RBBP8NL

Summary

RBBP8NL (RBBP8 N-terminal like, HGNC:16144) is a protein-coding gene on chromosome 20q13.33, encoding RBBP8 N-terminal-like protein (Q8NC74).

Located in extracellular space.

Source: NCBI Gene 140893 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 141 total
• MANE Select transcript: NM_080833

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16144
Approved symbol	RBBP8NL
Name	RBBP8 N-terminal like
Location	20q13.33
Locus type	gene with protein product
Status	Approved
Aliases	dJ908M14.3
Ensembl gene	ENSG00000130701
Ensembl biotype	protein_coding
Entrez	140893

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000252998

RefSeq mRNA: 1 — MANE Select: NM_080833 NM_080833

CCDS: CCDS13498

Canonical transcript exons

ENST00000252998 — 14 exons

Exon	Start	End
ENSE00000897915	62415121	62415287
ENSE00000991932	62413821	62414556
ENSE00000991933	62413401	62413545
ENSE00000991934	62412830	62412900
ENSE00000991935	62412624	62412753
ENSE00000991936	62410237	62410996
ENSE00001175442	62416164	62416236
ENSE00001175453	62416760	62416872
ENSE00001175464	62417224	62417319
ENSE00001175472	62418423	62418465
ENSE00001175484	62415788	62415945
ENSE00001239799	62415578	62415660
ENSE00001239849	62419587	62419730
ENSE00001379909	62427460	62427539

Expression profiles

Bgee: expression breadth ubiquitous, 108 present calls, max score 93.12.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5778 / max 19.9516, expressed in 196 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188269	0.5778	196

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	93.12	gold quality
upper arm skin	UBERON:0004263	91.57	gold quality
vena cava	UBERON:0004087	88.67	gold quality
left ventricle myocardium	UBERON:0006566	88.17	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.60	gold quality
lower esophagus mucosa	UBERON:0035834	87.11	gold quality
myocardium	UBERON:0002349	86.33	gold quality
parotid gland	UBERON:0001831	85.35	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	85.35	gold quality
pons	UBERON:0000988	82.74	silver quality
epithelial cell of pancreas	CL:0000083	82.11	gold quality
vastus lateralis	UBERON:0001379	81.83	gold quality
cardia of stomach	UBERON:0001162	81.19	gold quality
quadriceps femoris	UBERON:0001377	80.39	gold quality
pharyngeal mucosa	UBERON:0000355	79.89	silver quality
inferior vagus X ganglion	UBERON:0005363	79.77	gold quality
heart right ventricle	UBERON:0002080	79.71	gold quality
pylorus	UBERON:0001166	79.64	silver quality
trachea	UBERON:0003126	79.53	silver quality
nipple	UBERON:0002030	78.92	gold quality
lateral globus pallidus	UBERON:0002476	78.80	silver quality
pancreatic ductal cell	CL:0002079	78.77	silver quality
pericardium	UBERON:0002407	78.76	gold quality
saphenous vein	UBERON:0007318	78.74	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	78.68	gold quality
biceps brachii	UBERON:0001507	78.24	gold quality
thymus	UBERON:0002370	77.84	gold quality
cerebellar vermis	UBERON:0004720	77.42	silver quality
superior vestibular nucleus	UBERON:0007227	77.25	gold quality
renal medulla	UBERON:0000362	77.21	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting RBBP8NL, 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-6778-3P	99.96	67.29	2693
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-6513-3P	99.59	69.77	1102
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-4293	99.22	65.46	1263
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-92A-1-5P	98.28	64.51	631
HSA-MIR-6893-3P	97.79	64.91	1238
HSA-MIR-6890-3P	97.50	65.71	997
HSA-MIR-370-3P	97.09	64.92	1221
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-541-3P	96.07	66.11	1271
HSA-MIR-654-5P	96.07	66.18	1280
HSA-MIR-6805-5P	95.79	64.86	670
HSA-MIR-1237-5P	95.38	62.21	451
HSA-MIR-4488	95.38	62.00	443
HSA-MIR-4697-5P	95.38	61.72	457

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbbp8l	ENSDARG00000087032
mus_musculus	Rbbp8nl	ENSMUSG00000038980
rattus_norvegicus	Rbbp8nl	ENSRNOG00000057245
caenorhabditis_elegans		WBGENE00008082

Paralogs (1): RBBP8 (ENSG00000101773)

