SPATA6L

Summary

SPATA6L (spermatogenesis associated 6 like, HGNC:25472) is a protein-coding gene on chromosome 9p24.2-p24.1, encoding Spermatogenesis associated 6-like protein (Q8N4H0).

Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm head-tail coupling apparatus.

Source: NCBI Gene 55064 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 91 total — 2 pathogenic
• MANE Select transcript: NM_001353486

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25472
Approved symbol	SPATA6L
Name	spermatogenesis associated 6 like
Location	9p24.2-p24.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10058
Ensembl gene	ENSG00000106686
Ensembl biotype	protein_coding
Entrez	55064

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 7 protein_coding, 5 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 2 retained_intron

ENST00000223517, ENST00000381890, ENST00000406861, ENST00000451763, ENST00000461761, ENST00000471669, ENST00000475086, ENST00000485616, ENST00000485981, ENST00000486047, ENST00000496798, ENST00000497383, ENST00000498087, ENST00000682582, ENST00000707146, ENST00000707147, ENST00000888411, ENST00000958227

RefSeq mRNA: 10 — MANE Select: NM_001353486 NM_001039395, NM_001353484, NM_001353485, NM_001353486, NM_001353487, NM_001353488, NM_001353489, NM_001353490, NM_001353491, NM_001416130

CCDS: CCDS43785, CCDS6453

Canonical transcript exons

ENST00000682582 — 12 exons

Exon	Start	End
ENSE00003497471	4625327	4625566
ENSE00003549899	4605347	4605440
ENSE00003555898	4629091	4629168
ENSE00003559606	4617923	4618110
ENSE00003582984	4604179	4604269
ENSE00003603814	4622408	4622510
ENSE00003610598	4635275	4635399
ENSE00003623197	4618864	4618898
ENSE00003652783	4656041	4656089
ENSE00003691315	4661899	4662036
ENSE00003917733	4666212	4666480
ENSE00003919938	4598316	4600809

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 91.82.

FANTOM5 (CAGE): breadth broad, TPM avg 1.3724 / max 82.3464, expressed in 496 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99802	0.9296	396
205416	0.3513	176
99801	0.0916	36

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	91.82	gold quality
right uterine tube	UBERON:0001302	87.82	gold quality
sperm	CL:0000019	86.68	gold quality
secondary oocyte	CL:0000655	84.23	gold quality
left testis	UBERON:0004533	84.02	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.69	gold quality
male germ cell	CL:0000015	83.57	gold quality
right testis	UBERON:0004534	83.48	gold quality
bronchial epithelial cell	CL:0002328	83.04	gold quality
right lobe of liver	UBERON:0001114	81.58	gold quality
testis	UBERON:0000473	81.16	gold quality
adenohypophysis	UBERON:0002196	79.49	gold quality
body of pancreas	UBERON:0001150	78.76	gold quality
pituitary gland	UBERON:0000007	78.68	gold quality
epithelium of bronchus	UBERON:0002031	78.24	gold quality
bronchus	UBERON:0002185	77.49	gold quality
calcaneal tendon	UBERON:0003701	76.71	gold quality
pancreas	UBERON:0001264	76.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.80	silver quality
left lobe of thyroid gland	UBERON:0001120	75.79	gold quality
islet of Langerhans	UBERON:0000006	75.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.11	gold quality
thyroid gland	UBERON:0002046	75.10	gold quality
gall bladder	UBERON:0002110	75.05	gold quality
right lobe of thyroid gland	UBERON:0001119	74.73	gold quality
liver	UBERON:0002107	73.92	gold quality
right lung	UBERON:0002167	72.87	gold quality
metanephros cortex	UBERON:0010533	72.68	gold quality
cerebellar hemisphere	UBERON:0002245	72.50	gold quality
cerebellar cortex	UBERON:0002129	72.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.48

Regulation

Is transcription factor: no

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	spata6l	ENSDARG00000004874
mus_musculus	Spata6l	ENSMUSG00000064202
rattus_norvegicus	Spata6l	ENSRNOG00000015137
drosophila_melanogaster	CG14079	FBGN0036849

