ClinVar Genomic variation as it relates to human health
NM_004646.4(NPHS1):c.1099C>T (p.Arg367Cys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_004646.4(NPHS1):c.1099C>T (p.Arg367Cys)
Variation ID: 56421 Accession: VCV000056421.22
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 19q13.12 19: 35848708 (GRCh38) [ NCBI UCSC ] 19: 36339610 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jul 24, 2013 Oct 8, 2024 Mar 17, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_004646.4:c.1099C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004637.1:p.Arg367Cys missense NC_000019.10:g.35848708G>A NC_000019.9:g.36339610G>A NG_013356.2:g.25580C>T NG_051206.1:g.2074G>A LRG_693:g.25580C>T LRG_693t1:c.1099C>T LRG_693p1:p.Arg367Cys O60500:p.Arg367Cys - Protein change
- R367C
- Other names
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- Canonical SPDI
- NC_000019.10:35848707:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00004
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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NPHS1 | - | - |
GRCh38 GRCh37 |
1674 | 1858 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (9) |
criteria provided, multiple submitters, no conflicts
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Mar 17, 2024 | RCV000049834.19 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 30, 2023 | RCV001380444.5 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Oct 18, 2021 | RCV002294007.2 | |
NPHS1-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Jan 19, 2024 | RCV003415816.6 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Oct 18, 2021)
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criteria provided, single submitter
Method: clinical testing
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Inherited focal segmental glomerulosclerosis
Affected status: unknown
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002587324.1
First in ClinVar: Oct 29, 2022 Last updated: Oct 29, 2022 |
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Pathogenic
(Mar 17, 2024)
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criteria provided, single submitter
Method: clinical testing
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Finnish congenital nephrotic syndrome
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004191410.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(Oct 09, 2017)
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criteria provided, single submitter
Method: clinical testing
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Finnish congenital nephrotic syndrome
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919898.1
First in ClinVar: Jun 02, 2019 Last updated: Jun 02, 2019 |
Comment:
Variant summary: The NPHS1 c.1099C>T (p.Arg367Cys) variant involves the alteration of a conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant … (more)
Variant summary: The NPHS1 c.1099C>T (p.Arg367Cys) variant involves the alteration of a conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 10/246176 control chromosomes at a frequency of 0.0000406, which does not exceed the estimated maximal expected allele frequency of a pathogenic NPHS1 variant (0.0033541). The variant has been reported in affected individuals in the literature, and has been described as an Indian founder mutation (Sadowski_2015). In in vitro studies, the variant was shown to result in the absence of cell-surface localization (Liu_2001). In addition, one clinical diagnostic laboratory classified this variant as likely pathogenic. Taken together, this variant is classified as pathogenic. (less)
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Pathogenic
(May 27, 2022)
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criteria provided, single submitter
Method: clinical testing
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Finnish congenital nephrotic syndrome
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV001752515.2
First in ClinVar: Jul 18, 2021 Last updated: Dec 31, 2022 |
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Likely pathogenic
(Nov 16, 2023)
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criteria provided, single submitter
Method: clinical testing
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Finnish congenital nephrotic syndrome
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV004123119.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
A homozygous missense variant in exon 9 of the NPHS1 gene that results in the amino acid substitution of Cysteine for Arginine at codon 367 … (more)
A homozygous missense variant in exon 9 of the NPHS1 gene that results in the amino acid substitution of Cysteine for Arginine at codon 367 (p.Arg367Cys) was detected. The observed variant has previously been reported in patients affected with nephrotic syndrome [PMID:30013592]. The p.Arg367Cys variant has not been reported in the 1000 genomes databases and has a minor allele frequency of 0.002%, 0.004% and 0.003% in the gnomAD (v3.1), gnomdAD (v2.1) and topmed databases respectively. The in silico prediction of the variant are probably damaging by PolyPhen-2 (HumDiv) and damaging by SIFT, LRT and MutationTaster2. The reference codon is conserved across mammals. In summary, the variant meets our criteria to be classified as likely pathogenic. (less)
Clinical Features:
Proteinuria (present) , Seizure (present) , Pedal edema (present)
Age: 0-9 years
Sex: female
Method: DNA was used to perform targeted gene capture using a custom capture kit. Libraries were sequenced to mean >80-100X coverage on the Illumina sequencing platform. Sequence obtained were aligned to human references genome using BWA program and analyzed using Picard and GATK-Lite toolkit to identify variants in the targeted genes relevant to clinical indication.
