NM_004646.4(NPHS1):c.928G>A (p.Asp310Asn) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 2, 2024
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:: RCV000821998.7

Allele description [Variation Report for NM_004646.4(NPHS1):c.928G>A (p.Asp310Asn)]

NM_004646.4(NPHS1):c.928G>A (p.Asp310Asn)

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.928G>A (p.Asp310Asn)

HGVS:

NC_000019.10:g.35849060C>T
NG_013356.2:g.25228G>A
NG_051206.1:g.2426C>T
NM_004646.4:c.928G>AMANE SELECT
NP_004637.1:p.Asp310Asn
NP_004637.1:p.Asp310Asn
LRG_693t1:c.928G>A
LRG_693:g.25228G>A
LRG_693p1:p.Asp310Asn
NC_000019.9:g.36339962C>T
NM_004646.3:c.928G>A

Protein change:

D310N

Links:

dbSNP: rs763972372

NCBI 1000 Genomes Browser:

rs763972372

Molecular consequence:

NM_004646.4:c.928G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Clostridium botulinum strain CDC52271, whole genome shotgun sequencing project
gi|666366127|gb|JFGF00000000.1|JFGF 000

Nucleotide
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BarH-like homeobox 2 [Homo sapiens]
gi|119588147|gb|EAW67743.1||gnl|WGS |hCP48435

Protein
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Campylobacter jejuni genome assembly 7213_3#31, scaffold ERS070336.7213_3_31.36, whole genome shotgun sequence
gi|910092354|emb|CUTO01000036.1|

Nucleotide
Rattus norvegicus Mof4 family associated protein 1, mRNA (cDNA clone MGC:109522 ...
Rattus norvegicus Mof4 family associated protein 1, mRNA (cDNA clone MGC:109522 IMAGE:7324285), complete cds
gi|56789915|gb|BC088308.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000962775	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 2, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 16316524, 25729976, 25903641, 28204945, 28392951, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000962775

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 2, 2024)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

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

Citations

PubMed

[NPHS1 mutations in a Chinese family with congenital nephrotic syndrome].

Shi Y, Ding J, Liu JC, Wang H, Bu DF.

Zhonghua Er Ke Za Zhi. 2005 Nov;43(11):805-9. Chinese.

PubMed [citation]

PMID:: 16316524

Novel NPHS1 splice site mutations in a Chinese child with congenital nephrotic syndrome.

Fu R, Gou MF, Ma WH, He JJ, Luan Y, Liu J.

Genet Mol Res. 2015 Jan 23;14(1):433-9. doi: 10.4238/2015.January.23.17.

PubMed [citation]

PMID:: 25729976

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000962775.6

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 310 of the NPHS1 protein (p.Asp310Asn). This variant is present in population databases (rs763972372, gnomAD 0.02%). This missense change has been observed in individual(s) with nephrotic syndrome (PMID: 16316524, 25729976, 25903641, 28204945, 28392951). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 556151). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt NPHS1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

#	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

Last Updated: Sep 29, 2024

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