NRIP1

nuclear receptor interacting protein 1

Basic information

Region (hg38): 21:14961234-15065936

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 (101 variants)
• Inborn genetic diseases (50 variants)
• NRIP1-related condition (8 variants)
• Congenital anomalies of kidney and urinary tract 3 (5 variants)
• not specified (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				20	12	32
missense			85	11	12	108
nonsense						0
start loss						0
frameshift			2			2
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	89	31	25

Variants in NRIP1

This is a list of pathogenic ClinVar variants found in the NRIP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
21-14964724-ATTCT-A		not specified	Uncertain significance (Jan 08, 2024)
21-14964728-T-A		Inborn genetic diseases	Uncertain significance (Jun 05, 2023)
21-14964738-G-A		Congenital anomalies of kidney and urinary tract 3 • NRIP1-related disorder	Benign/Likely benign (Jan 18, 2024)
21-14964745-C-T		NRIP1-related disorder	Uncertain significance (Dec 26, 2023)
21-14964750-C-T		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
21-14964763-A-C		NRIP1-related disorder	Likely benign (May 22, 2023)
21-14964767-T-C		NRIP1-related disorder	Benign (Nov 03, 2023)
21-14964779-G-A		NRIP1-related disorder	Benign/Likely benign (Oct 22, 2023)
21-14964781-T-C		Inborn genetic diseases • NRIP1-related disorder	Conflicting classifications of pathogenicity (Oct 03, 2023)
21-14964785-T-G			Likely benign (Sep 26, 2022)
21-14964790-G-A			Benign (Apr 01, 2024)
21-14964792-G-A		Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
21-14964808-T-C			Uncertain significance (Apr 18, 2022)
21-14964829-T-C		Inborn genetic diseases	Uncertain significance (Oct 24, 2023)
21-14964844-A-C			Uncertain significance (Jul 22, 2022)
21-14964855-T-G		Inborn genetic diseases	Uncertain significance (Nov 29, 2021)
21-14964863-A-G			Benign (Jan 15, 2024)
21-14964880-T-C			Benign (Sep 04, 2023)
21-14964890-C-G		Inborn genetic diseases • NRIP1-related disorder	Conflicting classifications of pathogenicity (Dec 26, 2023)
21-14964899-A-T		Inborn genetic diseases	Uncertain significance (Jun 30, 2023)
21-14964906-G-C		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
21-14964931-C-T		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
21-14964949-G-C		Inborn genetic diseases	Uncertain significance (Aug 27, 2023)
21-14964954-G-A		Inborn genetic diseases	Uncertain significance (Oct 06, 2022)
21-14964958-C-A		NRIP1-related disorder	Conflicting classifications of pathogenicity (Jun 29, 2023)

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
• 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