RIMBP3B

Summary

RIMBP3B (RIMS binding protein 3B, HGNC:33891) is a protein-coding gene on chromosome 22q11.21, encoding RIMS-binding protein 3B (A6NNM3). Probable component of the manchette, a microtubule-based structure which plays a key role in sperm head morphogenesis during late stages of sperm development.

Predicted to enable benzodiazepine receptor binding activity. Predicted to be involved in fertilization and spermatid development. Predicted to be located in manchette. Predicted to be active in nucleus.

Source: NCBI Gene 440804 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 56 total — 1 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_001128635

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33891
Approved symbol	RIMBP3B
Name	RIMS binding protein 3B
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000274600
Ensembl biotype	protein_coding
OMIM	612700
Entrez	440804

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000620804

RefSeq mRNA: 1 — MANE Select: NM_001128635 NM_001128635

CCDS: CCDS46668

Canonical transcript exons

ENST00000620804 — 1 exons

Exon	Start	End
ENSE00003978226	21383751	21389478

Expression profiles

Bgee: expression breadth broad, 37 present calls, max score 83.19.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.19	gold quality
left testis	UBERON:0004533	75.81	gold quality
testis	UBERON:0000473	75.03	gold quality
right testis	UBERON:0004534	72.26	gold quality
granulocyte	CL:0000094	55.25	gold quality
stromal cell of endometrium	CL:0002255	53.74	gold quality
bone marrow cell	CL:0002092	50.13	gold quality
lymph node	UBERON:0000029	48.55	gold quality
ventricular zone	UBERON:0003053	47.53	silver quality
leukocyte	CL:0000738	47.00	silver quality
vermiform appendix	UBERON:0001154	46.66	gold quality
tonsil	UBERON:0002372	45.99	gold quality
monocyte	CL:0000576	45.65	silver quality
colonic epithelium	UBERON:0000397	45.21	gold quality
blood	UBERON:0000178	43.93	silver quality
islet of Langerhans	UBERON:0000006	42.75	gold quality
duodenum	UBERON:0002114	41.86	silver quality
spleen	UBERON:0002106	41.66	silver quality
bone marrow	UBERON:0002371	41.24	gold quality
mucosa of transverse colon	UBERON:0004991	41.02	silver quality
cortical plate	UBERON:0005343	40.09	gold quality
placenta	UBERON:0001987	38.53	gold quality
prefrontal cortex	UBERON:0000451	38.40	silver quality
descending thoracic aorta	UBERON:0002345	38.20	silver quality
fallopian tube	UBERON:0003889	37.32	silver quality
apex of heart	UBERON:0002098	37.25	silver quality
pancreas	UBERON:0001264	36.80	silver quality
right uterine tube	UBERON:0001302	36.57	silver quality
thoracic aorta	UBERON:0001515	35.99	silver quality
smooth muscle tissue	UBERON:0001135	35.65	silver quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-9067	yes	12.01
E-MTAB-10137	no	4.29
E-ANND-3	no	0.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting RIMBP3B, 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-3617-3P	99.98	67.86	918
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-4722-3P	99.35	65.22	1099
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-7851-3P	98.72	64.88	980
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-138-5P	98.43	70.49	1292
HSA-MIR-4518	98.12	66.82	1030
HSA-MIR-1266-5P	97.71	66.92	1052
HSA-MIR-5089-3P	97.50	67.82	758
HSA-MIR-526B-5P	97.41	67.99	1074
HSA-MIR-3187-3P	97.38	65.80	904
HSA-MIR-342-5P	97.25	64.10	817
HSA-MIR-4701-5P	96.45	68.41	1121
HSA-MIR-588	96.45	68.36	1127
HSA-MIR-524-3P	95.15	66.16	109
HSA-MIR-525-3P	95.15	65.95	109
HSA-MIR-3672	94.46	65.67	646
HSA-MIR-6864-3P	94.46	65.97	625

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000103792
mus_musculus	Rimbp3	ENSMUSG00000071636
rattus_norvegicus	Rimbp3	ENSRNOG00000030452
drosophila_melanogaster	Rbp	FBGN0262483
caenorhabditis_elegans		WBGENE00006513

Paralogs (4): TSPOAP1 (ENSG00000005379), RIMBP2 (ENSG00000060709), RIMBP3C (ENSG00000183246), RIMBP3 (ENSG00000275793)

Protein

Protein identifiers

RIMS-binding protein 3B — A6NNM3 (reviewed: A6NNM3)

Alternative names: RIMS-binding protein 3.2

All UniProt accessions (1): A6NNM3

UniProt curated annotations — full annotation on UniProt →

Function. Probable component of the manchette, a microtubule-based structure which plays a key role in sperm head morphogenesis during late stages of sperm development.

