SPDYE1

Summary

SPDYE1 (speedy/RINGO cell cycle regulator family member E1, HGNC:16408) is a protein-coding gene on chromosome 7p13, encoding Speedy protein E1 (Q8NFV5). It is a common-essential gene (DepMap: required in 92.4% of cancer cell lines).

This gene is located at chromosome 7p13 which is close to the Williams Beuren syndrome chromosome region 7q11.23.

Source: NCBI Gene 285955 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 92 total
• Cancer dependency (DepMap): dependent in 92.4% of screened cell lines (common-essential)
• MANE Select transcript: NM_001378423

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16408
Approved symbol	SPDYE1
Name	speedy/RINGO cell cycle regulator family member E1
Location	7p13
Locus type	gene with protein product
Status	Approved
Aliases	Ringo1, SPDYE
Ensembl gene	ENSG00000136206
Ensembl biotype	protein_coding
OMIM	617623
Entrez	285955

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000258704, ENST00000652520, ENST00000693451

RefSeq mRNA: 2 — MANE Select: NM_001378423 NM_001378423, NM_175064

CCDS: CCDS5475, CCDS94090

Canonical transcript exons

ENST00000693451 — 9 exons

Exon	Start	End
ENSE00000680685	44002590	44002817
ENSE00000680690	44007268	44007586
ENSE00001613923	44005142	44005227
ENSE00001619253	44003853	44003911
ENSE00001641351	44007709	44007813
ENSE00003842816	44001066	44001284
ENSE00003848046	43997897	43997959
ENSE00003929091	43999528	44000109
ENSE00003934441	44008667	44010124

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 81.44.

Top tissues by expression

136 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	81.44	gold quality
left testis	UBERON:0004533	76.14	gold quality
testis	UBERON:0000473	76.08	gold quality
right testis	UBERON:0004534	75.88	gold quality
monocyte	CL:0000576	68.68	gold quality
leukocyte	CL:0000738	68.23	gold quality
skeletal muscle tissue	UBERON:0001134	67.88	gold quality
sural nerve	UBERON:0015488	66.87	gold quality
granulocyte	CL:0000094	66.16	gold quality
blood	UBERON:0000178	64.93	gold quality
bone marrow	UBERON:0002371	64.86	gold quality
muscle tissue	UBERON:0002385	64.68	gold quality
bone marrow cell	CL:0002092	64.25	silver quality
muscle of leg	UBERON:0001383	64.02	gold quality
gastrocnemius	UBERON:0001388	63.68	gold quality
tonsil	UBERON:0002372	63.61	gold quality
apex of heart	UBERON:0002098	62.36	gold quality
right lobe of thyroid gland	UBERON:0001119	61.82	gold quality
stromal cell of endometrium	CL:0002255	61.69	gold quality
heart left ventricle	UBERON:0002084	60.86	gold quality
adrenal tissue	UBERON:0018303	60.86	gold quality
body of pancreas	UBERON:0001150	60.25	gold quality
right ovary	UBERON:0002118	60.01	gold quality
uterine cervix	UBERON:0000002	59.96	gold quality
metanephros cortex	UBERON:0010533	59.95	gold quality
small intestine Peyer’s patch	UBERON:0003454	59.76	gold quality
small intestine	UBERON:0002108	59.65	gold quality
spleen	UBERON:0002106	59.45	gold quality
stomach	UBERON:0000945	59.44	gold quality
thyroid gland	UBERON:0002046	59.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting SPDYE1, 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-3924	100.00	72.09	2394
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 92.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

• This paper mentioned accessions “AF412025-2035” and “WBSCR16-WBSCR23”, but AF412027 and WBSCR19 were not discussed in this paper, and the WBSCR19 information is not available from this paper. (PMID:12073013)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spdye4b	ENSMUSG00000029586
mus_musculus	Spdye4a	ENSMUSG00000039296
rattus_norvegicus	Spdye4	ENSRNOG00000058563

Paralogs (18): SPDYE5 (ENSG00000170092), SPDYE2B (ENSG00000173678), SPDYE4 (ENSG00000183318), SPDYE12 (ENSG00000184616), SPDYE16 (ENSG00000185040), SPDYE17 (ENSG00000186645), SPDYE2 (ENSG00000205238), SPDYE18 (ENSG00000205482), SPDYE3 (ENSG00000214300), SPDYE21 (ENSG00000230358), SPDYE6 (ENSG00000260097), SPDYE9 (ENSG00000262461), SPDYE8 (ENSG00000273520), SPDYE10 (ENSG00000274570), SPDYE11 (ENSG00000275976), SPDYE15 (ENSG00000286014), SPDYE13 (ENSG00000286038), SPDYE14 (ENSG00000286137)

Protein

Protein identifiers

Speedy protein E1 — Q8NFV5 (reviewed: Q8NFV5)

Alternative names: Williams-Beuren syndrome chromosomal region 19 protein

All UniProt accessions (2): A0A494C1S0, Q8NFV5

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Predominantly expressed in testis and heart.

Disease relevance. SPDYE1 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.

Similarity. Belongs to the Speedy/Ringo family.

RefSeq proteins (2): NP_001365352, NP_778234 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020984	Speedy	Family
IPR057742	Speedy_E	Family

Pfam: PF11357

UniProt features (5 total): sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NFV5-F1	60.83	0.20

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 54 (showing top): WANG_CLIM2_TARGETS_UP, TGACATY_UNKNOWN, chr7p13, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOMF_KINASE_BINDING, ZWANG_EGF_INTERVAL_UP, SRC_UP.V1_DN, MIR3662, MIR1277_5P, MIR559, MIR3121_3P, MIR548Y, MIR548BB_5P, MIR548AR_5P, MIR548AD_5P_MIR548AE_5P_MIR548AY_5P_MIR548B_5P_MIR548D_5P

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

GO Molecular Function (1): protein kinase binding (GO:0019901)

GO Cellular Component (0):

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

Protein interactions and networks

STRING

136 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPDYE1	NUTM2F	A1L443	627
SPDYE1	POM121L2	Q96KW2	412
SPDYE1	OR2A42	Q8NGT9	379
SPDYE1	A0A1B0GVM2	A0A1B0GVM2	366
SPDYE1	CTAGE6	Q86UF2	348
SPDYE1	POLR2J2	Q9GZM3	348
SPDYE1	CERCAM	Q5T4B2	326
SPDYE1	NUTM2G	Q5VZR2	318
SPDYE1	GTF2IRD2B	Q6EKJ0	307
SPDYE1	ZNHIT2	Q9UHR6	307
SPDYE1	GON4L	Q3T8J9	305
SPDYE1	GTF2IRD2	Q86UP8	305
SPDYE1	SLC17A4	Q9Y2C5	305
SPDYE1	H2AC7	P20671	300
SPDYE1	UBE2D4	Q9Y2X8	299

IntAct

0 interactions, top by confidence:

BioGRID (6): SPDYE1 (Negative Genetic), CDK1 (Affinity Capture-Western), CDK2 (Affinity Capture-Western), CDK5 (Affinity Capture-Western), CDKN1B (Affinity Capture-Western), SPDYE1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0J9YY54, A0A494C086, A0A494C0Z2, A0A494C191, A6NHP3, A6NIY4, A6NJR5, A6NNV3, B4DH59, F6SZT2, P0C6Y7, P0CI01, P0DKJ7, P0DKJ8, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, P79386, Q08AG5, Q13342, Q16666, Q3BBV2, Q495Y8, Q587J8, Q5JRC9, Q5QGU6, Q5RD14, Q5RKG3, Q63HK3, Q6ITT4, Q7TQI8, Q86T75, Q8IWY8, Q8N660, Q8NFV5

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	89
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1052 predictions. Top by Δscore:

Variant	Effect	Δscore
7:44001280:GCTTG:G	donor_gain	1.0000
7:44007584:GAGGT:G	donor_loss	1.0000
7:44007586:GGTG:G	donor_loss	1.0000
7:44008662:TCCA:T	acceptor_loss	1.0000
7:44008664:CA:C	acceptor_loss	1.0000
7:44008665:A:AG	acceptor_gain	1.0000
7:44008665:AGAAC:A	acceptor_loss	1.0000
7:44008666:G:GA	acceptor_gain	1.0000
7:44001281:C:G	donor_gain	0.9900
7:44002810:GCTGC:G	donor_gain	0.9900
7:44002869:G:GT	donor_gain	0.9900
7:44002870:A:T	donor_gain	0.9900
7:44003851:A:AG	acceptor_gain	0.9900
7:44003851:AGAG:A	acceptor_gain	0.9900
7:44003852:G:GG	acceptor_gain	0.9900
7:44003852:GAGG:G	acceptor_gain	0.9900
7:44007198:G:A	acceptor_gain	0.9900
7:44007266:A:AG	acceptor_gain	0.9900
7:44007267:G:GA	acceptor_gain	0.9900
7:44007267:GCT:G	acceptor_gain	0.9900
7:44007412:G:GT	donor_gain	0.9900
7:44007583:GGAG:G	donor_gain	0.9900
7:44007584:G:GT	donor_gain	0.9900
7:44007588:T:G	donor_loss	0.9900
7:44008666:GA:G	acceptor_gain	0.9900
7:44008666:GAA:G	acceptor_gain	0.9900
7:44008666:GAAC:G	acceptor_gain	0.9900
7:44008666:GAACA:G	acceptor_gain	0.9900
7:44001266:G:GT	donor_gain	0.9800
7:44002818:G:GG	donor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000432489 (7:44006520 C>T), RS1000466654 (7:44006116 C>A), RS1000765697 (7:44007669 G>A), RS1000966568 (7:43998914 A>G), RS1001334921 (7:43999183 G>C), RS1001426377 (7:44004427 A>C), RS1001457377 (7:44004039 T>TTC), RS1001710000 (7:44010605 G>A), RS1001936741 (7:43997854 T>C), RS1001986706 (7:43996129 TG>T), RS1003650387 (7:44009001 T>C), RS1003753460 (7:44009616 ATATT>A,ATATTTATT), RS1003769510 (7:44001376 G>A), RS1004024373 (7:44009324 T>C), RS1004128743 (7:44009372 T>C,G)

Disease associations

OMIM: gene MIM:617623 | 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

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
kojic acid	increases expression	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	decreases expression	1
2-palmitoylglycerol	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Zoledronic Acid	increases expression	1
Arsenic Trioxide	decreases expression, affects cotreatment	1
Cadmium	decreases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression, affects cotreatment	1
Aflatoxin B1	affects expression	1
Lactic Acid	increases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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