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NM_000272.5(NPHP1):c.(?_-45)_(*443_?)del AND Nephronophthisis 1

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Oct 10, 2018
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:
RCV001251510.5

Allele description [Variation Report for NM_000272.5(NPHP1):c.(?_-45)_(*443_?)del]

NM_000272.5(NPHP1):c.(?_-45)_(*443_?)del

Genes:
LOC126806306:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:110906815-110908014 [Gene]
NPHP1:nephrocystin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2q13
Genomic location:
Preferred name:
NM_000272.5(NPHP1):c.(?_-45)_(*443_?)del
Other names:
NPHP1, DEL
HGVS:
  • NC_000002.12:g.(?_110123336)_(110205062_?)del
  • NC_000002.11:g.(?_110880913)_(110962639_?)del
  • NM_000272.3:c.-94_*455del
Note:
The deletion has been described at the genomic level, resulting in the loss of the transcript.
Nucleotide change:
DEL
Links:
OMIM: 607100.0005

Condition(s)

Name:
Nephronophthisis 1 (NPHP1)
Synonyms:
Nephronophthisis familial juvenile
Identifiers:
MONDO: MONDO:0009728; MedGen: C1855681; Orphanet: 655; OMIM: 256100

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000023849OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2004)
germlineliterature only

PubMed (6)
[See all records that cite these PMIDs]

SCV001427156Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 10, 2018)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Large homozygous deletions of the 2q13 region are a major cause of juvenile nephronophthisis.

Konrad M, Saunier S, Heidet L, Silbermann F, Benessy F, Calado J, Le Paslier D, Broyer M, Gubler MC, Antignac C.

Hum Mol Genet. 1996 Mar;5(3):367-71.

PubMed [citation]
PMID:
8852662

A novel gene encoding an SH3 domain protein is mutated in nephronophthisis type 1.

Hildebrandt F, Otto E, Rensing C, Nothwang HG, Vollmer M, Adolphs J, Hanusch H, Brandis M.

Nat Genet. 1997 Oct;17(2):149-53.

PubMed [citation]
PMID:
9326933
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000023849.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (6)

Description

Nephronophthisis 1

Approximately 80% of patients with nephronophthisis (NPHP1; 256100) demonstrate a homozygous deletion of about 290 kb that encompasses the NPHP1 gene (Konrad et al., 1996; Hildebrandt et al., 1997; Saunier et al., 2000).

Senior-Loken Syndrome 1

Caridi et al. (1998) described Senior-Loken syndrome (SLSN1; 266900), the association of nephronophthisis with autosomal recessive retinitis pigmentosa, in patients with homozygous deletion of the NPHP1 gene.

Joubert Syndrome 4

In 2 sibs with a mild form of Joubert syndrome (JBTS4; 609583), Parisi et al. (2004) demonstrated homozygous deletion of the NPHP1 gene identical, by mapping, to that in subjects with nephronophthisis alone. A hallmark of that disorder is cerebellar vermis hypoplasia with prominent superior cerebellar peduncles, creating the 'molar tooth sign' (MTS) on axial MRI. Parisi et al. (2004) suggested that the MTS may be relatively common in patients with juvenile nephronophthisis without classic symptoms of JS.

In 4 patients with Joubert syndrome from 3 nonconsanguineous families, Parisi et al. (2006) identified homozygosity for deletion of the NPHP1 gene. The molar tooth sign in these patients had a distinctive appearance, with elongated but not thickened superior cerebellar peduncles.

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

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001427156.2

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

Description

A homozygous deletion encompassing the entire NPHP1 gene has been identified; NM_000272.3(NPHP1):c.(?_-94)_(*462_?)del. The deletion includes at least the entire NPHP1 gene (NP_000263.2), and potentially extends into the adjacent gene, MALL (NP_005425.1). The variant is present in the general population at a frequency of 0.24% (Javorszky, E., et al. (2017)). The variant has been previously described as pathogenic in multiple patients with nephronophthisis. This deletion is the most frequent known cause of nephronophthisis (Chaki, M., et al. (2011), Lindstrand, A., et al. (2014), Hildebrandt, F., et al. (1997), Saunier, S., et al. (2000)). Based on the information available at the time of curation, this variant has been classified as PATHOGENIC.

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

Last Updated: Sep 29, 2024