NRIP1

nuclear receptor interacting protein 1

Basic information

Region (hg38): 21:14961235-15065936

Links

ENSG00000180530

∙ NCBI:8204 ∙ OMIM:602490 ∙ HGNC:8001 ∙ Uniprot:P48552 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital anomalies of kidney and urinary tract 3 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital anomalies of the kidney and urinary tract 3	AD	Renal	Evidence or clinical applicability is unclear	Neurologic; Renal	21743468; 28381549

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NRIP1 gene.

not_provided (155 variants)
Inborn_genetic_diseases (148 variants)
NRIP1-related_disorder (51 variants)
Congenital_anomalies_of_kidney_and_urinary_tract_3 (15 variants)
not_specified (3 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Congenital_anomaly_of_kidney_and_urinary_tract (1 variants)
Long_QT_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRIP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003489.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				48 clinvar	11 clinvar	59
missense			201 clinvar	25 clinvar	11 clinvar	237
nonsense						0
start loss						0
frameshift	1 clinvar		5 clinvar	1 clinvar		7
splice donor/acceptor (+/-2bp)						0
Total	1	0	206	74	22

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRIP1	protein_coding	protein_coding	ENST00000400202	1	103766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00606	125698	0	38	125736	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.460	610	579	1.05	0.0000277	7665
Missense in Polyphen		198	201.32	0.98353		2754
Synonymous	-1.07	240	220	1.09	0.0000112	2226
Loss of Function	4.66	4	32.8	0.122	0.00000177	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000675	0.000675
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000973	0.0000791
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1. Also modulates transcriptional repression by nuclear hormone receptors. Positive regulator of the circadian clock gene expression: stimulates transcription of ARNTL/BMAL1, CLOCK and CRY1 by acting as a coactivator for RORA and RORC. {ECO:0000269|PubMed:10364267, ECO:0000269|PubMed:11509661, ECO:0000269|PubMed:11518808, ECO:0000269|PubMed:12554755, ECO:0000269|PubMed:15060175, ECO:0000269|PubMed:21628546, ECO:0000269|PubMed:7641693}.;
Pathway: Adipogenesis;Aryl Hydrocarbon Receptor;Pregnane X Receptor pathway;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;Ovarian Infertility Genes;Transcription factor regulation in adipogenesis;Liver steatosis AOP;mechanism of gene regulation by peroxisome proliferators via ppara;Circadian Clock;Coregulation of Androgen receptor activity;FOXA1 transcription factor network;Validated nuclear estrogen receptor alpha network;Retinoic acid receptors-mediated signaling (Consensus)

Recessive Scores

pRec: 0.199

Intolerance Scores

loftool: 0.0754
rvis_EVS: 1.39
rvis_percentile_EVS: 94.64

Haploinsufficiency Scores

pHI: 0.826
hipred: Y
hipred_score: 0.762
ghis: 0.446

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.112

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Nrip1
Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; digestive/alimentary phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;ovarian follicle rupture;circadian rhythm;lipid storage;androgen receptor signaling pathway;circadian regulation of gene expression;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;cellular response to estradiol stimulus
Cellular component: histone deacetylase complex;nuclear chromatin;nucleus;nucleoplasm;nucleolus;nuclear speck
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;transcription coactivator activity;transcription corepressor activity;protein binding;estrogen receptor binding;nuclear hormone receptor binding;glucocorticoid receptor binding;histone deacetylase binding;retinoid X receptor binding;androgen receptor binding