Paralogs (1): SPATA6 (ENSG00000132122)

Protein

Protein identifiers

Spermatogenesis associated 6-like protein — Q8N4H0 (reviewed: Q8N4H0)

All UniProt accessions (4): Q8N4H0, A0AA34QVF8, D3DRI0, F8W9P2

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the SPATA6 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N4H0-1	1	yes
Q8N4H0-2	2
Q8N4H0-3	3

RefSeq proteins (10): NP_001034484, NP_001340413, NP_001340414, NP_001340415, NP_001340416, NP_001340417, NP_001340418, NP_001340419, NP_001340420, NP_001403059 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032732	SPATA6_N	Domain
IPR042769	SPATA6_fam	Family

Pfam: PF14909

UniProt features (12 total): splice variant 4, sequence variant 2, modified residue 2, chain 1, region of interest 1, sequence conflict 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4H0-F1	56.82	0.17

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 260, 263

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOMF_CYTOSKELETAL_PROTEIN_BINDING, GOMF_MYOSIN_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, RAO_BOUND_BY_SALL4_ISOFORM_A, GOMF_MYOSIN_LIGHT_CHAIN_BINDING, MIR559, MIR3529_3P, MIR548Y, MIR548BB_5P, MIR548AR_5P, MIR548AD_5P_MIR548AE_5P_MIR548AY_5P_MIR548B_5P_MIR548D_5P, MIR548AK_MIR548AM_5P_MIR548C_5P_MIR548H_5P_MIR548O_5P_MIR548AU_5P

GO Biological Process (1): spermatogenesis (GO:0007283)

GO Molecular Function (1): myosin light chain binding (GO:0032027)

GO Cellular Component (1): sperm head-tail coupling apparatus (GO:0120212)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	1
male gamete generation	1
myosin binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

382 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA6L	TTLL5	Q6EMB2	508
SPATA6L	DRC9	Q9H095	502
SPATA6L	DMAC1	Q96GE9	476
SPATA6L	SPATA1	Q5VX52	445
SPATA6L	BRD10	Q5HYC2	412
SPATA6L	DPY19L2	Q6NUT2	404
SPATA6L	SPATA4	Q8NEY3	381
SPATA6L	SLC26A8	Q96RN1	371
SPATA6L	RCL1	Q9Y2P8	370
SPATA6L	OVCA2	Q8WZ82	370
SPATA6L	PLPP6	Q8IY26	369
SPATA6L	AK3	Q9UIJ7	368
SPATA6L	CATSPER3	Q86XQ3	366
SPATA6L	EXOSC9	Q06265	360
SPATA6L	SMC1B	Q8NDV3	354

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CFTR	SPATA6L	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (9): KIF4A (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), ZBTB1 (Affinity Capture-MS), KIF4A (Affinity Capture-MS), ZBTB1 (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), SPATA6L (Affinity Capture-MS), SPATA6L (Positive Genetic), SPATA6L (PCA)

ESM2 similar proteins: A1A5R8, A6H694, A6PVS8, B8A5Y1, D3Z6S9, F1MCA7, P62283, P62285, P62287, P62288, P62289, P62290, P62291, P62292, P62293, P62294, P62296, P62297, P62932, P70587, Q05C16, Q14DL3, Q3U3V8, Q3V0J4, Q497N7, Q4R3V2, Q4R739, Q4V8G0, Q53TS8, Q5CZC0, Q5RA75, Q6AXY2, Q6AYL8, Q6P2D8, Q6PUR7, Q7PCK7, Q7T3T8, Q7Z7J5, Q80TE7, Q86WZ0

Diamond homologs: B2RV46, Q2KJG1, Q3U6K5, Q6AYJ3, Q8N4H0, Q99MU5, Q9NWH7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	69
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1047891	GRCh37/hg19 9p24.3-22.1(chr9:204193-18654812)	Pathogenic
2427400	NC_000009.11:g.(?3828272)(5126791_?)del	Pathogenic

