NRIP3

Summary

NRIP3 (nuclear receptor interacting protein 3, HGNC:1167) is a protein-coding gene on chromosome 11p15.4, encoding Nuclear receptor-interacting protein 3 (Q9NQ35).

Predicted to enable aspartic-type endopeptidase activity. Predicted to be involved in proteolysis.

Source: NCBI Gene 56675 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 48 total
• MANE Select transcript: NM_020645

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1167
Approved symbol	NRIP3
Name	nuclear receptor interacting protein 3
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000175352
Ensembl biotype	protein_coding
OMIM	613125
Entrez	56675

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000309166, ENST00000525100, ENST00000531090, ENST00000531142, ENST00000534759, ENST00000696747, ENST00000696748

RefSeq mRNA: 1 — MANE Select: NM_020645 NM_020645

CCDS: CCDS31422

Canonical transcript exons

ENST00000309166 — 7 exons

Exon	Start	End
ENSE00001103155	8983875	8983969
ENSE00001187319	8988118	8988282
ENSE00001267536	8985711	8985850
ENSE00001303381	8987548	8987630
ENSE00002175155	9003762	9004001
ENSE00003668786	8984072	8984124
ENSE00003968248	8980576	8983560

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 97.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.8619 / max 262.6677, expressed in 1236 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118535	8.8619	1236

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
lateral nuclear group of thalamus	UBERON:0002736	97.91	gold quality
cerebellar vermis	UBERON:0004720	97.77	gold quality
secondary oocyte	CL:0000655	94.86	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.68	gold quality
pons	UBERON:0000988	94.59	gold quality
substantia nigra pars compacta	UBERON:0001965	94.48	gold quality
dorsal root ganglion	UBERON:0000044	94.33	gold quality
cerebellum	UBERON:0002037	94.24	gold quality
cerebellar cortex	UBERON:0002129	94.20	gold quality
cerebellar hemisphere	UBERON:0002245	94.14	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.07	gold quality
middle temporal gyrus	UBERON:0002771	93.36	gold quality
sperm	CL:0000019	93.26	gold quality
oocyte	CL:0000023	92.48	gold quality
superior vestibular nucleus	UBERON:0007227	91.96	gold quality
Ammon’s horn	UBERON:0001954	91.29	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.85	gold quality
male germ cell	CL:0000015	90.72	gold quality
prefrontal cortex	UBERON:0000451	90.60	gold quality
endothelial cell	CL:0000115	90.49	gold quality
adult organism	UBERON:0007023	90.33	gold quality
lateral globus pallidus	UBERON:0002476	90.06	gold quality
left testis	UBERON:0004533	89.96	gold quality
right testis	UBERON:0004534	89.68	gold quality
frontal cortex	UBERON:0001870	89.49	gold quality
parietal lobe	UBERON:0001872	89.45	gold quality
ventral tegmental area	UBERON:0002691	89.44	gold quality
postcentral gyrus	UBERON:0002581	89.29	gold quality
occipital lobe	UBERON:0002021	89.16	gold quality
primary visual cortex	UBERON:0002436	89.12	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	12.52
E-GEOD-137537	yes	4.97
E-ANND-3	yes	4.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

163 targeting NRIP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-106A-5P	99.90	73.94	2683

Literature-anchored findings (GeneRIF, showing 1)

• NRIP3 is a novel translocation partner of MLL in acute myeloid leukemia (PMID:19454493)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Nrip3	ENSMUSG00000034825
rattus_norvegicus	Nrip3	ENSRNOG00000013290
drosophila_melanogaster	rngo	FBGN0030753
caenorhabditis_elegans		WBGENE00015308

Paralogs (4): NRIP2 (ENSG00000053702), UBAC2 (ENSG00000134882), DDI1 (ENSG00000170967), DDI2 (ENSG00000197312)

Protein

Protein identifiers

Nuclear receptor-interacting protein 3 — Q9NQ35 (reviewed: Q9NQ35)

Alternative names: Sarcoma antigen NY-SAR-105

All UniProt accessions (6): A0A8Q3WME3, B7Z3Y4, E9PIW3, Q9NQ35, H0YCM9, H0YEG7

RefSeq proteins (1): NP_065696* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019103	Peptidase_aspartic_DDI1-type	Domain
IPR021109	Peptidase_aspartic_dom_sf	Homologous_superfamily
IPR033821	NRIP_C	Domain

