SPATA31A6

Summary

SPATA31A6 (SPATA31 subfamily A member 6, HGNC:32006) is a protein-coding gene on chromosome 9p11.2, encoding Spermatogenesis-associated protein 31A6 (Q5VVP1). May play a role in spermatogenesis. It is a selective cancer dependency (DepMap: 26.1% of cell lines).

Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle.

Source: NCBI Gene 389730 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 378 total
• Cancer dependency (DepMap): dependent in 26.1% of screened cell lines
• MANE Select transcript: NM_001145196

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32006
Approved symbol	SPATA31A6
Name	SPATA31 subfamily A member 6
Location	9p11.2
Locus type	gene with protein product
Status	Approved
Aliases	OTTHUMG00000013224
Ensembl gene	ENSG00000185775
Ensembl biotype	protein_coding
Entrez	389730

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000332857, ENST00000496386

RefSeq mRNA: 1 — MANE Select: NM_001145196 NM_001145196

CCDS: CCDS75837

Canonical transcript exons

ENST00000332857 — 4 exons

Exon	Start	End
ENSE00001665791	42183659	42183876
ENSE00001742463	42185069	42185126
ENSE00001810627	42186011	42189887
ENSE00003470782	42185695	42185755

Expression profiles

Bgee: expression breadth tissue_specific, 10 present calls, max score 49.34.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	49.34	gold quality
testis	UBERON:0000473	48.17	gold quality
right testis	UBERON:0004534	44.81	gold quality
lower esophagus mucosa	UBERON:0035834	43.30	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
sural nerve	UBERON:0015488	35.03	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
prefrontal cortex	UBERON:0000451	32.61	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
Ammon’s horn	UBERON:0001954	30.79	silver quality
urinary bladder	UBERON:0001255	30.12	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
liver	UBERON:0002107	29.47	gold quality
monocyte	CL:0000576	29.35	gold quality
blood	UBERON:0000178	29.25	gold quality
leukocyte	CL:0000738	29.19	gold quality
right uterine tube	UBERON:0001302	28.42	gold quality
ectocervix	UBERON:0012249	28.24	gold quality
frontal cortex	UBERON:0001870	28.21	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
placenta	UBERON:0001987	27.46	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	27.30	gold quality
Brodmann (1909) area 9	UBERON:0013540	27.17	gold quality
tonsil	UBERON:0002372	27.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting SPATA31A6, 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-5011-5P	100.00	83.46	5820
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-519A-2-5P	98.78	71.74	1401
HSA-MIR-520B-5P	98.78	71.74	1401
HSA-MIR-4752	98.71	68.04	833
HSA-MIR-4684-5P	98.29	67.99	1650
HSA-MIR-6810-5P	98.29	66.21	975
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-376C-3P	97.63	68.88	1263
HSA-MIR-3190-3P	97.61	66.95	1406
HSA-MIR-5586-3P	95.51	67.00	805

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 26.1% of screened cell lines.

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31	ENSMUSG00000056223
rattus_norvegicus	Spata31	ENSRNOG00000018202

Paralogs (13): SPATA31C2 (ENSG00000177910), SPATA31E1 (ENSG00000177992), SPATA31D3 (ENSG00000186788), SPATA31F3 (ENSG00000187791), SPATA31D4 (ENSG00000189357), SPATA31A1 (ENSG00000204849), SPATA31F1 (ENSG00000205108), SPATA31D1 (ENSG00000214929), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A3 (ENSG00000275969), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Spermatogenesis-associated protein 31A6 — Q5VVP1 (reviewed: Q5VVP1)

Alternative names: Protein FAM75A6

All UniProt accessions (1): Q5VVP1

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in spermatogenesis.

Subcellular location. Membrane.

Similarity. Belongs to the SPATA31 family.

RefSeq proteins (1): NP_001138668* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (15 total): compositionally biased region 7, region of interest 6, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VVP1-F1	39.06	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): GOBP_MALE_GAMETE_GENERATION, chr9p11, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, MIR548D_3P, MIR548H_3P_MIR548Z, MIR548BB_3P, MIR548AC, MIR519A_2_5P_MIR520B_5P, MIR4684_5P, MIR6833_5P, MIR5586_3P, GOBP_SEXUAL_REPRODUCTION, GOBP_REPRODUCTIVE_PROCESS, GOBP_MULTICELLULAR_ORGANISMAL_REPRODUCTIVE_PROCESS

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

GO Molecular Function (0):

GO Cellular Component (1): 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
cellular developmental process	1
cellular anatomical structure	1

Protein interactions and networks

STRING

90 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31A6	SMKR1	H3BMG3	608
SPATA31A6	ANKRD20A4P	Q4UJ75	601
SPATA31A6	ZNF705G	A8MUZ8	599
SPATA31A6	DCAF8L2	P0C7V8	544
SPATA31A6	KLRG2	A4D1S0	474
SPATA31A6	SPNS3	Q6ZMD2	457
SPATA31A6	TOP6BL	Q8N6T0	436
SPATA31A6	WSCD2	Q2TBF2	435
SPATA31A6	PPP4R3C	Q6ZMV5	417
SPATA31A6	ATP13A4	Q4VNC1	379
SPATA31A6	DMXL1	Q9Y485	374
SPATA31A6	RAX2	Q96IS3	357
SPATA31A6	ASIC4	Q96FT7	348
SPATA31A6	PPP4R3B	Q5MIZ7	324
SPATA31A6	PPP4R3A	Q6IN85	324

