RIBC1

Summary

RIBC1 (RIB43A domain with coiled-coils 1, HGNC:26537) is a protein-coding gene on chromosome Xp11.22, encoding RIB43A-like with coiled-coils protein 1 (Q8N443).

Predicted to be involved in flagellated sperm motility. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Predicted to be active in axonemal A tubule inner sheath and sperm flagellum.

Source: NCBI Gene 158787 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 71 total — 1 pathogenic
• MANE Select transcript: NM_001031745

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26537
Approved symbol	RIBC1
Name	RIB43A domain with coiled-coils 1
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32783
Ensembl gene	ENSG00000158423
Ensembl biotype	protein_coding
Entrez	158787

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 17 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000329209, ENST00000375327, ENST00000414955, ENST00000457095, ENST00000490702, ENST00000868179, ENST00000868180, ENST00000868181, ENST00000868182, ENST00000868183, ENST00000929472, ENST00000929473, ENST00000929474, ENST00000947944, ENST00000947945, ENST00000947946, ENST00000947947, ENST00000947948

RefSeq mRNA: 3 — MANE Select: NM_001031745 NM_001031745, NM_001267053, NM_144968

CCDS: CCDS14353, CCDS35299, CCDS59168

Canonical transcript exons

ENST00000375327 — 8 exons

Exon	Start	End
ENSE00001038808	53428003	53428084
ENSE00001038836	53430396	53430790
ENSE00001095112	53423314	53423402
ENSE00001095118	53422873	53423004
ENSE00001235782	53429854	53429972
ENSE00001466716	53430907	53431115
ENSE00003757056	53426277	53426393
ENSE00003786826	53428283	53428627

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 95.08.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6410 / max 49.1683, expressed in 327 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196424	0.2909	134
196425	0.2066	102
196423	0.1435	48

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	95.08	gold quality
bronchial epithelial cell	CL:0002328	95.01	gold quality
bronchus	UBERON:0002185	93.41	gold quality
sperm	CL:0000019	92.62	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.96	gold quality
left testis	UBERON:0004533	89.62	gold quality
right testis	UBERON:0004534	89.27	gold quality
testis	UBERON:0000473	87.41	gold quality
mucosa of paranasal sinus	UBERON:0005030	85.52	gold quality
oviduct epithelium	UBERON:0004804	83.36	gold quality
fallopian tube	UBERON:0003889	81.59	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.55	gold quality
epithelium of nasopharynx	UBERON:0001951	79.26	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.77	gold quality
nasal cavity epithelium	UBERON:0005384	77.11	gold quality
right adrenal gland cortex	UBERON:0035827	75.88	gold quality
adenohypophysis	UBERON:0002196	75.69	gold quality
right adrenal gland	UBERON:0001233	74.81	gold quality
pituitary gland	UBERON:0000007	74.51	gold quality
left adrenal gland cortex	UBERON:0035825	73.43	gold quality
left adrenal gland	UBERON:0001234	72.89	gold quality
nasal cavity mucosa	UBERON:0001826	72.56	gold quality
adrenal cortex	UBERON:0001235	71.60	gold quality
adult organism	UBERON:0007023	70.77	gold quality
ventricular zone	UBERON:0003053	70.57	gold quality
kidney epithelium	UBERON:0004819	70.45	gold quality
islet of Langerhans	UBERON:0000006	70.06	gold quality
germinal epithelium of ovary	UBERON:0001304	69.93	silver quality
adrenal gland	UBERON:0002369	69.63	gold quality
left uterine tube	UBERON:0001303	68.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting RIBC1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-146A-3P	99.13	68.99	1881
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-194-5P	99.01	69.65	1465
HSA-MIR-6760-5P	98.87	66.73	1515
HSA-MIR-1288-5P	98.85	67.01	734
HSA-MIR-935	98.82	69.36	1072

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ribc1	ENSDARG00000055739
mus_musculus	Ribc1	ENSMUSG00000025257
rattus_norvegicus	Ribc1	ENSRNOG00000003081
drosophila_melanogaster	CG7264	FBGN0036214

Paralogs (1): RIBC2 (ENSG00000128408)

Protein

Protein identifiers

RIB43A-like with coiled-coils protein 1 — Q8N443 (reviewed: Q8N443)

All UniProt accessions (2): A0A0C4DFR2, Q8N443

UniProt curated annotations — full annotation on UniProt →

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

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme.

