SPATA24

Summary

SPATA24 (spermatogenesis associated 24, HGNC:27322) is a protein-coding gene on chromosome 5q31.2, encoding Spermatogenesis-associated protein 24 (Q86W54). Binds DNA with high affinity but does not bind to TATA boxes.

Predicted to enable DNA binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Located in cytosol and nucleoplasm.

Source: NCBI Gene 202051 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_194296

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27322
Approved symbol	SPATA24
Name	spermatogenesis associated 24
Location	5q31.2
Locus type	gene with protein product
Status	Approved
Aliases	T6441, CCDC161
Ensembl gene	ENSG00000170469
Ensembl biotype	protein_coding
OMIM	621086
Entrez	202051

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000302091, ENST00000450845, ENST00000451821, ENST00000507779, ENST00000509959, ENST00000512761, ENST00000514983, ENST00000939688

RefSeq mRNA: 1 — MANE Select: NM_194296 NM_194296

CCDS: CCDS47274

Canonical transcript exons

ENST00000450845 — 6 exons

Exon	Start	End
ENSE00001128168	139397041	139397143
ENSE00001128179	139401755	139401825
ENSE00001128190	139401915	139402045
ENSE00001128200	139402628	139402693
ENSE00001798155	139396767	139396929
ENSE00002060306	139403944	139404089

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 98.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.9038 / max 78.9399, expressed in 1131 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63752	1.9038	1131

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gingival epithelium	UBERON:0001949	98.39	silver quality
left testis	UBERON:0004533	97.67	gold quality
right testis	UBERON:0004534	97.52	gold quality
superficial temporal artery	UBERON:0001614	95.94	silver quality
testis	UBERON:0000473	95.06	gold quality
sperm	CL:0000019	93.68	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.56	gold quality
germinal epithelium of ovary	UBERON:0001304	90.62	gold quality
right uterine tube	UBERON:0001302	90.43	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.65	gold quality
apex of heart	UBERON:0002098	88.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.38	gold quality
gastrocnemius	UBERON:0001388	86.02	gold quality
muscle of leg	UBERON:0001383	85.52	gold quality
heart left ventricle	UBERON:0002084	85.00	gold quality
cardiac ventricle	UBERON:0002082	84.63	gold quality
right atrium auricular region	UBERON:0006631	84.07	gold quality
adult organism	UBERON:0007023	83.78	gold quality
cardiac atrium	UBERON:0002081	83.22	gold quality
mucosa of transverse colon	UBERON:0004991	82.81	gold quality
heart	UBERON:0000948	82.68	gold quality
adenohypophysis	UBERON:0002196	82.41	gold quality
pituitary gland	UBERON:0000007	82.17	gold quality
islet of Langerhans	UBERON:0000006	81.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	80.62	gold quality
visceral pleura	UBERON:0002401	80.22	silver quality
adult mammalian kidney	UBERON:0000082	79.69	gold quality
lower lobe of lung	UBERON:0008949	79.36	gold quality
ventricular zone	UBERON:0003053	78.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.86

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata24	ENSMUSG00000024352
rattus_norvegicus	Spata24	ENSRNOG00000019976

Protein

Protein identifiers

Spermatogenesis-associated protein 24 — Q86W54 (reviewed: Q86W54)

Alternative names: Testis protein T6441 homolog

All UniProt accessions (6): Q86W54, D6R9Q3, D6RBC8, H0Y992, H0YAD3, Q8N799

UniProt curated annotations — full annotation on UniProt →

Function. Binds DNA with high affinity but does not bind to TATA boxes. Synergises with GMNN and TBP in activation of TATA box-containing promoters and with GMNN and TBPL1 in activation of the NF1 TATA-less promoter. May play a role in cytoplasm movement and removal during spermiogenesis.

Subunit / interactions. Homodimer. Interacts with CBX3, CBX5, GMNN, GTF2B, TBPL1 and the polycomb proteins PHCF2, RNF2 and SCMH1 but not with CBX1 or PCGF2.

Subcellular location. Cytoplasm. Nucleus. Nucleolus. Nucleoplasm.