Protein

Protein identifiers

RBBP8 N-terminal-like protein — Q8NC74 (reviewed: Q8NC74)

All UniProt accessions (1): Q8NC74

RefSeq proteins (1): NP_543023* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019518	CtIP_N	Domain
IPR033316	RBBP8-like	Family

Pfam: PF10482

UniProt features (18 total): compositionally biased region 10, sequence variant 4, region of interest 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NC74-F1	56.11	0.20

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): HATADA_METHYLATED_IN_LUNG_CANCER_DN, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, MARTENS_TRETINOIN_RESPONSE_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, CSHL1_TARGET_GENES, GREB1_TARGET_GENES, KMT2D_TARGET_GENES, TEAD2_TARGET_GENES, WDHD1_TARGET_GENES, ZNF592_TARGET_GENES, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_DN, BLANCO_MELO_BETA_INTERFERON_TREATED_BRONCHIAL_EPITHELIAL_CELLS_DN, BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_INFECTION_DN, BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_DEL_NS1_INFECTION_DN

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): obsolete extracellular space (GO:0005615)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

356 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBBP8NL	TM9SF4	Q92544	690
RBBP8NL	CABLES2	Q9BTV7	599
RBBP8NL	SOX15	P35717	511
RBBP8NL	POFUT1	Q9H488	501
RBBP8NL	KIF3B	O15066	499
RBBP8NL	PLAGL2	Q9UPG8	453
RBBP8NL	RCHY1	Q96PM5	450
RBBP8NL	PDPN	Q86YL7	435
RBBP8NL	KIAA1614	Q5VZ46	434
RBBP8NL	RPS21	P35265	430
RBBP8NL	ENC1	O14682	424
RBBP8NL	GPR85	P60893	423
RBBP8NL	KDF1	Q8NAX2	408
RBBP8NL	KBTBD11	O94819	394
RBBP8NL	DMRTC2	Q8IXT2	393

IntAct

29 interactions, top by confidence:

A	B	Type	Score
RBBP8NL	POLR3C	psi-mi:“MI:0915”(physical association)	0.560
RBBP8NL	EGLN3	psi-mi:“MI:0915”(physical association)	0.560
RBBP8NL	CHIA	psi-mi:“MI:0915”(physical association)	0.560
PHF1	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.560
LARP1B	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.560
CTBP2	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.560
PIN1	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.560
NCK2	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.560
ARPC3	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.560
NFKB1	NFKB1	psi-mi:“MI:0914”(association)	0.350
POLR3C	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
EGLN3	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
CHIA	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
PHF1	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
LARP1B	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
CTBP2	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
PIN1	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
ARPC3	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000
NCK2	RBBP8NL	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): RBBP8NL (Affinity Capture-RNA), RBBP8NL (Two-hybrid), RBBP8NL (Two-hybrid), RBBP8NL (Two-hybrid), RBBP8NL (Two-hybrid), RBBP8NL (Two-hybrid), CHIA (Two-hybrid), LARP1B (Two-hybrid), CTBP2 (Two-hybrid), POLR3C (Two-hybrid), RBBP8NL (Cross-Linking-MS (XL-MS)), RBBP8NL (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PPE3, A0A1W2PR82, A0A2Z4LIS9, A2VE02, A4D1S0, A5PKC7, A5PL33, A6H7B4, A6NEL2, A6QP24, A6QPM6, A8MTW9, A8MYA2, D3ZAQ5, D4AAA5, E7EW31, O75474, O75638, O89113, O94850, P0C7X2, P14652, P50617, P70339, Q2KIS6, Q3UN58, Q5JPB2, Q5VZ46, Q6GQX2, Q6NZ36, Q6ZSJ8, Q6ZW13, Q76NI1, Q7TNS8, Q80TS7, Q86UU5, Q8IWN7, Q8N6K4, Q8N944

Diamond homologs: A6QNQ6, B1WC58, F1R983, F6SNN2, Q6GNV6, Q80YR6, Q8NC74, Q99708, Q9ZRT1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	113
Likely benign	17
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2413 predictions. Top by Δscore:

