SPDYC

Summary

SPDYC (speedy/RINGO cell cycle regulator family member C, HGNC:32681) is a protein-coding gene on chromosome 11q13.1, encoding Speedy protein C (Q5MJ68). Promotes progression through the cell cycle via binding and activation of CDK1 and CDK2.

Enables protein kinase binding activity. Predicted to be located in nucleus.

Source: NCBI Gene 387778 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 54 total
• MANE Select transcript: NM_001008778

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32681
Approved symbol	SPDYC
Name	speedy/RINGO cell cycle regulator family member C
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Aliases	Ringo2
Ensembl gene	ENSG00000204710
Ensembl biotype	protein_coding
OMIM	614030
Entrez	387778

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000377185

RefSeq mRNA: 1 — MANE Select: NM_001008778 NM_001008778

CCDS: CCDS31606

Canonical transcript exons

ENST00000377185 — 7 exons

Exon	Start	End
ENSE00001473038	65173183	65173374
ENSE00001473039	65172684	65173014
ENSE00001473040	65172434	65172605
ENSE00001473042	65172246	65172331
ENSE00001473044	65171943	65172001
ENSE00001473046	65171327	65171499
ENSE00001473048	65170233	65170261

Expression profiles

Bgee: expression breadth broad, 45 present calls, max score 92.54.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.2819 / max 78.6583, expressed in 88 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
115034	1.2819	88

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.54	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.88	gold quality
right lobe of liver	UBERON:0001114	72.06	gold quality
monocyte	CL:0000576	68.90	gold quality
leukocyte	CL:0000738	68.27	gold quality
liver	UBERON:0002107	66.51	gold quality
blood	UBERON:0000178	57.24	gold quality
right testis	UBERON:0004534	49.29	gold quality
testis	UBERON:0000473	48.81	gold quality
left testis	UBERON:0004533	48.80	gold quality
placenta	UBERON:0001987	47.08	gold quality
granulocyte	CL:0000094	46.47	silver quality
bone marrow cell	CL:0002092	40.72	gold quality
skeletal muscle tissue	UBERON:0001134	40.67	silver quality
muscle tissue	UBERON:0002385	38.87	silver quality
gall bladder	UBERON:0002110	37.35	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
sural nerve	UBERON:0015488	36.89	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
mucosa of transverse colon	UBERON:0004991	36.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.93	gold quality
muscle of leg	UBERON:0001383	35.87	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
gastrocnemius	UBERON:0001388	35.00	silver quality
tonsil	UBERON:0002372	34.30	gold quality
spleen	UBERON:0002106	34.20	silver quality
lymph node	UBERON:0000029	34.13	silver quality
upper lobe of left lung	UBERON:0008952	34.06	gold quality
smooth muscle tissue	UBERON:0001135	33.84	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-75688	yes	69.02
E-ANND-3	no	1.48

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• CDK-Speedy/Ringo C complexes positively regulate cell cycle progression during the late S and G(2) phases of the cell cycle. (PMID:18802405)
• Results indicate a role for RINGO C in the mitotic checkpoint, which might be mediated by defective recruitment of SAC components and deregulation of the activity of Aurora kinase B. (PMID:20605920)

Cross-species orthologs

0 orthologs

Paralogs (1): SPDYA (ENSG00000163806)

Protein

Protein identifiers

Speedy protein C — Q5MJ68 (reviewed: Q5MJ68)

Alternative names: Rapid inducer of G2/M progression in oocytes C

All UniProt accessions (1): Q5MJ68

UniProt curated annotations — full annotation on UniProt →

Function. Promotes progression through the cell cycle via binding and activation of CDK1 and CDK2. Involved in the spindle-assembly checkpoint. Required for recruitment of MAD2L1, BUBR1 and BUB1 to kinetochores. Required for the correct localization of the active form of Aurora B in prometaphase.

Subunit / interactions. Interacts with CDK1 and CDK2. Interacts with AURKB.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in a variety of tissues including bone marrow, kidney, small intestine, liver, placenta and testis.

Domain organisation. The C-terminus is required for CDK2-activation, but not CDK2-binding.

Similarity. Belongs to the Speedy/Ringo family.

RefSeq proteins (1): NP_001008778* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020984	Speedy	Family
IPR052316	Speedy-Ringo_regulator	Family

Pfam: PF11357

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5MJ68-F1	75.94	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): chr11q13, KEGG_OOCYTE_MEIOSIS, GOMF_KINASE_BINDING, MARTENS_TRETINOIN_RESPONSE_UP, DACH1_TARGET_GENES, ZNF592_TARGET_GENES, KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION, HAY_BONE_MARROW_PLATELET, GTF2A2_TARGET_GENES, CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN

GO Biological Process (1): positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)

GO Molecular Function (2): protein kinase binding (GO:0019901), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of cyclin-dependent protein serine/threonine kinase activity	1
cyclin-dependent protein serine/threonine kinase activity	1
positive regulation of cell cycle	1
positive regulation of protein serine/threonine kinase activity	1
positive regulation of cyclin-dependent protein kinase activity	1
kinase binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

472 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPDYC	OR5H1	A6NKK0	472
SPDYC	ACSM4	P0C7M7	447
SPDYC	NUP210L	Q5VU65	419
SPDYC	BTBD18	B2RXH4	415
SPDYC	KLHL26	Q53HC5	404
SPDYC	PHGR1	C9JFL3	391
SPDYC	RBM46	Q8TBY0	388
SPDYC	MCMDC2	Q4G0Z9	373
SPDYC	CCDC178	Q5BJE1	366
SPDYC	CATSPER4	Q7RTX7	359
SPDYC	ZNF687	Q8N1G0	358
SPDYC	PLPPR1	Q8TBJ4	352
SPDYC	CCDC63	Q8NA47	349
SPDYC	GXYLT1	Q4G148	349
SPDYC	FAM184A	Q8NB25	348

IntAct

15 interactions, top by confidence:

A	B	Type	Score
PAX6	SPDYC	psi-mi:“MI:0915”(physical association)	0.560
SPDYC	LZTS1	psi-mi:“MI:0915”(physical association)	0.560
SPDYC	FCF1	psi-mi:“MI:0915”(physical association)	0.560
ARPP19	SPDYC	psi-mi:“MI:0915”(physical association)	0.560
SPDYC	CDK1	psi-mi:“MI:0914”(association)	0.530
SPDYC	RBFOX3	psi-mi:“MI:0914”(association)	0.350
SPDYC	PAX6	psi-mi:“MI:0915”(physical association)	0.000
SPDYC	ARPP19	psi-mi:“MI:0915”(physical association)	0.000
SPDYC	LZTS1	psi-mi:“MI:0915”(physical association)	0.000
SPDYC	FCF1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): SPDYC (Two-hybrid), SPDYC (Two-hybrid), SPDYC (Two-hybrid), SPDYC (Two-hybrid), DPP9 (Affinity Capture-MS), CDK2 (Affinity Capture-MS), CKS1B (Affinity Capture-MS), CKS2 (Affinity Capture-MS), RBFOX3 (Affinity Capture-MS), CDK1 (Affinity Capture-MS), HERC1 (Affinity Capture-MS), CDK1 (Affinity Capture-Western), CDK2 (Affinity Capture-Western), CDKN1B (Affinity Capture-Western)

ESM2 similar proteins: A0A0J9YX57, A0A0J9YY54, A0A494C086, A0A494C0Z2, A0A494C191, A0A494C1R9, A2A6M5, A2A9R3, A6NHP3, A6NIY4, A6NJR5, A6NKD2, A6NLX3, A6NNV3, B1AUS7, F6SZT2, O19110, P0C6Y7, P0CI01, P0CV98, P0CV99, P0CW00, P0CW01, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, Q01534, Q12967, Q16666, Q495Y7, Q495Y8, Q587J8, Q5IBH6, Q5MJ68, Q5RD14

Diamond homologs: A0A494C086, A0A494C0Z2, A0A494C191, A6NHP3, A6NIY4, A6NJR5, A6NKU9, A6NLX3, A6NNV3, P0CI01, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, Q495Y7, Q495Y8, Q5IBH6, Q5IBH7, Q5MJ68, Q5MJ70, Q8NFV5, Q8R496, Q9PU13, Q9YGL1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1151 predictions. Top by Δscore:

Variant	Effect	Δscore
11:65171997:A:G	donor_gain	1.0000
11:65172241:TGCA:T	acceptor_loss	1.0000
11:65172243:CA:C	acceptor_loss	1.0000
11:65172244:A:AG	acceptor_gain	1.0000
11:65172244:A:G	acceptor_loss	1.0000
11:65172245:G:GG	acceptor_gain	1.0000
11:65172245:GT:G	acceptor_gain	1.0000
11:65172245:GTA:G	acceptor_gain	1.0000
11:65172245:GTAT:G	acceptor_gain	1.0000
11:65172245:GTATC:G	acceptor_gain	1.0000
11:65172298:GCGA:G	donor_gain	1.0000
11:65172327:GCCCT:G	donor_gain	1.0000
11:65172328:CCCT:C	donor_gain	1.0000
11:65172332:G:GG	donor_gain	1.0000
11:65170260:GG:G	donor_gain	0.9900
11:65170261:GG:G	donor_gain	0.9900
11:65170262:G:GG	donor_gain	0.9900
11:65170262:GT:G	donor_loss	0.9900
11:65170263:T:TC	donor_loss	0.9900
11:65171896:T:TA	acceptor_gain	0.9900
11:65171935:A:AG	acceptor_gain	0.9900
11:65171936:C:G	acceptor_gain	0.9900
11:65171941:A:AG	acceptor_gain	0.9900
11:65171942:G:GG	acceptor_gain	0.9900
11:65171942:GA:G	acceptor_gain	0.9900
11:65171997:ATAAG:A	donor_loss	0.9900
11:65171998:TAAGG:T	donor_loss	0.9900
11:65171999:AAG:A	donor_loss	0.9900
11:65172000:AGGT:A	donor_loss	0.9900
11:65172001:GGTG:G	donor_loss	0.9900

AlphaMissense

1916 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:65172714:T:A	W183R	0.994
11:65172714:T:C	W183R	0.994
11:65171963:T:C	F74L	0.993
11:65171965:C:A	F74L	0.993
11:65171965:C:G	F74L	0.993
11:65171997:A:T	D85V	0.993
11:65172531:T:C	F148L	0.992
11:65172533:C:A	F148L	0.992
11:65172533:C:G	F148L	0.992
11:65172570:T:C	F161L	0.992
11:65172572:C:A	F161L	0.992
11:65172572:C:G	F161L	0.992
11:65172716:G:C	W183C	0.992
11:65172716:G:T	W183C	0.992
11:65172476:A:C	K129N	0.991
11:65172476:A:T	K129N	0.991
11:65172532:T:C	F148S	0.991
11:65172545:G:C	R152S	0.991
11:65172545:G:T	R152S	0.991
11:65172274:T:C	F96S	0.990
11:65172321:T:C	F112L	0.988
11:65172323:C:A	F112L	0.988
11:65172323:C:G	F112L	0.988
11:65172484:T:C	I132T	0.988
11:65171997:A:C	D85A	0.987
11:65172273:T:C	F96L	0.987
11:65172275:C:A	F96L	0.987
11:65172275:C:G	F96L	0.987
11:65171964:T:C	F74S	0.986
11:65172322:T:C	F112S	0.986

dbSNP variants (sampled 300 via entrez): RS1000401035 (11:65169132 G>C), RS1001139298 (11:65168321 C>T), RS1002607662 (11:65171026 A>G), RS1003487679 (11:65170681 T>C), RS1003527877 (11:65169880 A>G), RS1004479635 (11:65171690 A>AC), RS1005677358 (11:65169960 G>A), RS1006050375 (11:65168437 C>T), RS1006409965 (11:65168285 A>T), RS1006582259 (11:65173279 G>T), RS1007121407 (11:65170496 C>G,T), RS1007451708 (11:65169083 C>G), RS1008048625 (11:65172622 A>G,T), RS1009211218 (11:65170007 GC>G), RS1009866876 (11:65169856 C>A)

Disease associations

OMIM: gene MIM:614030 | 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

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

Chemical	Actions (top 5)	PubMed papers
decabromobiphenyl ether	affects expression	1
sodium arsenite	increases expression	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
theaflavin-3,3’-digallate	affects expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Acetaminophen	increases expression	1
Arsenic	affects methylation	1
Cyclosporine	decreases methylation	1

Clinical trials (associated diseases)

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