NM_004646.4(NPHS1):c.791C>G (p.Pro264Arg) AND not provided

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Feb 1, 2024
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:: RCV000712435.29

Allele description [Variation Report for NM_004646.4(NPHS1):c.791C>G (p.Pro264Arg)]

NM_004646.4(NPHS1):c.791C>G (p.Pro264Arg)

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.791C>G (p.Pro264Arg)

HGVS:

NC_000019.10:g.35849285G>C
NG_013356.2:g.25003C>G
NG_051206.1:g.2651G>C
NM_004646.4:c.791C>GMANE SELECT
NP_004637.1:p.Pro264Arg
NP_004637.1:p.Pro264Arg
LRG_693t1:c.791C>G
LRG_693:g.25003C>G
LRG_693p1:p.Pro264Arg
NC_000019.9:g.36340187G>C
NM_004646.3:c.791C>G
O60500:p.Pro264Arg

Protein change:

P264R

Links:

UniProtKB: O60500#VAR_064199; dbSNP: rs34982899

NCBI 1000 Genomes Browser:

rs34982899

Molecular consequence:

NM_004646.4:c.791C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000842928	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Feb 6, 2018)	germline	clinical testing	PubMed (19) [See all records that cite these PMIDs] 23595123, 24371179, 20981092, 27884173, 21228398, 26346198, 27535533, 11317351, 25804400, 22565185, 26560236, 23349334, 11854170, 17371932, 18443213, 19808243, 19812541, 20507940, 26467025
SCV001730745	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001744373	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001936457	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Apr 14, 2020)	germline	clinical testing	Citation Link,
SCV002543911	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Jun 1, 2023)	germline	clinical testing	Citation Link,
SCV005207028	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	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	yes	6	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A molecular genetic analysis of childhood nephrotic syndrome in a cohort of Saudi Arabian families.

Al-Hamed MH, Al-Sabban E, Al-Mojalli H, Al-Harbi N, Faqeih E, Al Shaya H, Alhasan K, Al-Hissi S, Rajab M, Edwards N, Al-Abbad A, Al-Hassoun I, Sayer JA, Meyer BF.

J Hum Genet. 2013 Jul;58(7):480-9. doi: 10.1038/jhg.2013.27. Epub 2013 Apr 18.

PubMed [citation]

PMID:: 23595123

Novel and known nephrin gene (NPHS1) mutations in two Greek cases with congenital nephrotic syndrome including a complex genotype.

Fylaktou I, Megremis S, Mitsioni A, Kitsiou-Tzeli S, Kosma K, Bitsori M, Stefanidis CJ, Kanavakis E, Traeger Synodinos J.

J Genet. 2013 Dec;92(3):577-81. No abstract available.

PubMed [citation]

PMID:: 24371179

See all PubMed Citations (21)

Details of each submission

From Athena Diagnostics, SCV000842928.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (19)

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001730745.4

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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001744373.3

#	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 GeneDx, SCV001936457.1

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

Description

This variant is associated with the following publications: (PMID: 20507940, 24371179, 23595123, 20981092, 18443213, 21228398, 11854170, 27535533, 27884173, 26346198)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV002543911.16

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	clinical testing	not provided

Description

NPHS1: BP4, BS1, BS2

#	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		6	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005207028.1

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

#	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

Last Updated: Oct 20, 2024

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