NM_004646.4(NPHS1):c.2515del (p.Gln839fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 18, 2022
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:: RCV001853055.5

Allele description [Variation Report for NM_004646.4(NPHS1):c.2515del (p.Gln839fs)]

NM_004646.4(NPHS1):c.2515del (p.Gln839fs)

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.2515del (p.Gln839fs)

HGVS:

NC_000019.10:g.35842277del
NG_013356.2:g.32016del
NM_004646.4:c.2515delMANE SELECT
NP_004637.1:p.Gln839fs
LRG_693:g.32016del
NC_000019.9:g.36333174del
NC_000019.9:g.36333179del
NM_004646.3:c.2515delC

Protein change:

Q839fs

Links:

dbSNP: rs386833918

NCBI 1000 Genomes Browser:

rs386833918

Molecular consequence:

NM_004646.4:c.2515del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002197172	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 18, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 19321760, 11317351, 11854170, 12039988, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002197172

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 18, 2022)

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

NPHS1 gene mutation in Japanese patients with congenital nephrotic syndrome.

Aya K, Shimizu J, Ohtomo Y, Satomura K, Suzuki H, Yan K, Sado Y, Morishima T, Tanaka H.

Nephrol Dial Transplant. 2009 Aug;24(8):2411-4. doi: 10.1093/ndt/gfp122. Epub 2009 Mar 25.

PubMed [citation]

PMID:: 19321760

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

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002197172.4

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

Description

This premature translational stop signal has been observed in individual(s) with congenital nephrotic syndrome (PMID: 19321760). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln839Argfs*8) 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). ClinVar contains an entry for this variant (Variation ID: 56479). 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 7, 2025

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