RIMBP3C

Summary

RIMBP3C (RIMS binding protein 3C, HGNC:33892) is a protein-coding gene on chromosome 22q11.21, encoding RIMS-binding protein 3C (A6NJZ7). 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 150221 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 10 total — 1 pathogenic
• MANE Select transcript: NM_001128633

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33892
Approved symbol	RIMBP3C
Name	RIMS binding protein 3C
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000183246
Ensembl biotype	protein_coding
OMIM	612701
Entrez	150221

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000433039

RefSeq mRNA: 1 — MANE Select: NM_001128633 NM_001128633

CCDS: CCDS46669

Canonical transcript exons

ENST00000433039 — 1 exons

Exon	Start	End
ENSE00001685980	21545666	21551461

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 69.73.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	69.73	gold quality
testis	UBERON:0000473	66.29	gold quality
left testis	UBERON:0004533	65.37	gold quality
stromal cell of endometrium	CL:0002255	63.86	gold quality
granulocyte	CL:0000094	51.07	silver quality
ganglionic eminence	UBERON:0004023	45.70	gold quality
ventricular zone	UBERON:0003053	44.32	gold quality
cortical plate	UBERON:0005343	44.10	gold quality
bone marrow cell	CL:0002092	43.05	gold quality
lymph node	UBERON:0000029	42.12	silver quality
bone marrow	UBERON:0002371	41.41	gold quality
blood	UBERON:0000178	39.05	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
lower esophagus mucosa	UBERON:0035834	37.06	gold quality
islet of Langerhans	UBERON:0000006	37.04	gold quality
prefrontal cortex	UBERON:0000451	37.00	silver quality
sural nerve	UBERON:0015488	36.16	gold quality
tonsil	UBERON:0002372	35.80	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.60	gold quality
urinary bladder	UBERON:0001255	35.38	silver quality
placenta	UBERON:0001987	35.10	silver quality
skeletal muscle tissue	UBERON:0001134	34.79	gold quality
muscle tissue	UBERON:0002385	34.45	gold quality
vermiform appendix	UBERON:0001154	34.43	gold quality
cortex of kidney	UBERON:0001225	34.25	gold quality
frontal cortex	UBERON:0001870	34.02	silver quality
primary visual cortex	UBERON:0002436	34.02	gold quality
gall bladder	UBERON:0002110	33.71	silver quality
liver	UBERON:0002107	33.44	gold quality
smooth muscle tissue	UBERON:0001135	33.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting RIMBP3C, 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-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-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), RIMBP3B (ENSG00000274600), RIMBP3 (ENSG00000275793)

Protein

Protein identifiers

RIMS-binding protein 3C — A6NJZ7 (reviewed: A6NJZ7)

Alternative names: RIMS-binding protein 3.3

All UniProt accessions (1): A6NJZ7

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). May interact with FASLG.

Subcellular location. Cytoplasm. Cytoskeleton.

Similarity. Belongs to the RIMBP family.

RefSeq proteins (1): NP_001122105* (*=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-A6NJZ7-F1	58.95	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (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, GOCC_MANCHETTE, GOMF_BENZODIAZEPINE_RECEPTOR_BINDING, MIR4701_5P, MIR588, GSE10273_LOW_IL7_VS_HIGH_IL7_AND_IRF4_IN_IRF4_8_NULL_PRE_BCELL_DN, ZSCAN4_TARGET_GENES

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

578 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RIMBP3C	RIMS2	Q9UQ26	561
RIMBP3C	LRRC74B	Q6ZQY2	548
RIMBP3C	FN1	P02751	542
RIMBP3C	FAM86B2	P0C5J1	541
RIMBP3C	GAB4	Q2WGN9	530
RIMBP3C	CCT8L2	Q96SF2	526
RIMBP3C	SRC	P12931	494
RIMBP3C	GPR162	Q16538	473
RIMBP3C	ATP5MGL	Q7Z4Y8	448
RIMBP3C	TSPO	P30536	436
RIMBP3C	SLC35E4	Q6ICL7	433
RIMBP3C	CCDC54	Q8NEL0	428
RIMBP3C	TSACC	Q96A04	419
RIMBP3C	TDRD15	B5MCY1	419
RIMBP3C	GOLGA8Q	H3BV12	417

