SPATA12

Summary

SPATA12 (spermatogenesis associated 12, HGNC:23221) is a protein-coding gene on chromosome 3p14.3, encoding Spermatogenesis-associated protein 12 (Q7Z6I5).

This gene is expressed primarily in testis and may play a role in testicular development and spermatogenesis. The encoded protein may be upregulated in response to ultraviolet-C radiation.

Source: NCBI Gene 353324 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_181727

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23221
Approved symbol	SPATA12
Name	spermatogenesis associated 12
Location	3p14.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000186451
Ensembl biotype	protein_coding
OMIM	609869
Entrez	353324

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000334325, ENST00000867038

RefSeq mRNA: 1 — MANE Select: NM_181727 NM_181727

CCDS: CCDS2879

Canonical transcript exons

ENST00000334325 — 2 exons

Exon	Start	End
ENSE00001340109	57073366	57075432
ENSE00001340240	57060664	57060786

Expression profiles

Bgee: expression breadth broad, 65 present calls, max score 94.74.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2715 / max 30.7086, expressed in 121 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36981	0.1944	95
36980	0.0772	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.74	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.06	gold quality
left testis	UBERON:0004533	83.85	gold quality
right testis	UBERON:0004534	83.52	gold quality
testis	UBERON:0000473	81.29	gold quality
adult organism	UBERON:0007023	66.82	gold quality
pancreatic ductal cell	CL:0002079	56.81	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
epithelial cell of pancreas	CL:0000083	54.26	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
tonsil	UBERON:0002372	53.38	silver quality
right adrenal gland	UBERON:0001233	52.80	gold quality
colonic epithelium	UBERON:0000397	52.73	silver quality
right adrenal gland cortex	UBERON:0035827	51.76	gold quality
left adrenal gland	UBERON:0001234	51.48	gold quality
adrenal gland	UBERON:0002369	50.68	gold quality
left adrenal gland cortex	UBERON:0035825	50.68	gold quality
tibialis anterior	UBERON:0001385	50.27	silver quality
myocardium	UBERON:0002349	50.25	gold quality
medial globus pallidus	UBERON:0002477	50.19	gold quality
adrenal cortex	UBERON:0001235	50.15	gold quality
bone marrow cell	CL:0002092	49.59	gold quality
gall bladder	UBERON:0002110	49.04	gold quality
deltoid	UBERON:0001476	47.97	gold quality
globus pallidus	UBERON:0001875	47.95	gold quality
islet of Langerhans	UBERON:0000006	47.11	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
ileal mucosa	UBERON:0000331	46.90	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.61

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, JUN

miRNA regulators (miRDB)

63 targeting SPATA12, 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-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-199A-5P	99.51	69.71	1107

Literature-anchored findings (GeneRIF, showing 4)

• Didital differential display can be confirmed by SPATA12 as a novel computational biology-based approach for identification of the testis-specific expression of genes. (PMID:15603706)
• putative function of SPATA12 is to maintain the cell in a differentiated state and/or to suppress cell proliferation in the human testis. (PMID:17251597)
• AP-1 is founded to be a potential transcriptional activator of SPATA12. The promoter activity of SPATA12 was drastically declined after AP-1 binding site mutation or deletion. (PMID:22981541)
• SPATA12 could be induced under UV-C stress. (PMID:24205157)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Spermatogenesis-associated protein 12 — Q7Z6I5 (reviewed: Q7Z6I5)

Alternative names: Spermatogenesis-related protein 5

All UniProt accessions (2): A0A140VJV7, Q7Z6I5

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in testis.

RefSeq proteins (1): NP_859078* (*=MANE)

Domains & families (InterPro)

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z6I5-F1	42.63	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): chr3p14, KMT2D_TARGET_GENES, TFEB_TARGET_GENES, MIR5696, MIR4729, MIR6780B_5P, MIR4725_3P, MIR12119, MIR5581_3P, MIR4679, MIR3135B, MIR6880_5P, GSE15659_NAIVE_VS_PTPRC_NEG_CD4_TCELL_DN, GSE15659_NAIVE_CD4_TCELL_VS_RESTING_TREG_DN, GSE15659_NAIVE_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_DN

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

260 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA12	C3orf22	Q8N5N4	541
SPATA12	RNASE12	Q5GAN4	480
SPATA12	CHD2	O14647	479
SPATA12	C12orf56	Q8IXR9	479
SPATA12	SMIM17	P0DL12	475
SPATA12	SH2D7	A6NKC9	447
SPATA12	C1orf167	Q5SNV9	447
SPATA12	CC2D2B	Q6DHV5	447
SPATA12	C22orf42	Q6IC83	447
SPATA12	ANKRD62	A6NC57	446
SPATA12	SPMAP2	Q9P2T0	443
SPATA12	SPDYE4	A6NLX3	433
SPATA12	CLPSL1	A2RUU4	419
SPATA12	EPCIP	Q9NYP8	419
SPATA12	RD3L	P0DJH9	418

IntAct

108 interactions, top by confidence:

