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NM_004646.4(NPHS1):c.713-1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 28, 2023
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:
RCV003854992.2

Allele description [Variation Report for NM_004646.4(NPHS1):c.713-1G>A]

NM_004646.4(NPHS1):c.713-1G>A

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.713-1G>A
HGVS:
  • NC_000019.10:g.35849364C>T
  • NG_013356.2:g.24924G>A
  • NG_051206.1:g.2730C>T
  • NM_004646.4:c.713-1G>AMANE SELECT
  • LRG_693:g.24924G>A
  • NC_000019.9:g.36340266C>T
Molecular consequence:
  • NM_004646.4:c.713-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004661657Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 28, 2023) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Novel NPHS1 Gene Mutations in two Chinese Infants with Congenital Nephrotic Syndrome.

Li P.

Indian J Pediatr. 2017 Jun;84(6):489-490. doi: 10.1007/s12098-017-2296-2. Epub 2017 Feb 4. No abstract available.

PubMed [citation]
PMID:
28160156

Analysis of 14 Patients With Congenital Nephrotic Syndrome.

Chen Y, Zhang Y, Wang F, Zhang H, Zhong X, Xiao H, Yao Y, Jiang Y, Ding J, Hou X.

Front Pediatr. 2019;7:341. doi: 10.3389/fped.2019.00341. Erratum in: Front Pediatr. 2019 Nov 13;7:471. doi: 10.3389/fped.2019.00471.

PubMed [citation]
PMID:
31456999
PMCID:
PMC6700319
See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004661657.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individuals with congenital nephrotic syndrome (PMID: 28160156, 31456999). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 6 of the NPHS1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NPHS1 are known to be pathogenic (PMID: 11317351, 11854170, 12039988).

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

Last Updated: Sep 29, 2024