NM_004646.4(NPHS1):c.1175T>C (p.Leu392Pro) AND not provided

Germline classification:: Benign/Likely benign (4 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:: RCV000712419.14

Allele description [Variation Report for NM_004646.4(NPHS1):c.1175T>C (p.Leu392Pro)]

NM_004646.4(NPHS1):c.1175T>C (p.Leu392Pro)

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.1175T>C (p.Leu392Pro)

HGVS:

NC_000019.10:g.35848393A>G
NG_013356.2:g.25895T>C
NG_051206.1:g.1759A>G
NM_004646.4:c.1175T>CMANE SELECT
NP_004637.1:p.Leu392Pro
NP_004637.1:p.Leu392Pro
LRG_693t1:c.1175T>C
LRG_693:g.25895T>C
LRG_693p1:p.Leu392Pro
NC_000019.9:g.36339295A>G
NM_004646.3:c.1175T>C
O60500:p.Leu392Pro

Protein change:

L392P

Links:

UniProtKB: O60500#VAR_049971; dbSNP: rs34320609

NCBI 1000 Genomes Browser:

rs34320609

Molecular consequence:

NM_004646.4:c.1175T>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000842911	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Mar 9, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19812541, 28724397, 26467025
SCV001106458	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]
SCV001826607	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jul 21, 2021)	germline	clinical testing	Citation Link,
SCV005207022	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]

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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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Nephrin mutations cause childhood- and adult-onset focal segmental glomerulosclerosis.

Santín S, García-Maset R, Ruíz P, Giménez I, Zamora I, Peña A, Madrid A, Camacho JA, Fraga G, Sánchez-Moreno A, Cobo MA, Bernis C, Ortiz A, de Pablos AL, Pintos G, Justa ML, Hidalgo-Barquero E, Fernández-Llama P, Ballarín J, Ars E, Torra R; FSGS Spanish Study Group..

Kidney Int. 2009 Dec;76(12):1268-76. doi: 10.1038/ki.2009.381. Epub 2009 Oct 7.

PubMed [citation]

PMID:: 19812541

Partial uniparental isodisomy of chromosome 16 unmasks a deleterious biallelic mutation in IFT140 that causes Mainzer-Saldino syndrome.

Helm BM, Willer JR, Sadeghpour A, Golzio C, Crouch E, Vergano SS, Katsanis N, Davis EE.

Hum Genomics. 2017 Jul 19;11(1):16. doi: 10.1186/s40246-017-0111-9.

PubMed [citation]

PMID:: 28724397
PMCID:: PMC5517791

See all PubMed Citations (5)

Details of each submission

From Athena Diagnostics, SCV000842911.1

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001106458.6

#	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 GeneDx, SCV001826607.1

#	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 Breakthrough Genomics, Breakthrough Genomics, SCV005207022.1

#	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: Sep 29, 2024

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