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Finnish congenital nephrotic syndrome
(Autosomal recessive inheritance)
Affected status: no
Allele origin:
unknown
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Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
Accession: SCV004190110.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Sex: male
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Likely pathogenic
(Sep 30, 2021)
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criteria provided, single submitter
Method: clinical testing
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Finnish congenital nephrotic syndrome
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002020153.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Aug 30, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001578525.4
First in ClinVar: May 10, 2021 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects NPHS1 function (PMID: 11726550). Advanced modeling … (more)
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects NPHS1 function (PMID: 11726550). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NPHS1 protein function. ClinVar contains an entry for this variant (Variation ID: 56421). This missense change has been observed in individuals with nephrotic syndrome (PMID: 21415313, 24742477, 31655822). This variant is present in population databases (rs386833865, gnomAD 0.01%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 367 of the NPHS1 protein (p.Arg367Cys). (less)
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Pathogenic
(May 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Finnish congenital nephrotic syndrome
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004047683.2
First in ClinVar: Oct 28, 2023 Last updated: Oct 08, 2024 |
Comment:
The observed missense c.1099C>T(p.Arg367Cys) variant in NPHS1 gene has been reported in homozygous or compound heterozygous state in individual(s) affected with nephrotic Syndrome (Sinha R, … (more)
The observed missense c.1099C>T(p.Arg367Cys) variant in NPHS1 gene has been reported in homozygous or compound heterozygous state in individual(s) affected with nephrotic Syndrome (Sinha R, et. al., 2020; Lovric S, et. al., 2014). Experimental studies have shown that this missense change affects NPHS1 function (Liu L, et. al., 2001). This variant is present with an allele frequency of 0.004% in gnomAD Exomes database. This variant has been reported to the ClinVar database as Likely pathogenic/ Pathogenic(multiple submissions). Multiple lines of computational evidence (Polyphen - probably damaging , SIFT - damaging and MutationTaster - disease causing) predict a damaging effect on protein structure and function for this variant. The amino acid change p.Arg367Cys in NPHS1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 367 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. (less)
Clinical Features:
Abnormality of the kidney (present)
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Finnish congenital nephrotic syndrome
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001460543.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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probable-pathogenic
(-)
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no assertion criteria provided
Method: not provided
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Finnish congenital nephrotic syndrome
Affected status: not provided
Allele origin:
unknown
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Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082243.1
First in ClinVar: Jul 24, 2013 Last updated: Jul 24, 2013
Comment:
FinDis database variant: FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference
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Comment:
Converted during submission to Likely pathogenic.
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Pathogenic
(Jan 19, 2024)
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no assertion criteria provided
Method: clinical testing
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NPHS1-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004116198.3
First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024 |
Comment:
The NPHS1 c.1099C>T variant is predicted to result in the amino acid substitution p.Arg367Cys. This variant has been repeatedly reported in the compound heterozygous or … (more)
The NPHS1 c.1099C>T variant is predicted to result in the amino acid substitution p.Arg367Cys. This variant has been repeatedly reported in the compound heterozygous or homozygous state in individuals with congenital nephrotic syndrome (Lenkkeri et al. 1999. PubMed ID: 9915943; Liu L et al. 2001. PubMed ID: 11726550; Lovric S et al. 2014. PubMed ID: 24742477; Sinha R et al. 2019. PubMed ID: 31655822; Koziell A et al. 2002. PubMed ID: 11854170; Joshi A et al. 2021. PubMed ID: 33980730). This variant is reported as a possible founder variant from India (Sadowski et al. 2015. PubMed ID: 25349199). This variant is reported in 0.013% of alleles in individuals of South Asian descent in gnomAD. This variant is interpreted as pathogenic. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Congenital Nephrotic Syndrome in India in the Current Era: A Multicenter Case Series. | Sinha R | Nephron | 2020 | PMID: 31655822 |
Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome. | Lovric S | Clinical journal of the American Society of Nephrology : CJASN | 2014 | PMID: 24742477 |
Clinical utility of genetic testing in children and adults with steroid-resistant nephrotic syndrome. | Santín S | Clinical journal of the American Society of Nephrology : CJASN | 2011 | PMID: 21415313 |
Genotype-phenotype correlations in non-Finnish congenital nephrotic syndrome. | Machuca E | Journal of the American Society of Nephrology : JASN | 2010 | PMID: 20507940 |
Nineteen novel NPHS1 mutations in a worldwide cohort of patients with congenital nephrotic syndrome (CNS). | Schoeb DS | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2010 | PMID: 20172850 |
Thirteen novel NPHS1 mutations in a large cohort of children with congenital nephrotic syndrome. | Heeringa SF | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2008 | PMID: 18503012 |
Genotype/phenotype correlations of NPHS1 and NPHS2 mutations in nephrotic syndrome advocate a functional inter-relationship in glomerular filtration. | Koziell A | Human molecular genetics | 2002 | PMID: 11854170 |
Defective nephrin trafficking caused by missense mutations in the NPHS1 gene: insight into the mechanisms of congenital nephrotic syndrome. | Liu L | Human molecular genetics | 2001 | PMID: 11726550 |
Structure of the gene for congenital nephrotic syndrome of the finnish type (NPHS1) and characterization of mutations. | Lenkkeri U | American journal of human genetics | 1999 | PMID: 9915943 |
Text-mined citations for rs386833865 ...
HelpRecord last updated Oct 13, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.