SPATA45

Summary

SPATA45 (spermatogenesis associated 45, HGNC:33709) is a protein-coding gene on chromosome 1q32.3, encoding Spermatogenesis-associated protein 45 (Q537H7).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_001024601

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33709
Approved symbol	SPATA45
Name	spermatogenesis associated 45
Location	1q32.3
Locus type	gene with protein product
Status	Approved
Aliases	LOC149643
Ensembl gene	ENSG00000185523
Ensembl biotype	protein_coding
Entrez	149643

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000332912

RefSeq mRNA: 1 — MANE Select: NM_001024601 NM_001024601

CCDS: CCDS31020

Canonical transcript exons

ENST00000332912 — 3 exons

Exon	Start	End
ENSE00001308240	212830141	212830261
ENSE00001443145	212847580	212847649
ENSE00001886891	212835873	212836187

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 86.47.

Top tissues by expression

233 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	86.47	gold quality
right testis	UBERON:0004534	77.42	gold quality
left testis	UBERON:0004533	76.05	gold quality
testis	UBERON:0000473	73.74	gold quality
islet of Langerhans	UBERON:0000006	56.45	gold quality
sperm	CL:0000019	56.39	gold quality
granulocyte	CL:0000094	50.93	silver quality
lower lobe of lung	UBERON:0008949	50.64	silver quality
lower esophagus mucosa	UBERON:0035834	50.15	gold quality
adrenal tissue	UBERON:0018303	49.39	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	49.34	gold quality
stromal cell of endometrium	CL:0002255	48.96	gold quality
spinal cord	UBERON:0002240	48.47	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	47.84	gold quality
adult organism	UBERON:0007023	47.81	silver quality
metanephros cortex	UBERON:0010533	46.71	gold quality
adenohypophysis	UBERON:0002196	46.54	gold quality
right coronary artery	UBERON:0001625	46.09	gold quality
substantia nigra	UBERON:0002038	45.47	gold quality
pituitary gland	UBERON:0000007	45.41	gold quality
midbrain	UBERON:0001891	44.76	gold quality
metanephros	UBERON:0000081	44.75	gold quality
bone marrow cell	CL:0002092	44.65	gold quality
amygdala	UBERON:0001876	44.41	gold quality
primary visual cortex	UBERON:0002436	44.41	gold quality
corpus callosum	UBERON:0002336	44.35	silver quality
hypothalamus	UBERON:0001898	44.28	gold quality
nasal cavity mucosa	UBERON:0001826	44.11	gold quality
right adrenal gland cortex	UBERON:0035827	43.86	gold quality
smooth muscle tissue	UBERON:0001135	43.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting SPATA45, 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-5692A	100.00	74.40	6850
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-593-3P	99.22	67.28	1327
HSA-MIR-603	98.58	68.28	1603

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	spata45	ENSDARG00000095457
mus_musculus	Spata45	ENSMUSG00000057072
rattus_norvegicus	SPATA45	ENSRNOG00000048659
rattus_norvegicus		ENSRNOG00000080983

Protein

Protein identifiers

Spermatogenesis-associated protein 45 — Q537H7 (reviewed: Q537H7)

All UniProt accessions (1): Q537H7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPATA45 family.

RefSeq proteins (1): NP_001019772* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038806	SPATA45_mammals	Family

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q537H7-F1	64.64	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 7 (showing top): TCCAGAG_MIR518C, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_1H_ACT_CD4_TCELL_DN, GSE29614_CTRL_VS_TIV_FLU_VACCINE_PBMC_2007_UP, chr1q32, GSE21546_UNSTIM_VS_ANTI_CD3_STIM_ELK1_KO_DP_THYMOCYTES_UP, GSE34156_NOD2_LIGAND_VS_NOD2_AND_TLR1_TLR2_LIGAND_24H_TREATED_MONOCYTE_UP, GSE20727_CTRL_VS_DNFB_ALLERGEN_TREATED_DC_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

184 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA45	SPMIP10	Q6ZNM6	676
SPATA45	TEX35	Q5T0J7	664
SPATA45	SPATA18	Q8TC71	626
SPATA45	OR6K3	Q8NGY3	580
SPATA45	SPEM1	Q8N4L4	540
SPATA45	SPATC1	Q76KD6	519
SPATA45	CBY2	Q8NA61	517
SPATA45	SPATA3	Q8NHX4	516
SPATA45	LENEP	Q9Y5L5	474
SPATA45	SPATA19	Q7Z5L4	463
SPATA45	C1orf141	Q5JVX7	446
SPATA45	ACTRT2	Q8TDY3	434
SPATA45	POTEH	Q6S545	432
SPATA45	LCE3C	Q5T5A8	426
SPATA45	SH3BP5L	Q7L8J4	419

IntAct

0 interactions, top by confidence:

BioGRID (1): SPATA45 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GVR7, A0PJW8, A2BYT2, A5FRX9, B8G1X0, C1DKL7, G3UWD5, O42659, O62953, O95567, O98453, P05899, P11690, P11794, P19718, P20920, P27975, P32544, P33482, P39971, P52776, P54446, P69516, P69517, P86209, Q02781, Q0ABH1, Q1X6Y0, Q3AMN4, Q3J8R8, Q3K5Z2, Q3MFB7, Q3ZZM0, Q537H7, Q57P89, Q5I162, Q5PHY6, Q6AY31, Q75003, Q7CQJ0

Diamond homologs: Q32P96, Q537H7, Q9CVW4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

427 predictions. Top by Δscore:

Variant	Effect	Δscore
1:212835918:G:C	donor_gain	1.0000
1:212830258:TTAT:T	acceptor_gain	0.9900
1:212830260:ATCT:A	acceptor_loss	0.9900
1:212830261:TC:T	acceptor_loss	0.9900
1:212830262:C:CC	acceptor_gain	0.9900
1:212830262:CTGA:C	acceptor_loss	0.9900
1:212830263:T:G	acceptor_loss	0.9900
1:212836183:CTGTC:C	acceptor_gain	0.9900
1:212836185:GTCCT:G	acceptor_loss	0.9900
1:212836188:C:CA	acceptor_loss	0.9900
1:212836188:C:CC	acceptor_gain	0.9900
1:212836189:T:C	acceptor_loss	0.9900
1:212847590:C:CT	donor_gain	0.9900
1:212847591:T:TT	donor_gain	0.9900
1:212830259:TAT:T	acceptor_gain	0.9800
1:212835871:A:AC	donor_gain	0.9700
1:212835872:C:CC	donor_gain	0.9700
1:212836184:TGTC:T	acceptor_gain	0.9700
1:212847577:TA:T	donor_loss	0.9600
1:212847578:A:T	donor_loss	0.9600
1:212847579:C:CA	donor_loss	0.9600
1:212830257:ATTAT:A	acceptor_gain	0.9500
1:212847589:A:AC	donor_gain	0.9400
1:212847591:TACCA:T	donor_gain	0.9400
1:212836195:CAAA:C	acceptor_loss	0.9300
1:212838198:A:AC	donor_gain	0.9300
1:212830270:A:AC	acceptor_gain	0.9200
1:212835917:AG:A	donor_gain	0.9200
1:212836186:TC:T	acceptor_gain	0.9200
1:212836187:CC:C	acceptor_gain	0.9200

AlphaMissense

659 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:212830248:A:C	F97L	0.946
1:212830248:A:T	F97L	0.946
1:212830250:A:G	F97L	0.946
1:212835883:A:C	F89L	0.934
1:212835883:A:T	F89L	0.934
1:212835885:A:G	F89L	0.934
1:212836064:C:G	R29P	0.908
1:212830246:C:T	G98E	0.907
1:212836065:G:T	R29S	0.907
1:212835927:A:G	W75R	0.899
1:212835927:A:T	W75R	0.899
1:212835997:G:C	F51L	0.885
1:212835997:G:T	F51L	0.885
1:212835999:A:G	F51L	0.885
1:212835886:G:C	H88Q	0.884
1:212835886:G:T	H88Q	0.884
1:212836015:T:A	R45S	0.884
1:212836015:T:G	R45S	0.884
1:212835934:C:A	R72S	0.883
1:212835934:C:G	R72S	0.883
1:212830247:C:G	G98R	0.880
1:212830247:C:T	G98R	0.880
1:212830252:A:T	I96K	0.874
1:212836024:G:C	S42R	0.867
1:212836024:G:T	S42R	0.867
1:212836026:T:G	S42R	0.867
1:212836040:C:G	R37P	0.864
1:212836000:G:C	H50Q	0.863
1:212836000:G:T	H50Q	0.863
1:212836042:T:A	E36D	0.850

dbSNP variants (sampled 300 via entrez): RS1000054221 (1:212847377 T>A), RS1000074166 (1:212840936 T>C), RS1000144371 (1:212840656 C>T), RS1000312387 (1:212834607 C>A,T), RS1000603879 (1:212842891 A>G), RS1000856555 (1:212840225 A>G), RS1000911441 (1:212841573 G>A), RS1001012252 (1:212846337 CACT>C), RS1001464687 (1:212846120 C>A,T), RS1001743990 (1:212842549 T>C), RS1002024903 (1:212844899 A>G), RS1002135389 (1:212848743 C>T), RS1002489710 (1:212839142 T>A), RS1002643948 (1:212842072 A>G), RS1002676896 (1:212845138 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004861_36	Itch intensity from mosquito bite	1.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008377	mosquito bite reaction itch intensity 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
Benzo(a)pyrene	decreases expression, decreases methylation	2
propionaldehyde	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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