NM_002292.4(LAMB2):c.4469G>A (p.Arg1490Gln) AND multiple conditions

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Mar 1, 2022
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:
RCV001989006.4

Allele description [Variation Report for NM_002292.4(LAMB2):c.4469G>A (p.Arg1490Gln)]

NM_002292.4(LAMB2):c.4469G>A (p.Arg1490Gln)

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.4469G>A (p.Arg1490Gln)
HGVS:
  • NC_000003.12:g.49122808C>T
  • NG_008094.1:g.15359G>A
  • NG_054716.1:g.3131G>A
  • NM_002292.4:c.4469G>AMANE SELECT
  • NP_002283.3:p.Arg1490Gln
  • NC_000003.11:g.49160241C>T
  • NM_002292.3:c.4469G>A
Protein change:
R1490Q
Links:
dbSNP: rs533452341
NCBI 1000 Genomes Browser:
rs533452341
Molecular consequence:
  • NM_002292.4:c.4469G>A - 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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002287278Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 8, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002815700Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 1, 2022) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002287278.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces arginine with glutamine at codon 1490 of the LAMB2 protein (p.Arg1490Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs533452341, ExAC 0.01%). This variant has not been reported in the literature in individuals affected with LAMB2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002815700.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024