SPATA46

Summary

SPATA46 (spermatogenesis associated 46, HGNC:27648) is a protein-coding gene on chromosome 1q23.3, encoding Spermatogenesis-associated protein 46 (Q5T0L3). Plays a role in spermiogenesis and fertilization.

Predicted to be involved in fusion of sperm to egg plasma membrane involved in single fertilization and spermatogenesis. Predicted to be located in membrane and nucleus. Predicted to be active in nuclear membrane.

Source: NCBI Gene 284680 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_182581

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27648
Approved symbol	SPATA46
Name	spermatogenesis associated 46
Location	1q23.3
Locus type	gene with protein product
Status	Approved
Aliases	TEKT2BP2
Ensembl gene	ENSG00000171722
Ensembl biotype	protein_coding
OMIM	617257
Entrez	284680

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 nonsense_mediated_decay

ENST00000367935, ENST00000493255, ENST00000910350, ENST00000910351, ENST00000910352

RefSeq mRNA: 1 — MANE Select: NM_182581 NM_182581

CCDS: CCDS1238

Canonical transcript exons

ENST00000367935 — 3 exons

Exon	Start	End
ENSE00001165805	162375290	162375403
ENSE00001445958	162373203	162374616
ENSE00001895130	162376688	162376854

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 87.72.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1289 / max 138.4831, expressed in 3 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15669	0.0701	3
15670	0.0521	3
15671	0.0043	3
15668	0.0025	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	87.72	gold quality
right testis	UBERON:0004534	87.60	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.45	silver quality
testis	UBERON:0000473	84.96	gold quality
adult organism	UBERON:0007023	78.65	gold quality
ganglionic eminence	UBERON:0004023	69.84	gold quality
pancreatic ductal cell	CL:0002079	66.91	silver quality
adrenal tissue	UBERON:0018303	62.56	gold quality
pituitary gland	UBERON:0000007	61.74	gold quality
right hemisphere of cerebellum	UBERON:0014890	60.46	gold quality
cerebellar cortex	UBERON:0002129	59.23	gold quality
adenohypophysis	UBERON:0002196	59.08	gold quality
cerebellar hemisphere	UBERON:0002245	59.05	gold quality
ventricular zone	UBERON:0003053	58.65	gold quality
ileal mucosa	UBERON:0000331	58.39	silver quality
cerebellum	UBERON:0002037	58.16	gold quality
mucosa of stomach	UBERON:0001199	57.88	gold quality
bone marrow cell	CL:0002092	57.86	silver quality
rectum	UBERON:0001052	57.82	gold quality
tibialis anterior	UBERON:0001385	57.63	silver quality
sperm	CL:0000019	57.08	gold quality
body of stomach	UBERON:0001161	57.07	gold quality
right lobe of liver	UBERON:0001114	56.47	gold quality
colonic epithelium	UBERON:0000397	55.77	silver quality
epithelial cell of pancreas	CL:0000083	55.49	gold quality
stomach	UBERON:0000945	55.05	gold quality
right adrenal gland	UBERON:0001233	54.66	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
minor salivary gland	UBERON:0001830	54.32	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting SPATA46, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-511-5P	98.97	70.94	2268
HSA-MIR-6830-3P	98.62	68.07	1760
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-4662A-5P	98.48	67.18	1007
HSA-MIR-4637	97.69	68.14	632
HSA-MIR-6831-3P	97.49	69.29	505

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata46	ENSMUSG00000042800
rattus_norvegicus	Spata46	ENSRNOG00000002972

Protein

Protein identifiers

Spermatogenesis-associated protein 46 — Q5T0L3 (reviewed: Q5T0L3)

All UniProt accessions (2): Q5T0L3, V9GYQ4

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in spermiogenesis and fertilization.

Subcellular location. Nucleus membrane.

Tissue specificity. Testis-specific.

