NM_004646.4(NPHS1):c.2172_2173del (p.Glu725fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 25, 2021
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:: RCV001853053.6

Allele description [Variation Report for NM_004646.4(NPHS1):c.2172_2173del (p.Glu725fs)]

NM_004646.4(NPHS1):c.2172_2173del (p.Glu725fs)

Gene:

NPHS1:NPHS1 adhesion molecule, nephrin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

19q13.12

Genomic location:

Preferred name:

NM_004646.4(NPHS1):c.2172_2173del (p.Glu725fs)

HGVS:

NC_000019.10:g.35844142_35844143del
NG_013356.2:g.30145_30146del
NM_004646.4:c.2172_2173delMANE SELECT
NP_004637.1:p.Glu725fs
LRG_693t1:c.2172_2173del
LRG_693:g.30145_30146del
NC_000019.9:g.36335044_36335045del
NM_004646.3:c.2172_2173del
NM_004646.3:c.2172_2173delTG

Protein change:

E725fs

Links:

dbSNP: rs386833906

Molecular consequence:

NM_004646.4:c.2172_2173del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV002235638	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 25, 2021)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 11317351, 11854170, 12039988, 16703378, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002235638

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 25, 2021)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

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

Citations

PubMed

Mutation spectrum in the nephrin gene (NPHS1) in congenital nephrotic syndrome.

Beltcheva O, Martin P, Lenkkeri U, Tryggvason K.

Hum Mutat. 2001 May;17(5):368-73.

PubMed [citation]

PMID:: 11317351

Genotype/phenotype correlations of NPHS1 and NPHS2 mutations in nephrotic syndrome advocate a functional inter-relationship in glomerular filtration.

Koziell A, Grech V, Hussain S, Lee G, Lenkkeri U, Tryggvason K, Scambler P.

Hum Mol Genet. 2002 Feb 15;11(4):379-88.

PubMed [citation]

PMID:: 11854170

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002235638.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Glu725Glyfs*25) in the NPHS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHS1 are known to be pathogenic (PMID: 11317351, 11854170, 12039988). This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with nephrotic syndrome (PMID: 16703378). ClinVar contains an entry for this variant (Variation ID: 56466). For these reasons, this variant has been classified as Pathogenic.

#	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: Apr 12, 2026

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