A	B	Type	Score
HOXA1	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	SMARCC1	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	CIDEC	psi-mi:“MI:0915”(physical association)	0.560
POGZ	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
KRTAP26-1	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
HGS	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
ANKS1A	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
CREB5	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
FRS3	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	A2M	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	APBB2	psi-mi:“MI:0915”(physical association)	0.560
CASP6	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	CHAT	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	DNM2	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	TOR1A	psi-mi:“MI:0915”(physical association)	0.560
SPATA12		psi-mi:“MI:0915”(physical association)	0.560
SPATA12	EIF2S3	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	FKBP1A	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	GSN	psi-mi:“MI:0915”(physical association)	0.560
HSPA2	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	MECP2	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	PMP22	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	SARS1	psi-mi:“MI:0915”(physical association)	0.560
SPATA12	SMN1	psi-mi:“MI:0915”(physical association)	0.560
DNALI1	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
BAG6	SPATA12	psi-mi:“MI:0915”(physical association)	0.560
KLF11	SPATA12	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (11): SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), SPATA12 (Two-hybrid), CIDEC (Two-hybrid), KRTAP26-1 (Two-hybrid)

ESM2 similar proteins: A4D1N5, A4D250, A6NM66, B1ANY3, C0HM98, C0HMD7, F2Z3F1, J3KSC0, O14603, O15544, P0C092, P0DMR3, P0DMU3, P24026, P49671, P87743, Q06250, Q0VFX4, Q14695, Q2M3A8, Q32KZ5, Q4R3X9, Q4VX62, Q52M75, Q5SR53, Q5SWW7, Q5T0J3, Q5W5W9, Q6AWC8, Q6ZP68, Q6ZUL3, Q6ZV80, Q6ZVU0, Q7Z4H9, Q7Z6I5, Q8JMY5, Q8N2C9, Q8N4M7, Q8N5N4, Q8NDY4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

228 predictions. Top by Δscore:

Variant	Effect	Δscore
3:57070214:G:GT	donor_gain	0.9800
3:57060787:G:GG	donor_gain	0.9700
3:57060782:GTCTT:G	donor_gain	0.9500
3:57070195:C:T	donor_gain	0.9200
3:57073364:A:AG	acceptor_gain	0.9200
3:57073365:G:GG	acceptor_gain	0.9200
3:57060785:TT:T	donor_gain	0.9100
3:57065792:GC:G	donor_gain	0.9100
3:57073513:ACT:A	donor_gain	0.8900
3:57070255:A:T	donor_gain	0.8800
3:57073514:C:G	donor_gain	0.8800
3:57060783:TCTTG:T	donor_loss	0.8600
3:57060785:TTGT:T	donor_loss	0.8600
3:57060786:TG:T	donor_loss	0.8600
3:57060788:T:TC	donor_loss	0.8600
3:57060789:G:GG	donor_loss	0.8600
3:57060790:AGT:A	donor_loss	0.8600
3:57060791:G:C	donor_loss	0.8600
3:57065793:C:G	donor_gain	0.8400
3:57070214:G:T	donor_gain	0.8200
3:57070206:GGGT:G	donor_gain	0.8000
3:57061318:AATGG:A	acceptor_gain	0.7800
3:57060784:CTT:C	donor_gain	0.7700
3:57073363:TA:T	acceptor_gain	0.7700
3:57073362:CTAG:C	acceptor_gain	0.7600
3:57073364:AG:A	acceptor_gain	0.7600
3:57073454:T:TA	donor_gain	0.7600
3:57073455:A:AA	donor_gain	0.7600
3:57060792:T:G	donor_loss	0.7500
3:57073365:GCCAA:G	acceptor_gain	0.7400

AlphaMissense

1221 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:57074196:T:C	F168L	0.851
3:57074198:T:A	F168L	0.851
3:57074198:T:G	F168L	0.851
3:57073908:T:C	F72L	0.753
3:57073910:T:A	F72L	0.753
3:57073910:T:G	F72L	0.753
3:57074079:T:C	F129L	0.742
3:57074081:T:A	F129L	0.742
3:57074081:T:G	F129L	0.742
3:57074211:T:C	F173L	0.701
3:57074213:T:A	F173L	0.701
3:57074213:T:G	F173L	0.701
3:57073751:G:C	W19C	0.640
3:57073751:G:T	W19C	0.640
3:57073790:G:C	W32C	0.613
3:57073790:G:T	W32C	0.613
3:57073701:A:C	S3R	0.592
3:57073703:T:A	S3R	0.592
3:57073703:T:G	S3R	0.592
3:57073760:G:C	K22N	0.589
3:57073760:G:T	K22N	0.589
3:57074123:G:C	W143C	0.565
3:57074123:G:T	W143C	0.565

dbSNP variants (sampled 300 via entrez): RS1000850072 (3:57074522 C>A), RS1000887899 (3:57069097 A>G), RS1000945770 (3:57062836 CT>C), RS1001403405 (3:57060311 A>AG), RS1001475705 (3:57062441 A>G), RS1001600981 (3:57060051 G>A), RS1001706044 (3:57068157 G>A), RS1001733455 (3:57075449 G>A), RS1001764689 (3:57075194 T>G), RS1002113864 (3:57062601 A>C), RS1002410746 (3:57061933 C>T), RS1002594335 (3:57067264 A>T), RS1002738111 (3:57074047 G>A), RS1003075128 (3:57059121 C>T), RS1003117193 (3:57067077 C>A)

Disease associations

OMIM: gene MIM:609869 | 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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
abrine	increases expression	1
Temozolomide	affects response to substance	1
Benzo(a)pyrene	increases expression	1
Carmustine	affects response to substance	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Tobacco Smoke Pollution	affects expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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