NM_014625.4(NPHS2):c.965G>A (p.Arg322Gln) AND Nephrotic syndrome, type 2

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Aug 29, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000671756.5

Allele description [Variation Report for NM_014625.4(NPHS2):c.965G>A (p.Arg322Gln)]

NM_014625.4(NPHS2):c.965G>A (p.Arg322Gln)

Genes:

NPHS2:NPHS2 stomatin family member, podocin [Gene - OMIM - HGNC]
AXDND1:axonemal dynein light chain domain containing 1 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q25.2

Genomic location:

Preferred name:

NM_014625.4(NPHS2):c.965G>A (p.Arg322Gln)

HGVS:

NC_000001.11:g.179551360C>T
NG_007535.1:g.29590G>A
NG_033075.1:g.190641C>T
NM_001297575.2:c.761G>A
NM_014625.4:c.965G>AMANE SELECT
NM_144696.6:c.3032-3152C>TMANE SELECT
NP_001284504.1:p.Arg254Gln
NP_055440.1:p.Arg322Gln
NP_055440.1:p.Arg322Gln
LRG_887t1:c.965G>A
LRG_887:g.29590G>A
LRG_887p1:p.Arg322Gln
NC_000001.10:g.179520495C>T
NM_014625.2:c.965G>A
NM_014625.3:c.965G>A

Protein change:

R254Q

Links:

dbSNP: rs776859868

NCBI 1000 Genomes Browser:

rs776859868

Molecular consequence:

NM_144696.6:c.3032-3152C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001297575.2:c.761G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014625.4:c.965G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Nephrotic syndrome, type 2 (NPHS2)
Synonyms:: Nephrotic syndrome, steroid-resistant, autosomal recessive; Hereditary nephrotic syndrome
Identifiers:: MONDO: MONDO:0010974; MedGen: C1868672; Orphanet: 656; OMIM: 600995

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000796775	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Dec 28, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002789415	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 8, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004049242	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004191545	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 29, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

NPHS2 (podicin) mutations in Turkish children with idiopathic nephrotic syndrome.

Berdeli A, Mir S, Yavascan O, Serdaroglu E, Bak M, Aksu N, Oner A, Anarat A, Donmez O, Yildiz N, Sever L, Tabel Y, Dusunsel R, Sonmez F, Cakar N.

Pediatr Nephrol. 2007 Dec;22(12):2031-40. Epub 2007 Sep 25.

PubMed [citation]

PMID:: 17899208

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Counsyl, SCV000796775.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002789415.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV004049242.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004191545.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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