Subunit / interactions. Interacts with LRGUK (via guanylate kinase-like domain). Interacts (via C-terminus) with HOOK1 (via coiled-coil region).

Subcellular location. Cytoplasm. Cytoskeleton.

Similarity. Belongs to the RIMBP family.

RefSeq proteins (1): NP_001122107* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001452	SH3_domain	Domain
IPR003961	FN3_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036028	SH3-like_dom_sf	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR040325	RIMBP1/2/3	Family
IPR057884	FN3_RIM-BP1/2/3	Domain
IPR057950	RIMB1/RIM3A-C-like_N	Domain

Pfam: PF07653, PF25523, PF25566

UniProt features (22 total): region of interest 7, compositionally biased region 6, domain 5, coiled-coil region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NNM3-F1	59.08	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_MALE_GAMETE_GENERATION, GOBP_CELL_CELL_SIGNALING, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_SYNAPTIC_SIGNALING, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_FERTILIZATION, GOMF_SIGNALING_RECEPTOR_BINDING, GOBP_NEUROMUSCULAR_SYNAPTIC_TRANSMISSION, NUYTTEN_EZH2_TARGETS_DN, GOCC_MANCHETTE, GOMF_BENZODIAZEPINE_RECEPTOR_BINDING, CDC5L_TARGET_GENES, ZNF184_TARGET_GENES, MIR4701_5P

GO Biological Process (4): spermatid development (GO:0007286), fertilization (GO:0009566), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (2): benzodiazepine receptor binding (GO:0030156), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytoskeleton (GO:0005856), manchette (GO:0002177), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
germ cell development	1
spermatid differentiation	1
sexual reproduction	1
reproductive process	1
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
signaling receptor binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
microtubule cytoskeleton	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

484 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RIMBP3B	TMEM191B	P0C7N4	620
RIMBP3B	RIMS2	Q9UQ26	591
RIMBP3B	FN1	P02751	542
RIMBP3B	ATP5MGL	Q7Z4Y8	540
RIMBP3B	DCAF5	Q96JK2	523
RIMBP3B	SLC35E4	Q6ICL7	507
RIMBP3B	SRC	P12931	494
RIMBP3B	CFAP73	A6NFT4	487
RIMBP3B	TDRD15	B5MCY1	481
RIMBP3B	TSPO	P30536	457
RIMBP3B	TMEM121B	Q9BXQ6	447
RIMBP3B	ZNF280A	P59817	446
RIMBP3B	CCDC116	Q8IYX3	434
RIMBP3B	PRSS37	A4D1T9	430
RIMBP3B	DDTL	A6NHG4	417
RIMBP3B	POTEH	Q6S545	417

IntAct

0 interactions, top by confidence:

BioGRID (1): RIMBP3B (Affinity Capture-MS)

ESM2 similar proteins: A0A140LIT1, A0A1B0GVG4, A0JNH6, A1A5D9, A6NC98, A6NGB0, A6NJZ7, A6NNM3, F6XLV1, O15049, O54887, P0C7N4, P58660, P60531, Q0D2H9, Q0P5D1, Q2KJ21, Q2TAC2, Q3LUD3, Q3T1I3, Q3TMW1, Q3V0F0, Q4QRL3, Q5JTB6, Q5RD60, Q66HR5, Q6NSJ2, Q6PHN1, Q6QZQ4, Q80VM7, Q8BP01, Q8C7U1, Q8CB62, Q8CGU1, Q8CHW5, Q8K2I2, Q8N137, Q8N283, Q8N6Y0, Q8R370

Diamond homologs: A6NJZ7, A6NNM3, O95153, Q3V0F0, Q80U40, Q9JIR1, Q9UFD9, O15034, Q7TNF8, Q8QFX1, Q9JIR0, A0A0K3AV08, A1CEK6, A1DFN5, A2QW93, E2RP94, Q0CJU8, Q15811, Q4WHP5, Q557J6, Q5BBL4, Q96B97

