NM_002292.4(LAMB2):c.4139A>G (p.Asn1380Ser) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 2022
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:: RCV002019620.4

Allele description [Variation Report for NM_002292.4(LAMB2):c.4139A>G (p.Asn1380Ser)]

NM_002292.4(LAMB2):c.4139A>G (p.Asn1380Ser)

Gene:

LAMB2:laminin subunit beta 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_002292.4(LAMB2):c.4139A>G (p.Asn1380Ser)

HGVS:

NC_000003.12:g.49123217T>C
NG_008094.1:g.14950A>G
NG_054716.1:g.2722A>G
NM_002292.4:c.4139A>GMANE SELECT
NP_002283.3:p.Asn1380Ser
NC_000003.11:g.49160650T>C

Protein change:

N1380S

Links:

dbSNP: rs372463037

NCBI 1000 Genomes Browser:

rs372463037

Molecular consequence:

NM_002292.4:c.4139A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Pierson syndrome
Synonyms:: Microcoria and congenital nephrotic syndrome; MICROCORIA-CONGENITAL NEPHROTIC SYNDROME
Identifiers:: MONDO: MONDO:0012184; MedGen: C1836876; Orphanet: 2670; OMIM: 609049

Name:: LAMB2-related infantile-onset nephrotic syndrome
Synonyms:: Nephrotic syndrome, type 5, with or without ocular abnormalities; NEPHROTIC SYNDROME, TYPE 5, WITHOUT OCULAR ABNORMALITIES; NEPHROTIC SYNDROME, TYPE 5, WITH OCULAR ABNORMALITIES
Identifiers:: MONDO: MONDO:0013621; MedGen: C3280113; Orphanet: 306507; OMIM: 614199

Recent activity

Clear Turn Off Turn On

Homo sapiens tripartite motif containing 35 (TRIM35), mRNA
Homo sapiens tripartite motif containing 35 (TRIM35), mRNA
gi|94536781|ref|NM_171982.3|

Nucleotide
RPS3A [Taeniopygia guttata]
RPS3A [Taeniopygia guttata]
Gene ID:100190288

Gene
kiaa0319l [Solea solea]
kiaa0319l [Solea solea]
Gene ID:131447416

Gene
KIAA0319L KIAA0319 like [Gallus gallus]
KIAA0319L KIAA0319 like [Gallus gallus]
Gene ID:419634

Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002287062	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2022)	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

SCV002287062

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2022)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002287062.3

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1498275). This variant has not been reported in the literature in individuals affected with LAMB2-related conditions. This variant is present in population databases (rs372463037, gnomAD 0.02%). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1380 of the LAMB2 protein (p.Asn1380Ser). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

ClinVar

Relating variation to medicine