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NM_000278.5(PAX2):c.97del (p.Leu33fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 28, 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:
RCV002876762.3

Allele description [Variation Report for NM_000278.5(PAX2):c.97del (p.Leu33fs)]

NM_000278.5(PAX2):c.97del (p.Leu33fs)

Gene:
PAX2:paired box 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q24.31
Genomic location:
Preferred name:
NM_000278.5(PAX2):c.97del (p.Leu33fs)
HGVS:
  • NC_000010.11:g.100749799del
  • NG_008680.2:g.19091del
  • NM_000278.5:c.97delMANE SELECT
  • NM_001304569.2:c.190del
  • NM_003987.5:c.97del
  • NM_003988.5:c.97del
  • NM_003989.5:c.97del
  • NM_003990.5:c.97del
  • NP_000269.3:p.Leu33fs
  • NP_001291498.1:p.Leu64fs
  • NP_003978.3:p.Leu33fs
  • NP_003979.2:p.Leu33fs
  • NP_003980.3:p.Leu33fs
  • NP_003981.3:p.Leu33fs
  • NC_000010.10:g.102509553del
  • NC_000010.10:g.102509556del
Protein change:
L33fs
Molecular consequence:
  • NM_000278.5:c.97del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001304569.2:c.190del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003987.5:c.97del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003988.5:c.97del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003989.5:c.97del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003990.5:c.97del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Renal coloboma syndrome (PAPRS)
Synonyms:
RENAL-COLOBOMA SYNDROME WITH MACULAR ABNORMALITIES; Papillorenal syndrome; Optic nerve coloboma with renal disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007352; MedGen: C1852759; Orphanet: 1475; OMIM: 120330
Name:
Focal segmental glomerulosclerosis 7 (FSGS7)
Identifiers:
MONDO: MONDO:0014451; MedGen: C4014925; Orphanet: 656; OMIM: 616002

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003240746Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 28, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

PAX2 gene mutation in a family with isolated renal hypoplasia.

Nishimoto K, Iijima K, Shirakawa T, Kitagawa K, Satomura K, Nakamura H, Yoshikawa N.

J Am Soc Nephrol. 2001 Aug;12(8):1769-1772. doi: 10.1681/ASN.V1281769.

PubMed [citation]
PMID:
11461952

Mutations in PAX2 associate with adult-onset FSGS.

Barua M, Stellacci E, Stella L, Weins A, Genovese G, Muto V, Caputo V, Toka HR, Charoonratana VT, Tartaglia M, Pollak MR.

J Am Soc Nephrol. 2014 Sep;25(9):1942-53. doi: 10.1681/ASN.2013070686. Epub 2014 Mar 27.

PubMed [citation]
PMID:
24676634
PMCID:
PMC4147972
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003240746.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PAX2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu33Tyrfs*5) in the PAX2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PAX2 are known to be pathogenic (PMID: 11461952, 24676634).

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

Last Updated: Sep 29, 2024