ClinVar Genomic variation as it relates to human health
NM_014625.4(NPHS2):c.855_856del (p.Arg286fs)
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_014625.4(NPHS2):c.855_856del (p.Arg286fs)
Variation ID: 188823 Accession: VCV000188823.30
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 1q25.2 1: 179552620-179552621 (GRCh38) [ NCBI UCSC ] 1: 179521755-179521756 (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 Apr 4, 2013 Oct 8, 2024 Mar 27, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_014625.4:c.855_856del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055440.1:p.Arg286fs frameshift NM_144696.6:c.3032-1891_3032-1890del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_001297575.2:c.651_652del NP_001284504.1:p.Arg218fs frameshift NM_014625.2:c.855_856del NM_014625.3:c.854_855delAA NP_055440.1:p.Arg286Thrfs frameshift NM_014625.3:c.855_856delAA frameshift NC_000001.11:g.179552621_179552622del NC_000001.10:g.179521756_179521757del NG_007535.1:g.28329_28330del NG_033075.1:g.191902_191903del LRG_887:g.28329_28330del LRG_887t1:c.855_856del LRG_887p1:p.Arg286fs - Protein change
- R286fs, R218fs
- Other names
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- Canonical SPDI
- NC_000001.11:179552619:TTT:T
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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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- 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
Help
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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AXDND1 | - | - | - |
GRCh38 GRCh37 |
70 | 283 |
NPHS2 | - | - |
GRCh38 GRCh37 |
347 | 562 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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 (6) |
criteria provided, multiple submitters, no conflicts
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Mar 27, 2024 | RCV000169166.14 | |
Pathogenic/Likely pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Dec 26, 2023 | RCV000730521.11 | |
Pathogenic (1) |
no assertion criteria provided
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- | RCV001003813.1 | |
Likely pathogenic (1) |
criteria provided, single submitter
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May 28, 2020 | RCV001171356.1 | |
Pathogenic (1) |
no assertion criteria provided
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Sep 16, 2020 | RCV001273611.1 | |
Pathogenic (2) |
criteria provided, single submitter
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Dec 30, 2020 | RCV001849326.3 | |
NPHS2-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Jun 20, 2024 | RCV003398864.6 |
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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Pathogenic
(Oct 01, 2018)
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criteria provided, single submitter
Method: clinical testing
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Idiopathic nephrotic syndrome
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919905.1
First in ClinVar: Jun 02, 2019 Last updated: Jun 02, 2019 |
Comment:
Variant summary: NPHS2 c.855_856delAA (p.Arg286ThrfsX17) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Variant summary: NPHS2 c.855_856delAA (p.Arg286ThrfsX17) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 6.5e-05 in 275798 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in NPHS2 causing Nephrotic Syndrome, Type 2 (6.5e-05 vs 0.0018), allowing no conclusion about variant significance. c.855_856delAA has been reported in the literature in multiple individuals affected with Steroid Resistant Nephrotic Syndrome. These data indicate that the variant is very likely to be associated with disease. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Likely pathogenic
(May 28, 2020)
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criteria provided, single submitter
Method: research
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Chronic kidney disease
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
unknown
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Cavalleri Lab, Royal College of Surgeons in Ireland
Accession: SCV001328303.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
PVS1, PM3
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Pathogenic
(Jan 03, 2020)
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criteria provided, single submitter
Method: clinical testing
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Nephrotic syndrome, type 2
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV001194121.2
First in ClinVar: Apr 06, 2020 Last updated: Jul 03, 2020 |
Comment:
NM_014625.2(NPHS2):c.855_856delAA(R286Tfs*17) is classified as pathogenic in the context of NPHS2-related nephrotic syndrome. Sources cited for classification include the following: PMID 11805166, 18823551, 19406966, 24742477 and … (more)
NM_014625.2(NPHS2):c.855_856delAA(R286Tfs*17) is classified as pathogenic in the context of NPHS2-related nephrotic syndrome. Sources cited for classification include the following: PMID 11805166, 18823551, 19406966, 24742477 and 15327385. Classification of NM_014625.2(NPHS2):c.855_856delAA(R286Tfs*17) is based on the following criteria: The variant causes a premature termination codon that is not expected to be targeted by nonsense-mediated mRNA decay; however, literature evidence strongly supports pathogenicity. Please note: this variant was assessed in the context of healthy population screening. (less)
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Pathogenic
(Dec 30, 2020)
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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: SCV002587370.1
First in ClinVar: Oct 29, 2022 Last updated: Oct 29, 2022 |
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Likely pathogenic
(May 13, 2021)
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criteria provided, single submitter
Method: clinical testing
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Nephrotic syndrome, type 2
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002020154.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Dec 26, 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: SCV001231677.3
First in ClinVar: Apr 15, 2020 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg286Thrfs*17) in the NPHS2 gene. While this is not anticipated to result in nonsense mediated decay, … (more)
This sequence change creates a premature translational stop signal (p.Arg286Thrfs*17) in the NPHS2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 98 amino acid(s) of the NPHS2 protein. This variant is present in population databases (rs749740335, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with steroid resistant nephrotic syndrome (PMID: 11805166, 18823551, 20947785, 21355056, 24509478). ClinVar contains an entry for this variant (Variation ID: 188823). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Mar 27, 2024)
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criteria provided, single submitter
Method: clinical testing
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Nephrotic syndrome, type 2