RefSeq proteins (1): NP_872387* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040879	Spt46-like	Family

Pfam: PF17734

UniProt features (4 total): sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T0L3-F1	56.40	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): GOBP_SINGLE_FERTILIZATION, GOBP_MEMBRANE_FUSION, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_MALE_GAMETE_GENERATION, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_PLASMA_MEMBRANE_FUSION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MEMBRANE_ORGANIZATION, GOBP_FERTILIZATION, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_MEMBRANE, GOCC_ORGANELLE_ENVELOPE, MIR511_5P, MIR4662A_5P

GO Biological Process (4): spermatogenesis (GO:0007283), fusion of sperm to egg plasma membrane involved in single fertilization (GO:0007342), fertilization (GO:0009566), cell differentiation (GO:0030154)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): nuclear membrane (GO:0031965), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	1
male gamete generation	1
single fertilization	1
cellular process involved in reproduction in multicellular organism	1
sexual reproduction	1
reproductive process	1
cellular developmental process	1
binding	1
nucleus	1
nuclear envelope	1
organelle membrane	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

246 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA46	SSMEM1	Q8WWF3	680
SPATA46	SPACA1	Q9HBV2	666
SPATA46	SPATA16	Q9BXB7	612
SPATA46	DPY19L2	Q6NUT2	590
SPATA46	SPATA25	Q9BR10	547
SPATA46	ARMC2	Q8NEN0	534
SPATA46	SPATA3	Q8NHX4	529
SPATA46	SPATA20	Q8TB22	527
SPATA46	SPATA6	Q9NWH7	517
SPATA46	PRSS54	Q6PEW0	507
SPATA46	SPATA9	Q9BWV2	498
SPATA46	AGBL5	Q8NDL9	498
SPATA46	SEPTIN12	Q8IYM1	496
SPATA46	FBXO43	Q4G163	465
SPATA46	ACTL7A	Q9Y615	458

IntAct

41 interactions, top by confidence:

A	B	Type	Score
HLCS	SPATA46	psi-mi:“MI:0915”(physical association)	0.740
RBPMS	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
SPATA46	RBPMS	psi-mi:“MI:0915”(physical association)	0.560
ENKD1	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
TRAF1	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
KRT34	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
TLX3	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
CRYAA	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
DYNC1H1	SPATA46	psi-mi:“MI:0915”(physical association)	0.560
SPATA46	ATN1	psi-mi:“MI:0915”(physical association)	0.560
SPATA46	HNRNPH3	psi-mi:“MI:0915”(physical association)	0.560
SPATA46	KLK6	psi-mi:“MI:0915”(physical association)	0.560
SPATA46	TYW5	psi-mi:“MI:0914”(association)	0.530
SPATA46	MDM4	psi-mi:“MI:0914”(association)	0.530
CCDC85B	SPATA46	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (43): C1orf111 (Two-hybrid), CSNK1A1 (Affinity Capture-MS), MGLL (Affinity Capture-MS), HLCS (Affinity Capture-MS), GAPVD1 (Affinity Capture-MS), TYW5 (Affinity Capture-MS), MDM4 (Affinity Capture-MS), SNX24 (Affinity Capture-MS), CEP95 (Affinity Capture-MS), C1orf111 (Two-hybrid), SNX24 (Affinity Capture-MS), MDM4 (Affinity Capture-MS), GAPVD1 (Affinity Capture-MS), CSNK1A1 (Affinity Capture-MS), TYW5 (Affinity Capture-MS)

ESM2 similar proteins: A0A0A6YY25, A0A5K7RLP0, A6NMK8, A8MVX0, B2RQL2, B2RXH4, C9JSJ3, D2J0Y4, O54824, P97303, Q01954, Q05AH6, Q0VET5, Q14005, Q1W617, Q2YDE2, Q3MHT3, Q3U0P1, Q3ULM6, Q3UXL4, Q4R7L6, Q5RC05, Q5T0L3, Q68CR7, Q6GQV1, Q6NS69, Q6NZK5, Q6P1D7, Q6PG16, Q6ZVT6, Q7Z4V0, Q80W88, Q80XI1, Q811R2, Q86T90, Q86YN6, Q8BHP2, Q8BLK9, Q8BP99, Q8BW86

Diamond homologs: A1A519, A6NMN3, E9PXT9, Q2YDE2, Q4FZF2, Q4R7L6, Q5T0L3, Q66LM5, Q66LM6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

542 predictions. Top by Δscore:

Variant	Effect	Δscore
1:162374617:C:CC	acceptor_gain	1.0000
1:162374613:CAGT:C	acceptor_gain	0.9900
1:162374614:AGT:A	acceptor_gain	0.9900
1:162374614:AGTCT:A	acceptor_loss	0.9900
1:162374615:GT:G	acceptor_gain	0.9900
1:162374616:TC:T	acceptor_loss	0.9900
1:162374617:C:CA	acceptor_loss	0.9900
1:162374618:T:G	acceptor_loss	0.9900
1:162374789:T:TA	donor_gain	0.9800
1:162375409:T:TC	acceptor_gain	0.9600
1:162374612:GCAGT:G	acceptor_gain	0.9500
1:162374613:CAGTC:C	acceptor_gain	0.9500
1:162374619:G:C	acceptor_loss	0.9500
1:162376682:GTTTA:G	donor_loss	0.9500
1:162376683:TTTAC:T	donor_loss	0.9500
1:162376684:TTAC:T	donor_loss	0.9500
1:162376685:TACCT:T	donor_loss	0.9500
1:162376686:A:G	donor_loss	0.9500
1:162376687:C:A	donor_loss	0.9500
1:162375401:TGT:T	acceptor_gain	0.9400
1:162374615:GTC:G	acceptor_gain	0.9200
1:162374616:TCT:T	acceptor_gain	0.9200
1:162374925:C:G	acceptor_gain	0.9200
1:162375404:C:CC	acceptor_gain	0.9200
1:162376735:A:AC	donor_gain	0.9200
1:162374472:TGCTG:T	donor_gain	0.9100
1:162376681:AGTTT:A	donor_loss	0.9100
1:162376688:C:G	donor_loss	0.9100
1:162374469:T:TA	donor_gain	0.9000
1:162374797:A:AC	donor_gain	0.9000

AlphaMissense

1728 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:162374204:G:C	F210L	0.995
1:162374204:G:T	F210L	0.995
1:162374206:A:G	F210L	0.995
1:162374201:G:C	S211R	0.990
1:162374201:G:T	S211R	0.990
1:162374203:T:G	S211R	0.990
1:162374534:G:C	S100R	0.990
1:162374534:G:T	S100R	0.990
1:162374536:T:G	S100R	0.990
1:162374281:A:G	C185R	0.987
1:162374205:A:G	F210S	0.985
1:162374260:A:C	Y192D	0.984
1:162374200:A:G	C212R	0.981
1:162374280:C:G	C185S	0.980
1:162374281:A:T	C185S	0.980
1:162374231:G:C	H201Q	0.979
1:162374231:G:T	H201Q	0.979
1:162374279:G:C	C185W	0.979
1:162374191:A:C	Y215D	0.978
1:162374272:A:G	C188R	0.978
1:162374265:C:G	R190P	0.977
1:162374556:C:G	R93P	0.977
1:162374199:C:T	C212Y	0.975
1:162374233:G:C	H201D	0.975
1:162374241:A:G	L198P	0.975
1:162374270:G:C	C188W	0.975
1:162374178:A:G	L219P	0.973
1:162374198:G:C	C212W	0.973
1:162374209:C:G	G209R	0.972
1:162374551:A:G	W95R	0.972

dbSNP variants (sampled 300 via entrez): RS1000966874 (1:162374828 C>T), RS1001235049 (1:162373470 C>T), RS1001809097 (1:162378829 A>G), RS1002067472 (1:162377427 T>C), RS1002133993 (1:162378537 A>G), RS1003810621 (1:162376469 A>G), RS1004150324 (1:162376288 T>C), RS1004271146 (1:162372866 A>G), RS1005701933 (1:162373837 G>T), RS1005932015 (1:162378092 G>C), RS1006058795 (1:162373002 G>A,T), RS1006111175 (1:162372778 T>C), RS1007939110 (1:162375856 C>T), RS1008404168 (1:162375533 C>G,T), RS1009771559 (1:162378751 G>A,T)

Disease associations

OMIM: gene MIM:617257 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST010538_3	Sum of carotid plaque area	5.000000e-06
GCST010539_2	Sum of stenosis	4.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006501	carotid plaque build

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
terbufos	decreases methylation	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression, increases abundance	1
DEET	decreases expression	1
Fonofos	decreases methylation	1
Estradiol	increases expression	1
Parathion	decreases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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