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
RIMBP3B	“down-regulates activity”	RIMS1	binding
RIMBP3B	“down-regulates activity”	RIMS2	binding
RIMBP3B	“down-regulates activity”	RIMS3	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	49
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
973580	NC_000022.10:g.21514655_22986816del	Pathogenic
1340046	GRCh37/hg19 22q11.21(chr22:21059669-21804716)x1	Likely pathogenic

SpliceAI

22 predictions. Top by Δscore:

Variant	Effect	Δscore
22:21389300:T:G	acceptor_gain	0.6400
22:21389294:A:AG	acceptor_gain	0.4900
22:21389305:G:T	acceptor_gain	0.4100
22:21389303:G:T	acceptor_gain	0.4000
22:21389211:TGC:T	acceptor_gain	0.3900
22:21389212:GCG:G	acceptor_gain	0.3900
22:21389292:C:G	acceptor_gain	0.3800
22:21389213:C:CT	acceptor_gain	0.3500
22:21389316:A:T	acceptor_gain	0.3400
22:21389304:C:T	acceptor_gain	0.3200
22:21389291:A:AG	acceptor_gain	0.2900
22:21389313:A:AG	acceptor_gain	0.2700
22:21389314:G:GG	acceptor_gain	0.2700
22:21389301:G:T	acceptor_gain	0.2600
22:21389099:G:GC	acceptor_gain	0.2400
22:21388374:C:T	donor_gain	0.2300
22:21389315:A:G	acceptor_gain	0.2300
22:21389130:C:G	acceptor_gain	0.2200
22:21389290:C:A	acceptor_gain	0.2200
22:21389196:TG:T	acceptor_gain	0.2000
22:21389237:T:A	acceptor_gain	0.2000
22:21389311:C:A	acceptor_gain	0.2000

AlphaMissense

10553 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:21387177:T:A	W1107R	0.988
22:21387177:T:C	W1107R	0.988
22:21387237:G:C	A1127P	0.987
22:21387179:G:C	W1107C	0.976
22:21387179:G:T	W1107C	0.976
22:21386484:T:C	F876L	0.971
22:21386486:C:A	F876L	0.971
22:21386486:C:G	F876L	0.971
22:21387172:T:A	V1105D	0.971
22:21385474:T:C	L539P	0.964
22:21387349:T:A	V1164E	0.961
22:21384453:T:C	F199L	0.957
22:21384455:C:A	F199L	0.957
22:21384455:C:G	F199L	0.957
22:21387090:T:C	F1078L	0.951
22:21387092:C:A	F1078L	0.951
22:21387092:C:G	F1078L	0.951
22:21385452:T:C	S532P	0.949
22:21386895:T:A	W1013R	0.949
22:21386895:T:C	W1013R	0.949
22:21387241:T:A	V1128E	0.948
22:21387375:T:C	S1173P	0.947
22:21387178:G:C	W1107S	0.946
22:21387234:T:G	Y1126D	0.945
22:21384268:G:C	R137P	0.943
22:21387226:T:A	V1123D	0.942
22:21387232:G:T	G1125V	0.939
22:21387353:A:C	R1165S	0.935
22:21387353:A:T	R1165S	0.935
22:21386986:T:C	F1043S	0.933

dbSNP variants (sampled 300 via entrez): RS1007518731 (22:21388296 G>C), RS1025949559 (22:21388668 A>C), RS1036275509 (22:21389182 T>G), RS1052037670 (22:21388193 G>A), RS1055937712 (22:21382541 G>A), RS113594192 (22:21383522 A>G), RS1156523195 (22:21382462 C>T), RS1157170767 (22:21382103 CAAAAAAA>C,CAA,CAAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA), RS1157386150 (22:21387659 G>A), RS1157479655 (22:21389319 T>C), RS1158604664 (22:21389360 C>T), RS1158936061 (22:21382893 T>C), RS1159027895 (22:21388570 C>T), RS1160571556 (22:21382236 G>A), RS1160957990 (22:21382704 C>G)

Disease associations

OMIM: gene MIM:612700 | disease phenotypes: MIM:611867

GenCC curated gene-disease

Mondo (1): chromosome 22q11.2 deletion syndrome, distal (MONDO:0012740)

Orphanet (1): Distal 22q11.2 microdeletion syndrome (Orphanet:261330)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C567511	Chromosome 22q11.2 Deletion Syndrome, Distal (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
abrine	decreases expression	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Smoke	decreases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	increases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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