NM_004646.4(NPHS1):c.1320C>T (p.Pro440=) AND Finnish congenital nephrotic syndrome

Germline classification:: Benign (3 submissions)
Last evaluated:: Jun 10, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000362998.6

Allele description [Variation Report for NM_004646.4(NPHS1):c.1320C>T (p.Pro440=)]

NM_004646.4(NPHS1):c.1320C>T (p.Pro440=)

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.1320C>T (p.Pro440=)

HGVS:

NC_000019.10:g.35848161G>A
NG_013356.2:g.26127C>T
NG_051206.1:g.1527G>A
NM_004646.4:c.1320C>TMANE SELECT
NP_004637.1:p.Pro440=
NP_004637.1:p.Pro440=
LRG_693t1:c.1320C>T
LRG_693:g.26127C>T
LRG_693p1:p.Pro440=
NC_000019.9:g.36339063G>A
NM_004646.3:c.1320C>T

Links:

dbSNP: rs392702

NCBI 1000 Genomes Browser:

rs392702

Molecular consequence:

NM_004646.4:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000677366	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (May 15, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15968559, 15086927, 26467025
SCV001460541	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing
SCV001738130	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jun 10, 2021)	germline	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

SCV000677366

Athena Diagnostics Inc

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(May 15, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV001460541

Natera, Inc.

no assertion criteria provided

Benign
(Sep 16, 2020)

germline

clinical testing

SCV001738130

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jun 10, 2021)

germline

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical features and outcome of childhood minimal change nephrotic syndrome: is genetics involved?

Lahdenkari AT, Suvanto M, Kajantie E, Koskimies O, Kestilä M, Jalanko H.

Pediatr Nephrol. 2005 Aug;20(8):1073-80. Epub 2005 Jun 21.

PubMed [citation]

PMID:: 15968559

Nephrin gene (NPHS1) in patients with minimal change nephrotic syndrome (MCNS).

Lahdenkari AT, Kestilä M, Holmberg C, Koskimies O, Jalanko H.

Kidney Int. 2004 May;65(5):1856-63.

PubMed [citation]

PMID:: 15086927

See all PubMed Citations (4)

Details of each submission

From Athena Diagnostics Inc, SCV000677366.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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

From Natera, Inc., SCV001460541.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV001738130.1

#	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

Last Updated: Mar 10, 2024

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