Variant	Effect	Δscore
20:62415808:C:CA	donor_gain	1.0000
20:62415820:T:TA	donor_gain	1.0000
20:62415825:AG:A	donor_gain	1.0000
20:62415825:AGCCT:A	donor_gain	1.0000
20:62415875:C:CT	acceptor_gain	1.0000
20:62416162:ACC:A	donor_gain	1.0000
20:62416163:CCC:C	donor_gain	1.0000
20:62416188:T:TA	donor_gain	1.0000
20:62416758:A:AC	donor_gain	1.0000
20:62416759:C:CT	donor_gain	1.0000
20:62416869:CAGC:C	acceptor_gain	1.0000
20:62416873:C:CC	acceptor_gain	1.0000
20:62417219:CCCAC:C	donor_loss	1.0000
20:62417220:CCA:C	donor_loss	1.0000
20:62417221:CACC:C	donor_loss	1.0000
20:62417222:A:AT	donor_loss	1.0000
20:62417223:C:CT	donor_loss	1.0000
20:62417248:T:TA	donor_gain	1.0000
20:62417315:CGTCC:C	acceptor_gain	1.0000
20:62417317:TCC:T	acceptor_gain	1.0000
20:62417318:CC:C	acceptor_gain	1.0000
20:62417318:CCC:C	acceptor_gain	1.0000
20:62417318:CCCTG:C	acceptor_loss	1.0000
20:62417319:CC:C	acceptor_gain	1.0000
20:62417319:CCTGT:C	acceptor_loss	1.0000
20:62417320:C:CC	acceptor_gain	1.0000
20:62419595:T:TA	donor_gain	1.0000
20:62412618:CTGTA:C	donor_loss	0.9900
20:62412619:TGTA:T	donor_loss	0.9900
20:62412620:GTAC:G	donor_loss	0.9900

AlphaMissense

4264 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:62417275:A:G	L50P	0.996
20:62417272:C:G	R51P	0.994
20:62417296:A:G	L43P	0.992
20:62417286:C:A	K46N	0.991
20:62417286:C:G	K46N	0.991
20:62416870:A:G	L68P	0.990
20:62417233:A:G	L64P	0.989
20:62417242:A:G	L61P	0.989
20:62416845:G:C	C76W	0.988
20:62416847:A:G	C76R	0.988
20:62417224:C:A	R67M	0.988
20:62417254:A:G	L57P	0.988
20:62416855:C:T	C73Y	0.987
20:62416856:A:G	C73R	0.987
20:62416872:C:A	R67S	0.987
20:62416872:C:G	R67S	0.987
20:62417230:T:A	E65V	0.987
20:62417266:T:G	Q53P	0.987
20:62419616:A:G	L11P	0.987
20:62416854:G:C	C73W	0.986
20:62416855:C:A	C73F	0.985
20:62417263:T:G	Q54P	0.985
20:62418450:A:G	L26P	0.985
20:62416867:C:G	R69P	0.984
20:62416846:C:G	C76S	0.983
20:62416847:A:T	C76S	0.983
20:62416855:C:G	C73S	0.983
20:62416856:A:T	C73S	0.983
20:62417283:G:C	N47K	0.983
20:62417283:G:T	N47K	0.983

dbSNP variants (sampled 300 via entrez): RS1000399386 (20:62424974 G>A), RS1000543361 (20:62425773 G>A), RS1000734976 (20:62426016 G>T), RS1000745131 (20:62415349 C>A,T), RS1001172203 (20:62412317 C>T), RS1001352871 (20:62428656 C>A), RS1001677183 (20:62419123 G>A), RS1001718259 (20:62424401 G>A), RS1001726603 (20:62412075 C>G,T), RS1001781155 (20:62414832 G>T), RS1001958285 (20:62420414 A>G), RS1002009127 (20:62420111 A>G), RS1002389412 (20:62411920 G>A,T), RS1002515184 (20:62415753 C>A,T), RS1002627672 (20:62418291 CCG>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001942_4	Prostate cancer	4.000000e-08
GCST005173_6	Coronary artery calcified atherosclerotic plaque (130 HU threshold) in type 2 diabetes	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Estradiol	decreases expression, affects cotreatment	3
(+)-JQ1 compound	decreases expression	2
bisphenol F	increases expression	1
dicrotophos	decreases expression	1
bisphenol A	decreases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases methylation	1
coumarin	increases phosphorylation	1
abrine	increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Plant Extracts	decreases expression, affects cotreatment	1
Tobacco Smoke Pollution	affects expression	1
Valproic Acid	increases methylation	1
Zearalenone	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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