Similarity. Belongs to the SPATA24 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86W54-1	1	yes
Q86W54-2	2

RefSeq proteins (1): NP_919272* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029176	SPATA24	Family

Pfam: PF15175

UniProt features (6 total): region of interest 2, chain 1, coiled-coil region 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86W54-F1	88.81	0.74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): GOBP_MALE_GAMETE_GENERATION, RICKMAN_METASTASIS_DN, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr5q31, GOCC_NUCLEOLUS, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, FEVR_CTNNB1_TARGETS_DN, FOSTER_KDM1A_TARGETS_DN, ARID5B_TARGET_GENES, DLX6_TARGET_GENES, HOXA10_TARGET_GENES, ZFP91_TARGET_GENES, GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP

GO Biological Process (2): spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (3): DNA binding (GO:0003677), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (6): male germ cell nucleus (GO:0001673), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
nuclear lumen	2
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
nucleic acid binding	1
protein binding	1
binding	1
germ cell nucleus	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

492 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA24	DNAJC18	Q9H819	673
SPATA24	SMIM33	A0A1B0GW64	665
SPATA24	LRCOL1	A6NCL2	581
SPATA24	ZSCAN2	Q7Z7L9	542
SPATA24	PROB1	E7EW31	540
SPATA24	FAM229B	Q4G0N7	533
SPATA24	FAM13B	Q9NYF5	513
SPATA24	SPATA21	Q7Z572	503
SPATA24	SPATA3	Q8NHX4	502
SPATA24	PKD2L2	Q9NZM6	488
SPATA24	SPMIP4	Q8N865	486
SPATA24	ECSCR	Q19T08	483
SPATA24	PAIP2	Q9BPZ3	449
SPATA24	LRRTM2	O43300	447
SPATA24	SPATA31E1	Q6ZUB1	447

IntAct

46 interactions, top by confidence:

A	B	Type	Score
SPATA24	CEP72	psi-mi:“MI:0915”(physical association)	0.740
CEP72	SPATA24	psi-mi:“MI:0915”(physical association)	0.740
CEP72	AHCYL1	psi-mi:“MI:0914”(association)	0.640
SPATA24	CALCOCO2	psi-mi:“MI:0915”(physical association)	0.560
SPATA24	KRT31	psi-mi:“MI:0915”(physical association)	0.560
SPATA24	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP4-2	SPATA24	psi-mi:“MI:0915”(physical association)	0.560
SPATA24	MID2	psi-mi:“MI:0915”(physical association)	0.560
KRT31	SPATA24	psi-mi:“MI:0915”(physical association)	0.560
LZTS2	SPATA24	psi-mi:“MI:0915”(physical association)	0.560
SPATA24	KRTAP4-2	psi-mi:“MI:0915”(physical association)	0.560
CALCOCO2	SPATA24	psi-mi:“MI:0915”(physical association)	0.560
SPATA24	GGPS1	psi-mi:“MI:0914”(association)	0.530
CDR2	IGSF3	psi-mi:“MI:0914”(association)	0.530
SPATA24	CDR2	psi-mi:“MI:0914”(association)	0.530
KRT40	SPATA24	psi-mi:“MI:0915”(physical association)	0.490
SPATA24	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
SPATA24	H1-2	psi-mi:“MI:0915”(physical association)	0.400
CAMK2D	SPATA24	psi-mi:“MI:0915”(physical association)	0.370
SPATA24	FLOT2	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (66): SPATA24 (Two-hybrid), SPATA24 (Two-hybrid), SPATA24 (Two-hybrid), SPATA24 (Two-hybrid), SPATA24 (Two-hybrid), SPATA24 (Two-hybrid), SPATA24 (Two-hybrid), SPATA24 (Proximity Label-MS), SPATA24 (Proximity Label-MS), SPATA24 (Proximity Label-MS), SPATA24 (Proximity Label-MS), SPATA24 (Proximity Label-MS), SPATA24 (Proximity Label-MS), SPATA24 (Proximity Label-MS), DCAF17 (Affinity Capture-MS)

