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NM_003489.4(NRIP1):c.279del (p.Asp92_Trp93insTer) AND Congenital anomalies of kidney and urinary tract 3

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 9, 2019
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:
RCV000735957.1

Allele description [Variation Report for NM_003489.4(NRIP1):c.279del (p.Asp92_Trp93insTer)]

NM_003489.4(NRIP1):c.279del (p.Asp92_Trp93insTer)

Gene:
NRIP1:nuclear receptor interacting protein 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
21q11.2
Genomic location:
Preferred name:
NM_003489.4(NRIP1):c.279del (p.Asp92_Trp93insTer)
HGVS:
  • NC_000021.9:g.14967915del
  • NG_050643.1:g.102990del
  • NM_003489.4:c.279delMANE SELECT
  • NP_003480.2:p.Asp92_Trp93insTer
  • NC_000021.8:g.16340236del
  • NM_003489.3:c.279delG
Links:
OMIM: 602490.0001; dbSNP: rs1555879360
NCBI 1000 Genomes Browser:
rs1555879360
Molecular consequence:
  • NM_003489.4:c.279del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Congenital anomalies of kidney and urinary tract 3
Identifiers:
MONDO: MONDO:0032646; MedGen: C4748921; OMIM: 618270

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000864146OMIM
no assertion criteria provided
Pathogenic
(Jan 9, 2019) 		germlineliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

A Dominant Mutation in Nuclear Receptor Interacting Protein 1 Causes Urinary Tract Malformations via Dysregulation of Retinoic Acid Signaling.

Vivante A, Mann N, Yonath H, Weiss AC, Getwan M, Kaminski MM, Bohnenpoll T, Teyssier C, Chen J, Shril S, van der Ven AT, Ityel H, Schmidt JM, Widmeier E, Bauer SB, Sanna-Cherchi S, Gharavi AG, Lu W, Magen D, Shukrun R, Lifton RP, Tasic V, et al.

J Am Soc Nephrol. 2017 Aug;28(8):2364-2376. doi: 10.1681/ASN.2016060694. Epub 2017 Apr 5.

PubMed [citation]
PMID:
28381549
PMCID:
PMC5533226

Details of each submission

From OMIM, SCV000864146.1

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

Description

In 7 affected members of a 3-generation Yemenite Jewish family (family H) with congenital anomalies of the kidney and urinary tract-3 (CAKUT3; 618270), Vivante et al. (2017) identified a heterozygous 1-bp deletion (c.279delG, NM_003489.3) in the NRIP1 gene, resulting in a frameshift and premature termination (Trp93fsTer). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family, although there was 1 possible unaffected mutation carrier, suggesting incomplete penetrance. The variant was not found in the 1000 Genomes Project, Exome Variant Server, or ExAC databases. In vitro functional expression studies in HEK293 cells showed that the mutation resulted in a loss of function and was unable to repress RA-mediated transcriptional activity.

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

Last Updated: Apr 23, 2022