RIBC2

Summary

RIBC2 (RIB43A domain with coiled-coils 2, HGNC:13241) is a protein-coding gene on chromosome 22q13.31, encoding RIB43A-like with coiled-coils protein 2 (Q9H4K1). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.

Predicted to be involved in flagellated sperm motility. Located in axonemal microtubule.

Source: NCBI Gene 26150 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 25 total
• MANE Select transcript: NM_015653

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13241
Approved symbol	RIBC2
Name	RIB43A domain with coiled-coils 2
Location	22q13.31
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp566F0546, FLJ25720
Ensembl gene	ENSG00000128408
Ensembl biotype	protein_coding
OMIM	621115
Entrez	26150

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding_CDS_not_defined, 1 protein_coding, 1 retained_intron

ENST00000466226, ENST00000614167, ENST00000621287

RefSeq mRNA: 1 — MANE Select: NM_015653 NM_015653

CCDS: CCDS14066

Canonical transcript exons

ENST00000614167 — 7 exons

Exon	Start	End
ENSE00003712373	45432284	45432509
ENSE00003730468	45425948	45426175
ENSE00003732033	45413693	45414015
ENSE00003733145	45414322	45414403
ENSE00003737017	45417602	45417946
ENSE00003737226	45422290	45422408
ENSE00003749600	45430900	45431066

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 93.32.

FANTOM5 (CAGE): breadth broad, TPM avg 2.5543 / max 100.1409, expressed in 804 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
192718	2.5543	804

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	93.32	gold quality
epithelium of bronchus	UBERON:0002031	92.87	gold quality
right uterine tube	UBERON:0001302	91.87	gold quality
bronchus	UBERON:0002185	91.57	gold quality
left testis	UBERON:0004533	88.71	gold quality
right testis	UBERON:0004534	88.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.49	gold quality
testis	UBERON:0000473	86.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.09	gold quality
epithelium of nasopharynx	UBERON:0001951	85.55	silver quality
mucosa of paranasal sinus	UBERON:0005030	85.37	silver quality
adult organism	UBERON:0007023	82.94	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	82.76	gold quality
ventricular zone	UBERON:0003053	77.36	gold quality
endometrium epithelium	UBERON:0004811	77.35	gold quality
nasal cavity epithelium	UBERON:0005384	76.07	silver quality
sperm	CL:0000019	73.04	silver quality
male germ cell	CL:0000015	72.38	silver quality
ganglionic eminence	UBERON:0004023	71.43	gold quality
adenohypophysis	UBERON:0002196	70.20	gold quality
pituitary gland	UBERON:0000007	69.96	gold quality
fallopian tube	UBERON:0003889	69.77	gold quality
frontal pole	UBERON:0002795	68.47	gold quality
nasal cavity mucosa	UBERON:0001826	67.83	gold quality
stromal cell of endometrium	CL:0002255	66.79	gold quality
paraflocculus	UBERON:0005351	66.02	gold quality
middle frontal gyrus	UBERON:0002702	65.77	gold quality
oviduct epithelium	UBERON:0004804	64.76	silver quality
smooth muscle tissue	UBERON:0001135	64.69	gold quality
rectum	UBERON:0001052	64.27	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	11.29
E-ANND-3	yes	4.84

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• A common variant rs2272804 in the 5’UTR of RIBC2 inhibits downstream gene expression by creating an upstream open reading frame. (PMID:32329860)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ribc2	ENSDARG00000075177
mus_musculus	Ribc2	ENSMUSG00000022431
rattus_norvegicus	Ribc2	ENSRNOG00000033502
drosophila_melanogaster	CG7264	FBGN0036214

Paralogs (1): RIBC1 (ENSG00000158423)

Protein

Protein identifiers

RIB43A-like with coiled-coils protein 2 — Q9H4K1 (reviewed: Q9H4K1)

All UniProt accessions (1): Q9H4K1

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.

Subunit / interactions. Microtubule inner protein component of sperm flagellar doublet microtubules.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium axoneme. Flagellum axoneme.

Tissue specificity. Expressed in airway epithelial cells.

Similarity. Belongs to the RIB43A family.

RefSeq proteins (1): NP_056468* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008805	RIB43A	Family

Pfam: PF05914

UniProt features (5 total): sequence variant 3, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7UNG	ELECTRON MICROSCOPY	3.6
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H4K1-F1	86.88	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): MODULE_52, YAGI_AML_WITH_INV_16_TRANSLOCATION, MODULE_16, CAGCTG_AP4_Q5, MODULE_118, MODULE_379, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, DOANE_RESPONSE_TO_ANDROGEN_DN, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GNF2_CCNA1, SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP, MODULE_88, MODULE_242, GATA4_Q3

GO Biological Process (1): flagellated sperm motility (GO:0030317)

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

GO Cellular Component (9): nucleus (GO:0005634), axonemal microtubule (GO:0005879), sperm flagellum (GO:0036126), axonemal A tubule inner sheath (GO:0160111), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
binding	1
intracellular membrane-bounded organelle	1
cytoplasmic microtubule	1
axoneme	1
9+2 motile cilium	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

1845 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RIBC2	TRIB1	Q96RU8	930
RIBC2	TRIB3	Q96RU7	920
RIBC2	TRIB2	Q92519	901
RIBC2	MAP2K1	Q02750	768
RIBC2	COP1	Q8NHY2	715
RIBC2	MAP2K4	P45985	662
RIBC2	CEP15	Q9HBI5	528
RIBC2	J3KS56	J3KS56	522
RIBC2	AKT1	P31749	513
RIBC2	MAP2K7	O14733	494
RIBC2	STK40	Q8N2I9	490
RIBC2	CCDC150	Q8NCX0	489
RIBC2	FAM217B	Q9NTX9	475
RIBC2	CCDC77	Q9BR77	473
RIBC2	CFAP36	Q96G28	460

IntAct

38 interactions, top by confidence:

A	B	Type	Score
YBX1	HNRNPR	psi-mi:“MI:0914”(association)	0.770
RIBC2	LRP2	psi-mi:“MI:0915”(physical association)	0.590
RIBC2	tax	psi-mi:“MI:0915”(physical association)	0.560
RIBC2	GFAP	psi-mi:“MI:0915”(physical association)	0.550
RIBC2	RAD54B	psi-mi:“MI:0915”(physical association)	0.550
GFAP	RIBC2	psi-mi:“MI:0915”(physical association)	0.550
RAD54B	RIBC2	psi-mi:“MI:0915”(physical association)	0.550
YBX1	HNRNPL	psi-mi:“MI:0914”(association)	0.530
	RIBC2	psi-mi:“MI:0915”(physical association)	0.490
RIBC2		psi-mi:“MI:0915”(physical association)	0.490
RIBC2	SNRPA1	psi-mi:“MI:0915”(physical association)	0.400
TRIM23	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
RIBC2	GTPBP3	psi-mi:“MI:0915”(physical association)	0.370
RIBC2	USHBP1	psi-mi:“MI:0915”(physical association)	0.370
RIBC2	BEGAIN	psi-mi:“MI:0915”(physical association)	0.370
MTUS2	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
TRIM37	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
ATRIP	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
RIBC2	TEX11	psi-mi:“MI:0915”(physical association)	0.370
JUP	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
TRAF2	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
RIBC2	EFEMP2	psi-mi:“MI:0915”(physical association)	0.370
CCDC85B	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
NINL	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
RIBC2	NRBP1	psi-mi:“MI:0915”(physical association)	0.370
KRT15	RIBC2	psi-mi:“MI:0915”(physical association)	0.370
RIBC2	HOOK2	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (30): RIBC2 (Two-hybrid), GTPBP3 (Two-hybrid), USHBP1 (Two-hybrid), BEGAIN (Two-hybrid), RIBC2 (Two-hybrid), RIBC2 (Two-hybrid), RIBC2 (Two-hybrid), TEX11 (Two-hybrid), RIBC2 (Two-hybrid), RIBC2 (Two-hybrid), EFEMP2 (Two-hybrid), RIBC2 (Two-hybrid), RIBC2 (Two-hybrid), NRBP1 (Two-hybrid), RIBC2 (Two-hybrid)

ESM2 similar proteins: A0A0R4IFG5, A0A480NP79, A0A974E306, A0AUP1, A0AUT1, A0JLY1, A4IJ21, A7S8T5, A8I9E8, D6REC4, E1BJL9, F1N7G5, O88346, P02641, Q0VC09, Q0VFZ6, Q1RM03, Q2KIQ2, Q2TA16, Q32KY1, Q32LJ7, Q32LN4, Q3TVW5, Q3USS3, Q4R698, Q4R7T8, Q4R8R3, Q5RE49, Q61884, Q6AXN9, Q6AXQ8, Q6AYL4, Q6PBA8, Q7T0Y4, Q7TNB2, Q7Z4T9, Q8BRC6, Q8N443, Q8NEF3, Q8NEH6

Diamond homologs: Q0VC09, Q32LJ7, Q4R698, Q6AXN9, Q6AYL4, Q8N443, Q9D0B8, Q9D4Q1, Q9H4K1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 33 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Dengue Virus-Host Interactions	6	11.9×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1242 predictions. Top by Δscore:

