NM_004646.4(NPHS1):c.808G>T (p.Gly270Cys) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 14, 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:: RCV003320551.1

Allele description [Variation Report for NM_004646.4(NPHS1):c.808G>T (p.Gly270Cys)]

NM_004646.4(NPHS1):c.808G>T (p.Gly270Cys)

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.808G>T (p.Gly270Cys)

HGVS:

NC_000019.10:g.35849268C>A
NG_013356.2:g.25020G>T
NG_051206.1:g.2634C>A
NM_004646.4:c.808G>TMANE SELECT
NP_004637.1:p.Gly270Cys
NP_004637.1:p.Gly270Cys
LRG_693t1:c.808G>T
LRG_693:g.25020G>T
LRG_693p1:p.Gly270Cys
NC_000019.9:g.36340170C>A
NM_004646.3:c.808G>T
O60500:p.Gly270Cys

Protein change:

G270C

Links:

UniProtKB: O60500#VAR_013035; dbSNP: rs386833961

NCBI 1000 Genomes Browser:

rs386833961

Molecular consequence:

NM_004646.4:c.808G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004025448	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Feb 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004025448

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Feb 14, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV004025448.1

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

Description

Published functional studies demonstrate a damaging effect resulting in protein misfolding and activation of the unfolded protein response (Drozdova et al., 2013); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11726550, 24303155, 9915943)

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

Last Updated: Dec 30, 2023

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