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NM_004646.4(NPHS1):c.1555C>T (p.Pro519Ser) AND not provided

Germline classification:
no classifications from unflagged records (1 submission)
Last evaluated:
Aug 8, 2024
Review status:
no classifications from unflagged records
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:
RCV002513691.3

Allele description [Variation Report for NM_004646.4(NPHS1):c.1555C>T (p.Pro519Ser)]

NM_004646.4(NPHS1):c.1555C>T (p.Pro519Ser)

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.1555C>T (p.Pro519Ser)
HGVS:
  • NC_000019.10:g.35846080G>A
  • NG_013356.2:g.28208C>T
  • NM_004646.4:c.1555C>TMANE SELECT
  • NP_004637.1:p.Pro519Ser
  • NP_004637.1:p.Pro519Ser
  • LRG_693t1:c.1555C>T
  • LRG_693:g.28208C>T
  • LRG_693p1:p.Pro519Ser
  • NC_000019.9:g.36336982G>A
  • NM_004646.3:c.1555C>T
  • O60500:p.Pro519Ser
Protein change:
P519S
Links:
UniProtKB: O60500#VAR_064210; dbSNP: rs386833884
NCBI 1000 Genomes Browser:
rs386833884
Molecular consequence:
  • NM_004646.4:c.1555C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
No clinical assertions found. See "Flagged submissions" below.
Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Nothing to display

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003294715.1

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

Description

This sequence change replaces proline with serine at codon 519 of the NPHS1 protein (p.Pro519Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine. This variant is present in population databases (rs386833884, ExAC 0.004%). This missense change has been observed in individuals with nephrotic syndrome (PMID: 18503012, 29474669, 30295827). ClinVar contains an entry for this variant (Variation ID: 56442). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003294715Labcorp Genetics (formerly Invitae), Labcorp
flagged submission
Reason: Outlier claim with insufficient supporting evidence
Notes: None

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 1, 2021) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Last Updated: Nov 3, 2024