Pfam: PF09668

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQ35-F1	72.88	0.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 167 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, AP1_01, BENPORATH_ES_WITH_H3K27ME3, GGGTGGRR_PAX4_03, MYCMAX_01, USF_01, TGANTCA_AP1_C, ATF4_Q2, USF_02, SENESE_HDAC1_TARGETS_UP, MODULE_207, NFE2_01, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP, LEE_TARGETS_OF_PTCH1_AND_SUFU_DN, AP1FJ_Q2

GO Biological Process (1): proteolysis (GO:0006508)

GO Molecular Function (2): aspartic-type endopeptidase activity (GO:0004190), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein metabolic process	1
endopeptidase activity	1
aspartic-type peptidase activity	1
binding	1

Protein interactions and networks

STRING

760 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NRIP3	OCIAD2	Q56VL3	460
NRIP3	OR8A1	Q8NGG7	445
NRIP3	ZDHHC2	Q9UIJ5	435
NRIP3	LHFPL2	Q6ZUX7	432
NRIP3	SSPN	Q14714	429
NRIP3	NELL2	Q99435	429
NRIP3	CCDC73	Q6ZRK6	418
NRIP3	IKZF2	Q9UKS7	400
NRIP3	AGTR1	P30556	399
NRIP3	TBC1D30	Q9Y2I9	392
NRIP3	RNF182	Q8N6D2	385
NRIP3	CXCL12	P48061	372
NRIP3	ZNF714	Q96N38	368
NRIP3	TAFA5	Q7Z5A7	350
NRIP3	MYO18B	Q8IUG5	348
NRIP3	ZNF624	Q9P2J8	348

IntAct

28 interactions, top by confidence:

A	B	Type	Score
KASH5	NRIP3	psi-mi:“MI:0915”(physical association)	0.720
NRIP3	KASH5	psi-mi:“MI:0915”(physical association)	0.720
EFHC1	NRIP3	psi-mi:“MI:0915”(physical association)	0.560
C14orf119	NRIP3	psi-mi:“MI:0915”(physical association)	0.560
NRIP3	C14orf119	psi-mi:“MI:0915”(physical association)	0.560
CDC37	NRIP3	psi-mi:“MI:0915”(physical association)	0.560
UBL5	NRIP3	psi-mi:“MI:0915”(physical association)	0.560
NUTF2	NRIP3	psi-mi:“MI:0915”(physical association)	0.560
NRIP3	CFTR	psi-mi:“MI:0915”(physical association)	0.370
CFTR	NRIP3	psi-mi:“MI:0915”(physical association)	0.370
NRIP3	DDI2	psi-mi:“MI:0914”(association)	0.350
DDI1	PHC3	psi-mi:“MI:0914”(association)	0.350
NRIP3	PSMG1	psi-mi:“MI:0914”(association)	0.350
NRIP3	KASH5	psi-mi:“MI:0915”(physical association)	0.000
CDC37	NRIP3	psi-mi:“MI:0915”(physical association)	0.000
NUTF2	NRIP3	psi-mi:“MI:0915”(physical association)	0.000
UBL5	NRIP3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (26): CCDC155 (Two-hybrid), NRIP3 (Affinity Capture-MS), DDI2 (Affinity Capture-MS), NRIP3 (Affinity Capture-MS), PSMG2 (Affinity Capture-MS), NRIP3 (Affinity Capture-RNA), NRIP3 (Two-hybrid), NRIP3 (Two-hybrid), NRIP3 (Two-hybrid), NRIP3 (Two-hybrid), C14orf119 (Two-hybrid), UBL5 (Two-hybrid), NRIP3 (Affinity Capture-Western), DDI1 (Affinity Capture-Western), DDI2 (Affinity Capture-MS)

ESM2 similar proteins: A4FUB7, B2RD01, F4HT77, F4JPP0, F6QXW0, P03010, P04146, P05400, P08770, P0CT34, P0CT35, P0CT37, P0CT38, P0CT39, P0CT40, P0CT41, P0CT42, P0CT43, P10394, P10401, P10978, P15629, P25601, P92512, P92516, P92520, P92523, P93293, Q09575, Q2HEW6, Q3EC60, Q4PSK1, Q4R6I1, Q53RT3, Q56Y74, Q5R7G1, Q5RBK0, Q5SVZ6, Q66H30, Q6NT04

Diamond homologs: Q5R7G1, Q9BQI9, Q9JHR9, Q9JJR9, Q9NQ35, Q10256

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

48 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1024 predictions. Top by Δscore:

