NC_000003.12:g.(?_49121216)_(49533209_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 23, 2019
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:: RCV001384888.10

Allele description [Variation Report for NC_000003.12:g.(?_49121216)_(49533209_?)del]

NC_000003.12:g.(?_49121216)_(49533209_?)del

Genes:

TCTA:T cell leukemia translocation altered [Gene - OMIM - HGNC]
AMT:aminomethyltransferase [Gene - OMIM - HGNC]
C3orf62:chromosome 3 open reading frame 62 [Gene - HGNC]
CIMIP7:ciliary microtubule inner protein 7 [Gene - HGNC]
CCDC71:coiled-coil domain containing 71 [Gene - HGNC]
DAG1:dystroglycan 1 [Gene - OMIM - HGNC]
GPX1:glutathione peroxidase 1 [Gene - OMIM - HGNC]
IHO1:interactor of HORMAD1 1 [Gene - OMIM - HGNC]
KLHDC8B:kelch domain containing 8B [Gene - OMIM - HGNC]
LAMB2:laminin subunit beta 2 [Gene - OMIM - HGNC]
NICN1:nicolin 1, tubulin polyglutamylase complex subunit [Gene - OMIM - HGNC]
RHOA:ras homolog family member A [Gene - OMIM - HGNC]
USP4:ubiquitin specific peptidase 4 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p21.31

Genomic location:

Chr3: 49158649 - 49570642 (on Assembly GRCh37)

Preferred name:

NC_000003.12:g.(?_49121216)_(49533209_?)del

HGVS:

NC_000003.12:g.(?_49121216)_(49533209_?)del
NC_000003.11:g.(?_49158649)_(49570642_?)del

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001584548	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 23, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15367484, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001584548

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 23, 2019)

germline

clinical testing

PubMed (2)
[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

Human laminin beta2 deficiency causes congenital nephrosis with mesangial sclerosis and distinct eye abnormalities.

Zenker M, Aigner T, Wendler O, Tralau T, Müntefering H, Fenski R, Pitz S, Schumacher V, Royer-Pokora B, Wühl E, Cochat P, Bouvier R, Kraus C, Mark K, Madlon H, Dötsch J, Rascher W, Maruniak-Chudek I, Lennert T, Neumann LM, Reis A.

Hum Mol Genet. 2004 Nov 1;13(21):2625-32. Epub 2004 Sep 14.

PubMed [citation]

PMID:: 15367484

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, SCV001584548.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the LAMB2 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with LAMB2-related conditions. Loss-of-function variants in LAMB2 are known to be pathogenic (PMID: 15367484). 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: Nov 24, 2024

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