IntAct

0 interactions, top by confidence:

BioGRID (2): SPATA31A6 (Affinity Capture-MS), SPATA31A6 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A096LP49, A6NGG8, A6NNH2, B1ASB6, B4DYI2, B6VQA5, C0HKD1, C0HKD2, C0HKD3, D2J0Y4, D6RGX4, E9QAF0, P0C874, P0DKV0, Q149B8, Q3KR64, Q4R736, Q4V8B5, Q5TZJ5, Q5VU36, Q5VVP1, Q5VWK0, Q5VYM1, Q5VYP0, Q63HN1, Q658T7, Q68A65, Q6NS69, Q6NXZ1, Q6PAC4, Q6ZQQ2, Q6ZU69, Q6ZUB0, Q6ZUB1, Q7TSA6, Q80X53, Q86Y26, Q8BHP2, Q8BHW6, Q8C0D9

Diamond homologs: B4DYI2, B6VQA5, E9QAF0, P0C874, P0DKV0, Q5TZJ5, Q5VU36, Q5VVP1, Q5VYP0, Q6ZQQ2, Q6ZUB0, Q6ZUB1, Q8IWB4, A6NFR6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	331
Likely benign	45
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

634 predictions. Top by Δscore:

Variant	Effect	Δscore
9:42185018:A:C	acceptor_gain	1.0000
9:42183875:C:CA	donor_loss	0.9900
9:42183875:CCTTT:C	donor_gain	0.9900
9:42183877:TAC:T	donor_loss	0.9900
9:42183878:TTACC:T	donor_loss	0.9900
9:42183879:CTTA:C	donor_loss	0.9900
9:42183880:CCTTA:C	donor_loss	0.9900
9:42185012:A:AC	acceptor_gain	0.9900
9:42185012:A:C	acceptor_gain	0.9900
9:42185013:A:T	acceptor_gain	0.9900
9:42185014:C:CT	acceptor_gain	0.9900
9:42185018:A:AC	acceptor_gain	0.9900
9:42185021:A:T	acceptor_gain	0.9900
9:42185022:C:CT	acceptor_gain	0.9900
9:42185030:C:CT	acceptor_gain	0.9900
9:42185032:C:CT	acceptor_gain	0.9900
9:42185049:G:C	acceptor_gain	0.9900
9:42185692:C:CC	acceptor_gain	0.9900
9:42185695:CAGC:C	acceptor_gain	0.9900
9:42185696:CCAG:C	acceptor_gain	0.9900
9:42185754:CCT:C	donor_gain	0.9900
9:42183875:C:CC	donor_gain	0.9800
9:42183876:A:AC	donor_gain	0.9800
9:42185695:CAG:C	acceptor_gain	0.9800
9:42185756:CACC:C	donor_loss	0.9800
9:42185757:TCA:T	donor_loss	0.9800
9:42185758:CTCA:C	donor_loss	0.9800
9:42185759:CCTCA:C	donor_loss	0.9800
9:42185029:G:T	acceptor_gain	0.9700
9:42185046:C:CT	acceptor_gain	0.9700

AlphaMissense

8782 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:42186948:T:C	F416L	0.963
9:42186950:C:A	F416L	0.963
9:42186950:C:G	F416L	0.963
9:42187041:T:C	F447L	0.956
9:42187043:C:A	F447L	0.956
9:42187043:C:G	F447L	0.956
9:42188061:T:C	F787L	0.898
9:42188063:C:A	F787L	0.898
9:42188063:C:G	F787L	0.898
9:42186954:G:C	G418R	0.884
9:42186951:T:A	W417R	0.878
9:42186951:T:C	W417R	0.878
9:42186972:A:C	S424R	0.867
9:42186974:C:A	S424R	0.867
9:42186974:C:G	S424R	0.867
9:42188127:T:A	W809R	0.866
9:42188127:T:C	W809R	0.866
9:42187035:T:C	F445L	0.855
9:42187037:C:A	F445L	0.855
9:42187037:C:G	F445L	0.855
9:42188129:G:C	W809C	0.844
9:42188129:G:T	W809C	0.844
9:42187671:T:C	F657L	0.831
9:42187673:C:A	F657L	0.831
9:42187673:C:G	F657L	0.831
9:42188727:T:C	F1009L	0.828
9:42188729:T:A	F1009L	0.828
9:42188729:T:G	F1009L	0.828
9:42187042:T:C	F447S	0.820
9:42187395:T:C	F565L	0.815

dbSNP variants (sampled 300 via entrez): RS1000170473 (9:42184385 G>A), RS1000234187 (9:42183527 T>TC), RS1001714171 (9:42184949 G>A,C,T), RS1002080020 (9:42185383 C>T), RS1002679511 (9:42188309 G>A), RS1003724059 (9:42190278 C>T), RS1004041879 (9:42182327 C>A,G), RS1005045846 (9:42186124 C>T), RS1005245360 (9:42185474 A>G,T), RS1006256644 (9:42188453 G>A), RS1006530051 (9:42187326 C>T), RS1007561637 (9:42189358 T>C), RS1009932892 (9:42182829 C>A), RS1010144818 (9:42187351 G>A,C,T), RS1011148320 (9:42190238 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Copper	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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