Variant	Effect	Δscore
11:8983873:A:AC	donor_gain	1.0000
11:8983874:C:CC	donor_gain	1.0000
11:8983874:CTTGT:C	donor_gain	1.0000
11:8983966:TGCA:T	acceptor_gain	1.0000
11:8983968:CA:C	acceptor_gain	1.0000
11:8983970:C:CC	acceptor_gain	1.0000
11:8984125:C:CC	acceptor_gain	1.0000
11:8987629:CA:C	acceptor_gain	1.0000
11:8987631:C:CC	acceptor_gain	1.0000
11:9003756:GCTCA:G	donor_loss	1.0000
11:9003757:CTCA:C	donor_loss	1.0000
11:9003758:TCACC:T	donor_loss	1.0000
11:9003759:CACC:C	donor_loss	1.0000
11:9003760:A:AC	donor_gain	1.0000
11:9003760:ACC:A	donor_loss	1.0000
11:9003761:C:CC	donor_gain	1.0000
11:9003761:C:T	donor_loss	1.0000
11:9003766:T:TA	donor_gain	1.0000
11:8983867:GCACT:G	donor_loss	0.9900
11:8983868:CACTC:C	donor_loss	0.9900
11:8983869:ACTCA:A	donor_loss	0.9900
11:8983870:CTCAC:C	donor_loss	0.9900
11:8983871:TCACT:T	donor_loss	0.9900
11:8983872:C:CC	donor_loss	0.9900
11:8983971:T:G	acceptor_loss	0.9900
11:8984122:CAT:C	acceptor_gain	0.9900
11:8984124:TCT:T	acceptor_loss	0.9900
11:8984125:C:A	acceptor_loss	0.9900
11:8985857:C:CT	acceptor_gain	0.9900
11:8987543:CT:C	donor_loss	0.9900

AlphaMissense

1567 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:9003831:G:C	F35L	0.999
11:9003831:G:T	F35L	0.999
11:9003833:A:G	F35L	0.999
11:8983941:A:G	L215P	0.998
11:8984097:C:T	G197D	0.998
11:8987580:A:C	N130K	0.998
11:8987580:A:T	N130K	0.998
11:8987602:A:T	V123D	0.998
11:9003808:A:G	L43P	0.998
11:8984085:A:G	L201P	0.997
11:8988128:A:T	V110D	0.997
11:9003832:A:G	F35S	0.997
11:8983962:A:T	I208K	0.996
11:8983969:A:G	C206R	0.996
11:8984085:A:T	L201H	0.996
11:8984098:C:G	G197R	0.996
11:9003805:A:G	L44P	0.996
11:9003805:A:T	L44Q	0.995
11:9003857:G:T	R27S	0.995
11:8983962:A:C	I208R	0.994
11:8988123:A:G	C112R	0.994
11:8985722:G:T	A184E	0.993
11:9003808:A:T	L43Q	0.993
11:9003817:G:A	S40F	0.993
11:9003821:C:G	D39H	0.993
11:9003832:A:C	F35C	0.993
11:9003846:C:A	K30N	0.993
11:9003846:C:G	K30N	0.993
11:8983904:A:C	F227L	0.992
11:8983904:A:T	F227L	0.992

dbSNP variants (sampled 300 via entrez): RS1000142204 (11:8980623 C>A), RS1000345231 (11:8983570 G>A,C), RS1000678136 (11:8982010 A>G), RS1001035623 (11:8995546 C>T), RS1001160011 (11:8982356 G>A), RS1001228424 (11:8994418 T>A,C), RS1001257322 (11:8987476 C>G,T), RS1001266994 (11:8996482 T>C), RS1001385359 (11:8987840 A>C), RS1002260334 (11:8982624 G>A,C), RS1002324933 (11:8996814 G>A), RS1002421143 (11:8989303 C>T), RS1002902170 (11:8985310 C>T), RS1002934512 (11:8985449 A>G), RS1002991146 (11:8999713 C>T)

Disease associations

OMIM: gene MIM:613125 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST010703_171	Brain morphology (MOSTest)	5.000000e-09
GCST012228_404	Waist-hip index	5.000000e-08
GCST012229_139	Hip index	2.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	8
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
cobaltous chloride	increases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
entinostat	decreases expression, increases expression	2
(+)-JQ1 compound	increases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Arsenic	increases expression, affects expression, affects cotreatment, increases abundance	2
Estradiol	affects expression, affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Silicon Dioxide	increases expression	2
Tobacco Smoke Pollution	increases expression	2
p-Chloromercuribenzoic Acid	decreases expression, affects cotreatment	2
aristolochic acid I	increases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	decreases expression	1
butyraldehyde	increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
potassium chromate(VI)	increases expression	1
pentanal	increases expression	1
dinophysistoxin 1	increases expression	1
Am 580	increases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
Temozolomide	decreases expression	1
Zoledronic Acid	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.