ESM2 similar proteins: A0JMQ7, A2BGP7, A4D2H0, A4FU28, B4F7A7, O75665, P0C219, P0CG41, Q05D60, Q15025, Q28BZ7, Q28C41, Q2T9X8, Q32LC2, Q499E4, Q4PJT6, Q4R7I4, Q5FWP9, Q5U3Z6, Q5U465, Q5XIA0, Q5XJA2, Q5ZJA3, Q6AXZ4, Q6NRH3, Q6P926, Q6PCG6, Q7M6Y5, Q80Z25, Q865V0, Q86UF2, Q86W54, Q86XR8, Q86YF9, Q86Z20, Q8BMD2, Q8CEE0, Q8IX94, Q8IYJ2, Q8IYX8

Diamond homologs: Q4PJT6, Q4R7I4, Q6P926, Q86W54

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 31 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
Loss of Nlp from mitotic centrosomes	5	37.8×	8e-06
Loss of proteins required for interphase microtubule organization from the centrosome	5	37.8×	8e-06
Anchoring of the basal body to the plasma membrane	7	37.7×	6e-08
AURKA Activation by TPX2	5	36.2×	8e-06
Recruitment of mitotic centrosome proteins and complexes	5	32.4×	1e-05
Regulation of PLK1 Activity at G2/M Transition	5	30.2×	1e-05
Recruitment of NuMA to mitotic centrosomes	5	27.8×	2e-05

GO biological processes:

GO term	Partners	Fold	FDR
cilium assembly	5	12.7×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1371 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:139401772:A:G	L123P	0.991
5:139401945:A:G	L95P	0.990
5:139401980:A:C	F83L	0.990
5:139401980:A:T	F83L	0.990
5:139401982:A:G	F83L	0.990
5:139397107:A:G	L141P	0.987
5:139401979:C:G	A84P	0.987
5:139401957:A:G	L91P	0.984
5:139403954:A:G	L36P	0.983
5:139401923:A:C	F102L	0.980
5:139401923:A:T	F102L	0.980
5:139401925:A:G	F102L	0.980
5:139401975:A:G	L85P	0.980
5:139403996:A:G	L22P	0.979
5:139402008:A:G	L74P	0.977
5:139401823:A:G	L106P	0.975
5:139401916:C:G	A105P	0.970
5:139403966:A:G	L32P	0.969
5:139401978:G:T	A84D	0.967
5:139402632:A:G	L60P	0.964
5:139396893:C:A	Q175H	0.963
5:139396893:C:G	Q175H	0.963
5:139397056:T:G	Q158P	0.963
5:139401955:A:G	S92P	0.963
5:139397077:A:G	L151S	0.960
5:139396894:T:G	Q175P	0.959
5:139397119:T:G	Q137P	0.957
5:139403993:C:G	R23P	0.956
5:139401981:A:G	F83S	0.952
5:139402027:C:G	A68P	0.952

dbSNP variants (sampled 300 via entrez): RS1000037209 (5:139395931 A>G), RS1000257218 (5:139393599 T>G), RS1000348803 (5:139393322 G>A,T), RS1000518419 (5:139394934 C>T), RS1000573454 (5:139400279 G>A,T), RS1000591429 (5:139394856 G>A,C), RS1000686286 (5:139394636 G>A), RS1000799559 (5:139401350 T>G), RS1001114950 (5:139393638 G>C,T), RS1001231277 (5:139394346 C>T), RS1001454042 (5:139401449 TAG>T), RS1001568333 (5:139392929 C>T), RS1001682220 (5:139394604 C>T), RS1001898730 (5:139394320 C>G,T), RS1001914949 (5:139394060 C>A,G)

Disease associations

OMIM: gene MIM:621086 | 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
GCST005951_151	Body mass index	6.000000e-07
GCST010725_68	Malaria	4.000000e-07
GCST010725_7	Malaria	2.000000e-06
GCST010796_3063	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-09
GCST010796_3064	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-12
GCST010796_3065	Electrocardiogram morphology (amplitude at temporal datapoints)	7.000000e-14
GCST010796_3066	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
dicrotophos	decreases expression	1
titanium dioxide	decreases methylation	1
Vorinostat	increases expression	1
Benzo(a)pyrene	increases methylation	1
Ethyl Methanesulfonate	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases expression	1

Clinical trials (associated diseases)

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