rs1568455470
Molecular consequence:
  • NM_004646.4:c.1440+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000915828Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)		Uncertain significance
(Oct 19, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000915828.1

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

Description

The NPHS1 c.1440+2T>C variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. A literature search was performed for the gene and cDNA change. No publications were found based on this search. This variant is not found in the 1000 Genomes Project, the Exome Sequencing Project, or the Exome Aggregation Consortium. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of splice donor variants and the lack of clarifying evidence, the c.1440+2T>C variant is classified as a variant of unknown significance but suspicious for pathogenicity for congenital nephrotic syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

Last Updated: Jun 10, 2023