NM_004646.4(NPHS1):c.808G>T (p.Gly270Cys) AND Finnish congenital nephrotic syndrome

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Oct 16, 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:: RCV000049936.4

Allele description [Variation Report for NM_004646.4(NPHS1):c.808G>T (p.Gly270Cys)]

NM_004646.4(NPHS1):c.808G>T (p.Gly270Cys)

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.808G>T (p.Gly270Cys)

HGVS:

NC_000019.10:g.35849268C>A
NG_013356.2:g.25020G>T
NG_051206.1:g.2634C>A
NM_004646.4:c.808G>TMANE SELECT
NP_004637.1:p.Gly270Cys
NP_004637.1:p.Gly270Cys
LRG_693t1:c.808G>T
LRG_693:g.25020G>T
LRG_693p1:p.Gly270Cys
NC_000019.9:g.36340170C>A
NM_004646.3:c.808G>T
O60500:p.Gly270Cys

Protein change:

G270C

Links:

UniProtKB: O60500#VAR_013035; dbSNP: rs386833961

NCBI 1000 Genomes Browser:

rs386833961

Molecular consequence:

NM_004646.4:c.808G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Finnish congenital nephrotic syndrome (NPHS1)
Synonyms:: NEPHROTIC SYNDROME, TYPE 1; Nephrosis 1, congenital, Finnish type; Congenital nephrotic syndrome 1
Identifiers:: MONDO: MONDO:0009732; MedGen: C0403399; Orphanet: 839; OMIM: 256300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000082345	Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)	no assertion criteria provided	probable-pathogenic	not provided	not provided	PubMed (2) [See all records that cite these PMIDs] 9915943, 11854170
SCV000746149	Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare	no assertion criteria provided	Pathogenic (Oct 4, 2017)	germline	clinical testing
SCV004191387	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 16, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000082345

Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)

no assertion criteria provided

probable-pathogenic

not provided

PubMed (2)
[See all records that cite these PMIDs]

SCV000746149

Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare

no assertion criteria provided

Pathogenic
(Oct 4, 2017)

germline

clinical testing

SCV004191387

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 16, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Description

FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference: SCV000082345

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	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
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

Citations

PubMed

Structure of the gene for congenital nephrotic syndrome of the finnish type (NPHS1) and characterization of mutations.

Lenkkeri U, Männikkö M, McCready P, Lamerdin J, Gribouval O, Niaudet PM, Antignac C K, Kashtan CE, Homberg C, Olsen A, Kestilä M, Tryggvason K.

Am J Hum Genet. 1999 Jan;64(1):51-61.

PubMed [citation]

PMID:: 9915943
PMCID:: PMC1377702

Genotype/phenotype correlations of NPHS1 and NPHS2 mutations in nephrotic syndrome advocate a functional inter-relationship in glomerular filtration.

Koziell A, Grech V, Hussain S, Lee G, Lenkkeri U, Tryggvason K, Scambler P.

Hum Mol Genet. 2002 Feb 15;11(4):379-88.

PubMed [citation]

PMID:: 11854170

See all PubMed Citations (3)

Details of each submission

From Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM), SCV000082345.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (2)

Description

Converted during submission to Likely pathogenic.

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

From Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare, SCV000746149.1

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

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

From Baylor Genetics, SCV004191387.1

#	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: Dec 30, 2023

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