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RIMBP3C	FASLG	psi-mi:“MI:0407”(direct interaction)	0.440
PNMA2	TARS3	psi-mi:“MI:0914”(association)	0.350

BioGRID (24): RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), RIMBP3C (Two-hybrid), NOXA1 (Two-hybrid), GPANK1 (Two-hybrid), C22orf39 (Two-hybrid), RIMBP3C (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
RIMBP3C	“down-regulates activity”	RIMS1	binding
RIMBP3C	“down-regulates activity”	RIMS2	binding
RIMBP3C	“down-regulates activity”	RIMS3	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	6
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
816205	GRCh37/hg19 22q11.21-11.22(chr22:21029655-22481498)x1	Pathogenic

SpliceAI

12 predictions. Top by Δscore:

Variant	Effect	Δscore
22:21551414:GCATA:G	donor_loss	0.4200
22:21551415:CATA:C	donor_loss	0.4200
22:21551416:ATACC:A	donor_loss	0.4200
22:21551417:TACC:T	donor_loss	0.4200
22:21551418:A:T	donor_loss	0.4200
22:21551419:C:A	donor_loss	0.4200
22:21551420:C:A	donor_loss	0.3900
22:21551413:GGCAT:G	donor_loss	0.3600
22:21551421:T:A	donor_loss	0.3200
22:21545903:ACTT:A	acceptor_gain	0.2800
22:21551416:A:T	donor_gain	0.2500
22:21551412:GGGC:G	donor_loss	0.2000

AlphaMissense

10555 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:21547658:A:G	W1107R	0.987
22:21547658:A:T	W1107R	0.987
22:21547598:C:G	A1127P	0.979
22:21547656:C:A	W1107C	0.975
22:21547656:C:G	W1107C	0.975
22:21550583:C:G	A132P	0.969
22:21548349:G:C	F876L	0.968
22:21548349:G:T	F876L	0.968
22:21548351:A:G	F876L	0.968
22:21550567:C:G	R137P	0.967
22:21550380:G:C	F199L	0.962
22:21550380:G:T	F199L	0.962
22:21550382:A:G	F199L	0.962
22:21550549:A:G	L143P	0.960
22:21550559:C:G	A140P	0.960
22:21547663:A:T	V1105D	0.957
22:21550573:A:G	L135P	0.953
22:21549383:A:G	S532P	0.952
22:21550561:A:G	L139P	0.952
22:21549361:A:G	L539P	0.951
22:21547486:A:T	V1164E	0.948
22:21547743:G:C	F1078L	0.947
22:21547743:G:T	F1078L	0.947
22:21547745:A:G	F1078L	0.947
22:21547460:A:G	S1173P	0.945
22:21547609:A:T	V1123D	0.942
22:21547940:A:G	W1013R	0.942
22:21547940:A:T	W1013R	0.942
22:21547657:C:G	W1107S	0.941
22:21550579:C:G	R133P	0.940

dbSNP variants (sampled 300 via entrez): RS1004145536 (22:21553402 G>T), RS1006536169 (22:21551641 C>T), RS1006755164 (22:21552725 T>C), RS1016542823 (22:21551665 G>A), RS1016659708 (22:21545343 A>G), RS1025357317 (22:21551963 A>G), RS1025833682 (22:21553075 CAG>C), RS1035176953 (22:21553453 G>A), RS1038041623 (22:21552937 G>T), RS1042261054 (22:21546117 G>A), RS1050932777 (22:21552580 C>A), RS1051468664 (22:21546576 C>A), RS1055109241 (22:21545984 G>A), RS1156595019 (22:21552649 C>T), RS1156612884 (22:21545705 G>A)

Disease associations

OMIM: gene MIM:612701 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
perfluorooctanoic acid	affects cotreatment, increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
perfluorooctane sulfonic acid	affects cotreatment, increases expression	1
perfluorohexanesulfonic acid	affects cotreatment, increases expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects response to substance, decreases expression	1
Copper	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Smoke	decreases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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