Variant	Effect	Δscore
22:45413955:G:GT	donor_gain	1.0000
22:45414006:GA:G	donor_gain	1.0000
22:45414007:A:T	donor_gain	1.0000
22:45414314:A:AG	acceptor_gain	1.0000
22:45414315:T:G	acceptor_gain	1.0000
22:45414318:ATAG:A	acceptor_gain	1.0000
22:45414318:ATAGG:A	acceptor_gain	1.0000
22:45414319:T:G	acceptor_gain	1.0000
22:45414319:TAGGG:T	acceptor_gain	1.0000
22:45414320:A:AG	acceptor_gain	1.0000
22:45414320:AG:A	acceptor_gain	1.0000
22:45414320:AGG:A	acceptor_gain	1.0000
22:45414320:AGGGA:A	acceptor_gain	1.0000
22:45414321:G:GA	acceptor_gain	1.0000
22:45414321:GG:G	acceptor_gain	1.0000
22:45414321:GGG:G	acceptor_gain	1.0000
22:45414321:GGGA:G	acceptor_gain	1.0000
22:45414321:GGGAG:G	acceptor_gain	1.0000
22:45414399:CTTTG:C	donor_gain	1.0000
22:45414400:TTTG:T	donor_gain	1.0000
22:45414401:TTG:T	donor_gain	1.0000
22:45414401:TTGG:T	donor_loss	1.0000
22:45414403:GGTGA:G	donor_loss	1.0000
22:45414404:G:A	donor_loss	1.0000
22:45414404:G:GG	donor_gain	1.0000
22:45414405:T:G	donor_loss	1.0000
22:45422288:A:AG	acceptor_gain	1.0000
22:45422289:G:GG	acceptor_gain	1.0000
22:45422289:GA:G	acceptor_gain	1.0000
22:45426167:G:GT	donor_gain	1.0000

AlphaMissense

2559 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:45417733:T:C	F115L	0.963
22:45417735:T:A	F115L	0.963
22:45417735:T:G	F115L	0.963
22:45432342:T:C	F377L	0.961
22:45432344:T:A	F377L	0.961
22:45432344:T:G	F377L	0.961
22:45417694:T:C	F102L	0.916
22:45417696:C:A	F102L	0.916
22:45417696:C:G	F102L	0.916
22:45426104:T:A	W278R	0.910
22:45426104:T:C	W278R	0.910
22:45417889:T:A	W167R	0.903
22:45417889:T:C	W167R	0.903
22:45417878:A:C	Q163P	0.898
22:45417858:G:C	R156S	0.896
22:45417858:G:T	R156S	0.896
22:45432333:T:C	F374L	0.891
22:45432335:C:A	F374L	0.891
22:45432335:C:G	F374L	0.891
22:45417826:T:C	F146L	0.879
22:45417828:C:A	F146L	0.879
22:45417828:C:G	F146L	0.879
22:45413989:T:C	F35L	0.878
22:45413991:C:A	F35L	0.878
22:45413991:C:G	F35L	0.878
22:45426109:G:C	K279N	0.872
22:45426109:G:T	K279N	0.872
22:45417902:A:C	Q171P	0.862
22:45417840:T:A	D150E	0.859
22:45417840:T:G	D150E	0.859

dbSNP variants (sampled 300 via entrez): RS1000327589 (22:45430254 G>T), RS1000386655 (22:45412437 G>T), RS1000663125 (22:45431543 A>G), RS1000715237 (22:45431744 C>G,T), RS1000848677 (22:45415589 T>G), RS1000887595 (22:45421043 CTG>C), RS1000977090 (22:45420752 C>T), RS1001264933 (22:45426072 C>A,T), RS1001383491 (22:45429277 A>G), RS1001473461 (22:45413134 C>T), RS1001573210 (22:45423766 T>C), RS1001809153 (22:45418489 C>G), RS1001871175 (22:45424900 C>G,T), RS1001942325 (22:45418298 A>C), RS1001979640 (22:45419544 G>C)

Disease associations

OMIM: gene MIM:621115 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST008151_93	Waist circumference	8.000000e-07
GCST008160_93	Waist circumference	8.000000e-07
GCST011946_16	White matter hyperintensity volume	6.000000e-06
GCST011947_18	White matter hyperintensity volume	1.000000e-06
GCST011949_32	White matter hyperintensity volume (adjusted for hypertension)	7.000000e-06
GCST011950_8	White matter hyperintensity volume (adjusted for hypertension)	1.000000e-06
GCST011953_18	White matter hyperintensity volume x hypertension interaction (2df)	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005665	white matter hyperintensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, affects splicing, decreases expression, increases expression	5
Benzo(a)pyrene	increases expression, increases methylation	2
GSK-J4	decreases expression	1
afuresertib	decreases expression	1
sotorasib	affects cotreatment, increases expression	1
bisphenol A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	increases expression	1
ferrous chloride	decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
abrine	decreases expression	1
licochalcone B	decreases expression	1
trametinib	increases expression, affects cotreatment	1
(+)-JQ1 compound	decreases expression	1
NVP-BKM120	increases expression, affects cotreatment	1
Resveratrol	increases expression, affects cotreatment	1
Acetaminophen	increases expression	1
Air Pollutants	increases expression, increases abundance	1
Cisplatin	increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Endosulfan	affects cotreatment, increases expression	1
Oxygen	decreases expression	1
Smoke	increases abundance, increases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Zearalenone	decreases expression	1
Aflatoxin B1	increases expression	1
Copper Sulfate	decreases expression	1
Vitamin K 3	affects expression	1

Clinical trials (associated diseases)

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