SpliceAI

3824 predictions. Top by Δscore:

Variant	Effect	Δscore
9:4567643:T:A	acceptor_gain	1.0000
9:4567649:T:A	acceptor_gain	1.0000
9:4567660:A:AG	acceptor_gain	1.0000
9:4567660:AACAT:A	acceptor_gain	1.0000
9:4567661:A:G	acceptor_gain	1.0000
9:4567662:C:G	acceptor_gain	1.0000
9:4567663:A:AG	acceptor_gain	1.0000
9:4567663:AT:A	acceptor_gain	1.0000
9:4567664:T:G	acceptor_gain	1.0000
9:4567664:T:TA	acceptor_gain	1.0000
9:4567664:TGCA:T	acceptor_loss	1.0000
9:4567665:GCAG:G	acceptor_loss	1.0000
9:4567666:CA:C	acceptor_loss	1.0000
9:4567667:A:AG	acceptor_gain	1.0000
9:4567667:AGTA:A	acceptor_loss	1.0000
9:4567668:G:GA	acceptor_gain	1.0000
9:4567668:GT:G	acceptor_gain	1.0000
9:4567668:GTA:G	acceptor_gain	1.0000
9:4567668:GTAC:G	acceptor_gain	1.0000
9:4567668:GTACA:G	acceptor_gain	1.0000
9:4567763:CCAAG:C	donor_loss	1.0000
9:4567764:CAAG:C	donor_loss	1.0000
9:4567765:AAGGT:A	donor_loss	1.0000
9:4567766:AGG:A	donor_loss	1.0000
9:4567769:T:A	donor_loss	1.0000
9:4572188:T:A	acceptor_gain	1.0000
9:4572202:A:AG	acceptor_gain	1.0000
9:4572203:G:GG	acceptor_gain	1.0000
9:4572203:GAAC:G	acceptor_gain	1.0000
9:4572385:TGTGG:T	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000016391 (9:4645437 G>C), RS1000030863 (9:4645331 T>G), RS1000033834 (9:4615360 C>T), RS1000109346 (9:4605787 A>G), RS1000112166 (9:4661002 T>A,C,G), RS1000129259 (9:4593406 C>A,T), RS1000208088 (9:4656604 G>C), RS1000227505 (9:4649041 A>ATG,ATT), RS1000236796 (9:4611101 C>T), RS1000301582 (9:4624185 T>C,G), RS1000322863 (9:4622930 A>G), RS1000349223 (9:4652740 C>T), RS1000358582 (9:4648405 ATTATAAGTTC>A), RS1000436809 (9:4624390 T>C), RS1000441433 (9:4660851 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): trigonocephaly (MONDO:0000156)

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST004601_112	Red blood cell count	7.000000e-12
GCST006292_7	Response to antipsychotic treatment in schizophrenia	2.000000e-07
GCST90002395_50	Mean platelet volume	6.000000e-10
GCST90002398_248	Neutrophil count	7.000000e-10
GCST90002400_458	Plateletcrit	9.000000e-12
GCST90002403_599	Red blood cell count	5.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004305	erythrocyte count
EFO:0004833	neutrophil count
EFO:0007985	platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

7 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs301434	SLC1A1, SPATA6L	3	0.00	1	Selective serotonin reuptake inhibitors
rs301435	SLC1A1, SPATA6L	3	0.00	1	Selective serotonin reuptake inhibitors
rs2228622	SLC1A1, SPATA6L		0.00	0
rs3087879	SLC1A1, SPATA6L	3	3.50	1	Selective serotonin reuptake inhibitors
rs3780412	SLC1A1, SPATA6L		0.00	0
rs3780413	SLC1A1, SPATA6L		0.00	0
rs10815019	SLC1A1, SPATA6L		0.00	0

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Nickel	decreases expression	2
Valproic Acid	affects expression, increases expression	2
aristolochic acid I	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Estradiol	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Mercuric Chloride	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Testosterone	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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