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004191531.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(Dec 01, 2017)
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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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Eurofins Ntd Llc (ga)
Accession: SCV000858264.1
First in ClinVar: Dec 16, 2018 Last updated: Dec 16, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Likely pathogenic
(Dec 15, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001805111.2
First in ClinVar: Aug 21, 2021 Last updated: Dec 24, 2022 |
Comment:
Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 98 amino acids are lost and replaced with 16 incorrect amino … (more)
Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 98 amino acids are lost and replaced with 16 incorrect amino acids (HGMD); This variant is associated with the following publications: (PMID: 24227627, 18823551, 12464671, 30295827, 15769810, 15327385, 15253708, 15322893, 30260545, 30655312, 25949442, 14978175, 11805166, 10742096, 17699384, 19145239, 32581362, 33144682, 31589614, 33226606) (less)
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Likely pathogenic
(Apr 11, 2023)
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criteria provided, single submitter
Method: clinical testing
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Nephrotic syndrome, type 2
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV004049257.1
First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023 |
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Pathogenic
(Apr 01, 2000)
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no assertion criteria provided
Method: literature only
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NEPHROTIC SYNDROME, TYPE 2
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000025877.2
First in ClinVar: Apr 04, 2013 Last updated: Mar 08, 2022 |
Comment on evidence:
In a family with autosomal recessive steroid-resistant nephrotic syndrome (600995) previously reported by Fuchshuber et al. (1995), Boute et al. (2000) identified a frameshift mutation … (more)
In a family with autosomal recessive steroid-resistant nephrotic syndrome (600995) previously reported by Fuchshuber et al. (1995), Boute et al. (2000) identified a frameshift mutation on the paternal allele of the NPHS2 gene of an affected patient. The frameshift resulted from deletion of 2 adenines at nucleotide 855 and 856 in exon 7. No mutation was found on the other allele. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: research
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Nephrotic range proteinuria
Affected status: yes
Allele origin:
unknown
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NIHR Bioresource Rare Diseases, University of Cambridge
Accession: SCV001162264.1
First in ClinVar: Feb 27, 2020 Last updated: Feb 27, 2020 |
Number of individuals with the variant: 1
Sex: male
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Steroid-resistant nephrotic syndrome
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001456811.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Pathogenic
(Jan 17, 2019)
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no assertion criteria provided
Method: literature only
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Focal segmental glomerulosclerosis
Affected status: yes
Allele origin:
germline
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Yale Center for Mendelian Genomics, Yale University
Study: Yale Center for Mendelian Genomics
Accession: SCV002106566.1 First in ClinVar: Mar 28, 2022 Last updated: Mar 28, 2022 |
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Pathogenic
(Jun 20, 2024)
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no assertion criteria provided
Method: clinical testing
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NPHS2-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004104805.2
First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024 |
Comment:
The NPHS2 c.855_856delAA variant is predicted to result in a frameshift and premature protein termination (p.Arg286Thrfs*17). Also known as Q285fsX302 or R285fx302X, this variant has … (more)
The NPHS2 c.855_856delAA variant is predicted to result in a frameshift and premature protein termination (p.Arg286Thrfs*17). Also known as Q285fsX302 or R285fx302X, this variant has been reported to be pathogenic for steroid-resistant nephrotic syndrome (SRNS) (Boute et al. 2000. PubMed ID: 10742096; Machuca et al. 2009. PubMed ID: 19145239; Santín et al. 2011. PubMed ID: 20947785). This variant is reported in 0.016% of alleles in individuals of European (non-Finnish) descent in gnomAD. Frameshift variants in NPHS2 are expected to be pathogenic. 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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Whole-genome sequencing of patients with rare diseases in a national health system. | Turro E | Nature | 2020 | PMID: 32581362 |
Whole-Exome Sequencing Enables a Precision Medicine Approach for Kidney Transplant Recipients. | Mann N | Journal of the American Society of Nephrology : JASN | 2019 | PMID: 30655312 |
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 |
Mutation-dependent recessive inheritance of NPHS2-associated steroid-resistant nephrotic syndrome. | Tory K | Nature genetics | 2014 | PMID: 24509478 |
Screening for NPHS2 mutations may help predict FSGS recurrence after transplantation. | Jungraithmayr TC | Journal of the American Society of Nephrology : JASN | 2011 | PMID: 21355056 |
Clinical value of NPHS2 analysis in early- and adult-onset steroid-resistant nephrotic syndrome. | Santín S | Clinical journal of the American Society of Nephrology : CJASN | 2011 | PMID: 20947785 |
Clinical features and long-term outcome of nephrotic syndrome associated with heterozygous NPHS1 and NPHS2 mutations. | Caridi G | Clinical journal of the American Society of Nephrology : CJASN | 2009 | PMID: 19406966 |
NPHS2 variation in focal and segmental glomerulosclerosis. | Tonna SJ | BMC nephrology | 2008 | PMID: 18823551 |
In vivo expression of podocyte slit diaphragm-associated proteins in nephrotic patients with NPHS2 mutation. | Zhang SY | Kidney international | 2004 | PMID: 15327385 |
NPHS2 mutation analysis shows genetic heterogeneity of steroid-resistant nephrotic syndrome and low post-transplant recurrence. | Weber S | Kidney international | 2004 | PMID: 15253708 |
Novel mutations in NPHS2 detected in both familial and sporadic steroid-resistant nephrotic syndrome. | Karle SM | Journal of the American Society of Nephrology : JASN | 2002 | PMID: 11805166 |
NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome. | Boute N | Nature genetics | 2000 | PMID: 10742096 |
Mapping a gene (SRN1) to chromosome 1q25-q31 in idiopathic nephrotic syndrome confirms a distinct entity of autosomal recessive nephrosis. | Fuchshuber A | Human molecular genetics | 1995 | PMID: 8589695 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NPHS2 | - | - | - | - |
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Text-mined citations for rs749740335 ...
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.