NM_000278.5(PAX2):c.131_152del (p.Leu44fs) AND Renal coloboma syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 1, 2012
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000014808.21

Allele description [Variation Report for NM_000278.5(PAX2):c.131_152del (p.Leu44fs)]

NM_000278.5(PAX2):c.131_152del (p.Leu44fs)

Gene:

PAX2:paired box 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q24.31

Genomic location:

Preferred name:

NM_000278.5(PAX2):c.131_152del (p.Leu44fs)

HGVS:

NC_000010.11:g.100749833_100749854del
NG_008680.2:g.19125_19146del
NM_000278.5:c.131_152delMANE SELECT
NM_001304569.2:c.224_245del
NM_003987.5:c.131_152del
NM_003988.5:c.131_152del
NM_003989.5:c.131_152del
NM_003990.5:c.131_152del
NP_000269.3:p.Leu44fs
NP_001291498.1:p.Leu75fs
NP_003978.3:p.Leu44fs
NP_003979.2:p.Leu44fs
NP_003980.3:p.Leu44fs
NP_003981.3:p.Leu44fs
NC_000010.10:g.102509590_102509611del

Protein change:

L44fs

Links:

OMIM: 167409.0003; dbSNP: rs76675173

NCBI 1000 Genomes Browser:

rs76675173

Molecular consequence:

NM_000278.5:c.131_152del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304569.2:c.224_245del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003987.5:c.131_152del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003988.5:c.131_152del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003989.5:c.131_152del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003990.5:c.131_152del - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000035063	OMIM	no assertion criteria provided	Pathogenic (Mar 1, 2012)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 9106533, 22213154

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000035063

OMIM

no assertion criteria provided

Pathogenic
(Mar 1, 2012)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PAX2 mutations.

Schimmenti LA, Cunliffe HE, McNoe LA, Ward TA, French MC, Shim HH, Zhang YH, Proesmans W, Leys A, Byerly KA, Braddock SR, Masuno M, Imaizumi K, Devriendt K, Eccles MR.

Am J Hum Genet. 1997 Apr;60(4):869-78.

PubMed [citation]

PMID:: 9106533
PMCID:: PMC1712484

Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database.

Bower M, Salomon R, Allanson J, Antignac C, Benedicenti F, Benetti E, Binenbaum G, Jensen UB, Cochat P, DeCramer S, Dixon J, Drouin R, Falk MJ, Feret H, Gise R, Hunter A, Johnson K, Kumar R, Lavocat MP, Martin L, Morinière V, Mowat D, et al.

Hum Mutat. 2012 Mar;33(3):457-66. doi: 10.1002/humu.22020. Epub 2012 Jan 31.

PubMed [citation]

PMID:: 22213154

Details of each submission

From OMIM, SCV000035063.1

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

Description

Schimmenti et al. (1997) demonstrated a deletion of 22 bp at positions 674 to 695, inclusive, in exon 2 of the PAX2 gene in a patient with the renal-coloboma syndrome (120330). The patient was an 11-year-old male who was found at age 3 months to have polyuria, severe proteinuria, and hypertension. Progressive end-stage renal failure developed at 2 years of age, requiring peritoneal dialysis. Renal ultrasound showed bilateral renal hypoplasia. Bilateral retinal and optic nerve colobomas were detected at 3 years of age. His IQ at 9 years was within the normal range. Both parents were clinically normal and did not carry the mutation.

Based on nucleotide numbering reflecting the cDNA transcript with +1 corresponding to the A of the ATG translation initiation codon in the reference sequence, Bower et al. (2012) referred to the 673_694del22 mutation as 129_150del, and to the predicted effect on the protein as Glu43Aspfs*33.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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