Similarity. Belongs to the RIB43A family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N443-1	1	yes
Q8N443-2	2
Q8N443-3	3

RefSeq proteins (3): NP_001026915, NP_001253982, NP_659405 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008805	RIB43A	Family

Pfam: PF05914

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

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N443-F1	83.60	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 102 (showing top): E2F_Q4, E2F_Q4_01, E2F4DP1_01, E2F1DP1_01, E2F_Q3, E2F1DP2_01, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, RFX1_02, E2F_Q6_01, TGGAAA_NFAT_Q4_01, GOCC_CYTOPLASMIC_REGION, E2F_Q3_01, GOCC_MOTILE_CILIUM

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

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

GO Cellular Component (7): 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
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

1863 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RIBC1	OR2T5	Q6IEZ7	545
RIBC1	MORN5	Q5VZ52	530
RIBC1	HSD17B10	Q99714	482
RIBC1	ZNF407	Q9C0G0	475
RIBC1	SMC1A	Q14683	474
RIBC1	DYNLT3	P51808	473
RIBC1	HUWE1	Q7Z6Z7	467
RIBC1	CYLC1	P35663	452
RIBC1	SCNM1	Q9BWG6	451
RIBC1	PABIR3	Q6P4D5	446
RIBC1	ERAL1	O75616	443
RIBC1	SPANXN3	Q5MJ09	436
RIBC1	ARHGEF10L	Q9HCE6	429
RIBC1	TCEANC	Q8N8B7	427
RIBC1	OR52M1	Q8NGK5	417

IntAct

102 interactions, top by confidence:

A	B	Type	Score
RINT1	RIBC1	psi-mi:“MI:0915”(physical association)	0.780
RIBC1	RINT1	psi-mi:“MI:0915”(physical association)	0.780
KRT31	RIBC1	psi-mi:“MI:0915”(physical association)	0.720
RIBC1	KRT31	psi-mi:“MI:0915”(physical association)	0.720
RIBC1	TRIM27	psi-mi:“MI:0915”(physical association)	0.560
RIBC1	KRT15	psi-mi:“MI:0915”(physical association)	0.560
RIBC1	GOLGA2	psi-mi:“MI:0915”(physical association)	0.560
RIBC1	TEX11	psi-mi:“MI:0915”(physical association)	0.560
EMILIN1	RIBC1	psi-mi:“MI:0915”(physical association)	0.560
TEX11	RIBC1	psi-mi:“MI:0915”(physical association)	0.560
GOLGA2	RIBC1	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	RIBC1	psi-mi:“MI:0915”(physical association)	0.560
RIBC1	LDOC1	psi-mi:“MI:0915”(physical association)	0.560
RIBC1	BORCS6	psi-mi:“MI:0915”(physical association)	0.560
TRIM23	RIBC1	psi-mi:“MI:0915”(physical association)	0.560
MKRN3	RIBC1	psi-mi:“MI:0915”(physical association)	0.560
TLE5	RIBC1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (80): RIBC1 (Two-hybrid), RIBC1 (Two-hybrid), RIBC1 (Two-hybrid), RIBC1 (Two-hybrid), RIBC1 (Two-hybrid), RIBC1 (Two-hybrid), RIBC1 (Two-hybrid), CNOT6 (Affinity Capture-MS), CNOT2 (Affinity Capture-MS), CNOT11 (Affinity Capture-MS), TNKS1BP1 (Affinity Capture-MS), CNOT6L (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), CNOT3 (Affinity Capture-MS), RQCD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IFG5, A0A480NP79, A0A974E306, A0AUT1, A0JLY1, A4IJ21, A5A6J4, A8I9E8, A8IRJ7, A8IUG5, E1BJL9, F1N7G5, M0R3K6, M1V4Y8, O95990, Q0VC09, Q0VFZ6, Q17QH9, Q1RM03, Q2KI00, Q2KIQ2, Q32LH1, Q3TGF2, Q3TVW5, Q4R698, Q4R7T8, Q4R8Y5, Q5NVP3, Q5RE49, Q5U4F3, Q5XIN9, Q61884, Q6AXN9, Q6AXQ8, Q6AYL4, Q6PBA8, Q6ZN84, Q78TU8, Q8BRC6, Q8N443

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	38
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
564845	GRCh37/hg19 Xp11.22(chrX:53372728-54106257)x2	Pathogenic

SpliceAI

1478 predictions. Top by Δscore:

Variant	Effect	Δscore
X:53426274:CAG:C	acceptor_loss	1.0000
X:53426275:A:AC	acceptor_loss	1.0000
X:53426276:GAT:G	acceptor_gain	1.0000
X:53427995:G:A	acceptor_gain	1.0000
X:53428072:G:GT	donor_gain	1.0000
X:53422425:C:CT	donor_gain	0.9900
X:53422426:T:TT	donor_gain	0.9900
X:53422429:TCCGG:T	donor_gain	0.9900
X:53422430:CCGGC:C	donor_gain	0.9900
X:53423001:G:GT	donor_gain	0.9900
X:53426269:T:TA	acceptor_gain	0.9900
X:53426275:A:AG	acceptor_gain	0.9900
X:53426275:AGAT:A	acceptor_gain	0.9900
X:53426276:G:GA	acceptor_gain	0.9900
X:53426276:GATG:G	acceptor_gain	0.9900
X:53426276:GATGT:G	acceptor_gain	0.9900
X:53426389:TGGGG:T	donor_gain	0.9900
X:53426390:GGGG:G	donor_gain	0.9900
X:53426390:GGGGG:G	donor_gain	0.9900
X:53426391:GGG:G	donor_gain	0.9900
X:53426391:GGGG:G	donor_gain	0.9900
X:53426392:GG:G	donor_gain	0.9900
X:53426392:GGG:G	donor_gain	0.9900
X:53426393:GG:G	donor_gain	0.9900
X:53427994:T:TA	acceptor_gain	0.9900
X:53427999:TCA:T	acceptor_loss	0.9900
X:53428000:CAG:C	acceptor_loss	0.9900
X:53428406:G:GT	donor_gain	0.9900
X:53428443:G:GT	donor_gain	0.9900
X:53429848:GTGTA:G	acceptor_loss	0.9900

AlphaMissense

2510 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:53430968:T:C	F374L	0.957
X:53430970:T:A	F374L	0.957
X:53430970:T:G	F374L	0.957
X:53428375:T:C	F98L	0.912
X:53428377:T:A	F98L	0.912
X:53428377:T:G	F98L	0.912
X:53430980:A:C	S378R	0.851
X:53430982:C:A	S378R	0.851
X:53430982:C:G	S378R	0.851
X:53426353:G:C	R26P	0.840
X:53428343:G:C	R87P	0.822
X:53426364:T:C	F30L	0.810
X:53426366:C:A	F30L	0.810
X:53426366:C:G	F30L	0.810
X:53428040:G:C	R52P	0.805
X:53426383:G:C	R36P	0.802
X:53430557:G:C	K275N	0.797
X:53430557:G:T	K275N	0.797
X:53428507:T:C	F142L	0.793
X:53428509:C:A	F142L	0.793
X:53428509:C:G	F142L	0.793
X:53426341:G:C	R22P	0.785
X:53428049:G:C	R55P	0.781
X:53430983:C:A	R379S	0.776
X:53426391:G:A	G39R	0.770
X:53426391:G:C	G39R	0.770
X:53428495:A:C	S138R	0.768
X:53428497:C:A	S138R	0.768
X:53428497:C:G	S138R	0.768
X:53430756:T:C	F342L	0.764

dbSNP variants (sampled 300 via entrez): RS1000061224 (X:53428777 A>T), RS1001748769 (X:53423352 C>A), RS1002252438 (X:53421662 T>C), RS1002401694 (X:53431199 G>A,T), RS1002923817 (X:53425432 A>C), RS1003386768 (X:53424832 G>A), RS1003969152 (X:53427387 C>G,T), RS1006775326 (X:53424657 G>A), RS1007238774 (X:53424193 A>G), RS1009169851 (X:53426567 T>C,G), RS1009547579 (X:53421712 T>C), RS1010148549 (X:53429738 C>T), RS1010586248 (X:53429246 C>T), RS1013022339 (X:53425957 C>T), RS1013354489 (X:53425494 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:309530

GenCC curated gene-disease

Mondo (1): intellectual disability, X-linked 1 (MONDO:0010656)

Orphanet (2): X-linked non-syndromic intellectual disability (Orphanet:777), Severe intellectual disability-progressive postnatal microcephaly-midline stereotypic hand movements syndrome (Orphanet:397933)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008103_88	Bipolar disorder	1.000000e-06

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C567906	Mental Retardation, X-Linked 1 (supp.)
C564489	Mental Retardation, X-Linked 78 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
Vorinostat	affects cotreatment, decreases expression	2
Estradiol	decreases reaction, increases expression, decreases expression	2
afuresertib	increases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
triphenyl phosphate	affects expression	1
3,3’-diindolylmethane	increases expression, decreases reaction	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Endosulfan	decreases expression	1
Smoke	increases expression, increases abundance	1
Tetrachlorodibenzodioxin	increases expression, decreases reaction	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01238250	Not specified	RECRUITING	Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight