SPATC1

Summary

SPATC1 (spermatogenesis and centriole associated 1, HGNC:30510) is a protein-coding gene on chromosome 8q24.3, encoding Speriolin (Q76KD6).

Predicted to enable gamma-tubulin binding activity. Located in centrosome.

Source: NCBI Gene 375686 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_198572

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30510
Approved symbol	SPATC1
Name	spermatogenesis and centriole associated 1
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC61633, SPATA15, SPERIOLIN
Ensembl gene	ENSG00000186583
Ensembl biotype	protein_coding
OMIM	610874
Entrez	375686

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000377470, ENST00000447830

RefSeq mRNA: 2 — MANE Select: NM_198572 NM_001134374, NM_198572

CCDS: CCDS47937, CCDS6413

Canonical transcript exons

ENST00000377470 — 5 exons

Exon	Start	End
ENSE00001340650	144041232	144041371
ENSE00001340651	144040568	144041107
ENSE00001696924	144039909	144040463
ENSE00001849109	144046627	144047114
ENSE00002273888	144012280	144012726

Expression profiles

Bgee: expression breadth ubiquitous, 121 present calls, max score 87.84.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7897 / max 53.2280, expressed in 164 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91456	0.2368	81
91458	0.1952	56
91457	0.1384	57
91455	0.0787	41
91459	0.0564	28
91461	0.0522	21
91460	0.0319	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	87.84	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.51	gold quality
left testis	UBERON:0004533	87.49	gold quality
sperm	CL:0000019	87.16	silver quality
testis	UBERON:0000473	83.87	gold quality
ileal mucosa	UBERON:0000331	67.40	silver quality
bone marrow cell	CL:0002092	67.15	silver quality
buccal mucosa cell	CL:0002336	67.02	gold quality
spleen	UBERON:0002106	63.25	gold quality
vermiform appendix	UBERON:0001154	62.91	gold quality
blood	UBERON:0000178	62.40	gold quality
tendon of biceps brachii	UBERON:0008188	61.99	gold quality
tibialis anterior	UBERON:0001385	59.84	silver quality
caecum	UBERON:0001153	57.96	gold quality
myocardium	UBERON:0002349	56.99	gold quality
deltoid	UBERON:0001476	56.28	gold quality
upper arm skin	UBERON:0004263	56.26	gold quality
adult organism	UBERON:0007023	56.19	gold quality
granulocyte	CL:0000094	56.01	gold quality
bone marrow	UBERON:0002371	55.38	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	54.70	gold quality
nasal cavity epithelium	UBERON:0005384	54.68	gold quality
right lobe of liver	UBERON:0001114	54.65	gold quality
heart left ventricle	UBERON:0002084	54.65	gold quality
trabecular bone tissue	UBERON:0002483	54.36	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
metanephros	UBERON:0000081	54.33	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
cardiac ventricle	UBERON:0002082	54.16	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

2 targeting SPATC1, 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-3151-5P	99.86	63.83	1069
HSA-MIR-134-3P	96.83	66.22	1001

Literature-anchored findings (GeneRIF, showing 1)

• Speriolin is a novel centrosomal protein present in the connecting piece region of human sperm that is transmitted to the zygote and can be detected throughout the first mitotic division. (PMID:20542897)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spatc1	ENSMUSG00000049653
rattus_norvegicus	Spatc1	ENSRNOG00000029590

Paralogs (1): SPATC1L (ENSG00000160284)

Protein

Protein identifiers

Speriolin — Q76KD6 (reviewed: Q76KD6)

Alternative names: Spermatogenesis and centriole-associated protein 1, Spermatogenesis-associated protein 15, Spermatogenic cell-specific Cdc20-binding protein

All UniProt accessions (2): A0A140VJV4, Q76KD6

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Found in a complex with CDC20, CDC27 and TUBG1. Interacts with CDC20.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Tissue specificity. Detected only in testis.

Similarity. Belongs to the speriolin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q76KD6-1	1	yes
Q76KD6-2	2

RefSeq proteins (2): NP_001127846, NP_940974* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026715	SPATC1	Family
IPR029384	Speriolin_C	Domain
IPR029385	Speriolin_N	Domain

Pfam: PF15058, PF15059

UniProt features (13 total): compositionally biased region 4, region of interest 3, splice variant 2, sequence conflict 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q76KD6-F1	57.80	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): TGACCTY_ERR1_Q2, GOCC_MICROTUBULE_ORGANIZING_CENTER, YGACNNYACAR_UNKNOWN, ATF1_Q6, GOCC_CENTROSOME, P53_DECAMER_Q2, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, P53_02, MARTENS_TRETINOIN_RESPONSE_UP, BRUINS_UVC_RESPONSE_LATE, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, chr8q24, NCOA2_TARGET_GENES, MIR1827

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): cytoplasm (GO:0005737), centrosome (GO:0005813), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1
centriole	1
microtubule organizing center	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

590 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATC1	ODF1	Q14990	885
SPATC1	CNTLN	Q9NXG0	793
SPATC1	PCNT	O95613	773
SPATC1	CDC20	Q12834	742
SPATC1	NUP85	Q9BW27	711
SPATC1	CDC27	P30260	711
SPATC1	CBY2	Q8NA61	549
SPATC1	TUBG1	P23258	548
SPATC1	CEP76	Q8TAP6	547
SPATC1	SPATA45	Q537H7	519
SPATC1	SPATA9	Q9BWV2	513
SPATC1	SPATA6	Q9NWH7	500
SPATC1	SPMIP10	Q6ZNM6	498
SPATC1	SPATA3	Q8NHX4	489
SPATC1	TEX35	Q5T0J7	485

IntAct

0 interactions, top by confidence:

BioGRID (8): CDC20 (Affinity Capture-Western), CDC27 (Affinity Capture-Western), TUBG1 (Affinity Capture-Western), SPATC1 (Two-hybrid), SPATC1 (Reconstituted Complex), SPATC1 (Affinity Capture-MS), SPATC1 (Cross-Linking-MS (XL-MS)), SPATC1 (Protein-peptide)

ESM2 similar proteins: A0A172M4N0, A1KXM5, B3A0Q2, B3A0Q7, B6KJ32, K9N4Q4, O96001, P04144, P04671, P05686, P06796, P08961, P0CU96, P0CV08, P0CV21, P0CV36, P0CV39, P0CV40, P0CV42, P0CV43, P0CV45, P0CV46, P0CV47, P0CV48, P0CV55, P0CV57, P0CV58, P10322, P19442, P34626, P86273, Q02596, Q04807, Q09239, Q196W1, Q1HVG4, Q41121, Q5BB76, Q76KD6, Q80Y39

Diamond homologs: Q148B6, Q76KD6, Q9D9W0, Q9H0A9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

3772 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:144041276:T:C	F451L	1.000
8:144041278:C:A	F451L	1.000
8:144041278:C:G	F451L	1.000
8:144041286:A:T	D454V	1.000
8:144041289:G:C	R455P	1.000
8:144041264:G:C	G447R	0.999
8:144041265:G:A	G447D	0.999
8:144041276:T:A	F451I	0.999
8:144041277:T:C	F451S	0.999
8:144041277:T:G	F451C	0.999
8:144041283:T:C	L453P	0.999
8:144041286:A:C	D454A	0.999
8:144041336:T:C	F471L	0.999
8:144041337:T:C	F471S	0.999
8:144041338:C:A	F471L	0.999
8:144041338:C:G	F471L	0.999
8:144046946:T:C	F589S	0.999
8:144041264:G:T	G447C	0.998
8:144041265:G:T	G447V	0.998
8:144041268:A:T	E448V	0.998
8:144041274:C:A	A450D	0.998
8:144041276:T:G	F451V	0.998
8:144041288:C:A	R455S	0.998
8:144041292:G:C	R456T	0.998
8:144041292:G:T	R456M	0.998
8:144041293:G:C	R456S	0.998
8:144041293:G:T	R456S	0.998
8:144041295:T:A	I457N	0.998
8:144041295:T:C	I457T	0.998
8:144041295:T:G	I457S	0.998

dbSNP variants (sampled 300 via entrez): RS1000037876 (8:144024288 C>A,G,T), RS1000043826 (8:144044904 G>A), RS1000049636 (8:144031225 C>T), RS1000104779 (8:144031449 T>C), RS1000322106 (8:144024821 T>C), RS1000495054 (8:144035989 T>A), RS1000702346 (8:144041804 C>T), RS1000711175 (8:144047138 T>C), RS1000816820 (8:144042042 G>C), RS1000929017 (8:144020064 C>G), RS1001011988 (8:144035667 C>T), RS1001054150 (8:144029845 T>G), RS1001105045 (8:144030155 C>T), RS1001170864 (8:144039472 C>T), RS1001445065 (8:144019843 T>A)

Disease associations

OMIM: gene MIM:610874 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004121_35	Fibrinogen levels	5.000000e-08
GCST005993_43	Mean corpuscular hemoglobin	2.000000e-09
GCST008103_86	Bipolar disorder	1.000000e-06
GCST008115_8	Bipolar I disorder	2.000000e-08
GCST010703_132	Brain morphology (MOSTest)	3.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004527	mean corpuscular hemoglobin
EFO:0009963	bipolar I disorder
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Endosulfan	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Nanotubes, Carbon	increases expression	1

Clinical trials (associated diseases)

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