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NM_004646.4(NPHS1):c.1292dup (p.Ser432fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 6, 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:
RCV003556132.2

Allele description [Variation Report for NM_004646.4(NPHS1):c.1292dup (p.Ser432fs)]

NM_004646.4(NPHS1):c.1292dup (p.Ser432fs)

Gene:
NPHS1:NPHS1 adhesion molecule, nephrin [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
19q13.12
Genomic location:
Preferred name:
NM_004646.4(NPHS1):c.1292dup (p.Ser432fs)
HGVS:
  • NC_000019.10:g.35848277dup
  • NG_013356.2:g.26012dup
  • NG_051206.1:g.1643dup
  • NM_004646.4:c.1292dupMANE SELECT
  • NP_004637.1:p.Ser432fs
  • LRG_693:g.26012dup
  • NC_000019.9:g.36339177_36339178insT
  • NC_000019.9:g.36339179dup
  • NM_004646.3:c.1292dupA
Protein change:
S432fs
Links:
dbSNP: rs386833877
NCBI 1000 Genomes Browser:
rs386833877
Molecular consequence:
  • NM_004646.4:c.1292dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004297306Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 6, 2023) 		germlineclinical testing

PubMed (4)
[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

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

Nephrin TRAP mice lack slit diaphragms and show fibrotic glomeruli and cystic tubular lesions.

Rantanen M, Palmén T, Pätäri A, Ahola H, Lehtonen S, Aström E, Floss T, Vauti F, Wurst W, Ruiz P, Kerjaschki D, Holthöfer H.

J Am Soc Nephrol. 2002 Jun;13(6):1586-94.

PubMed [citation]
PMID:
12039988
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004297306.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Ser432Valfs*16) 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 (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with NPHS1-related conditions (PMID: 11854170). This variant is also known as nt1291 (insA). ClinVar contains an entry for this variant (Variation ID: 56435). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024