NM_004646.4(NPHS1):c.1619C>A (p.Ala540Glu) AND NPHS1-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 22, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV003942697.2

Allele description [Variation Report for NM_004646.4(NPHS1):c.1619C>A (p.Ala540Glu)]

NM_004646.4(NPHS1):c.1619C>A (p.Ala540Glu)

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.1619C>A (p.Ala540Glu)

HGVS:

NC_000019.10:g.35846016G>T
NG_013356.2:g.28272C>A
NM_004646.4:c.1619C>AMANE SELECT
NP_004637.1:p.Ala540Glu
NP_004637.1:p.Ala540Glu
LRG_693t1:c.1619C>A
LRG_693:g.28272C>A
LRG_693p1:p.Ala540Glu
NC_000019.9:g.36336918G>T
NM_004646.3:c.1619C>A
p.ALA540GLU

Protein change:

A540E

Links:

dbSNP: rs149598144

NCBI 1000 Genomes Browser:

rs149598144

Molecular consequence:

NM_004646.4:c.1619C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: NPHS1-related disorder
Synonyms:: NPHS1-related condition
Identifiers:

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Pgk Phosphoglycerate kinase [Drosophila melanogaster]
Pgk Phosphoglycerate kinase [Drosophila melanogaster]
Gene ID:33461

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004771761	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Uncertain significance (Feb 22, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004771761

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Uncertain significance
(Feb 22, 2024)

germline

clinical testing

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004771761.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The NPHS1 c.1619C>A variant is predicted to result in the amino acid substitution p.Ala540Glu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.068% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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