SPATA31A3

Summary

SPATA31A3 (SPATA31 subfamily A member 3, HGNC:32003) is a protein-coding gene on chromosome 9q21.11, encoding Spermatogenesis-associated protein 31A3 (Q5VYP0). May play a role in spermatogenesis.

Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in membrane.

Source: NCBI Gene 727830 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 254 total
• MANE Select transcript: NM_001083124

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32003
Approved symbol	SPATA31A3
Name	SPATA31 subfamily A member 3
Location	9q21.11
Locus type	gene with protein product
Status	Approved
Aliases	OTTHUMG00000013164, DKFZp434B204
Ensembl gene	ENSG00000275969
Ensembl biotype	protein_coding
Entrez	727830

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000428649

RefSeq mRNA: 1 — MANE Select: NM_001083124 NM_001083124

CCDS: CCDS78400

Canonical transcript exons

ENST00000428649 — 4 exons

Exon	Start	End
ENSE00001645381	66991074	66991131
ENSE00001709331	66986304	66990189
ENSE00003750472	66990445	66990505
ENSE00003978258	66992333	66992550

Expression profiles

Bgee: expression breadth tissue_specific, 5 present calls, max score 62.13.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	62.13	gold quality
left testis	UBERON:0004533	62.08	gold quality
testis	UBERON:0000473	61.81	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.95	gold quality
muscle tissue	UBERON:0002385	33.23	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	33.16	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
prefrontal cortex	UBERON:0000451	30.26	gold quality
primary visual cortex	UBERON:0002436	30.06	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
right uterine tube	UBERON:0001302	29.75	gold quality
liver	UBERON:0002107	29.69	gold quality
superior frontal gyrus	UBERON:0002661	29.35	gold quality
monocyte	CL:0000576	28.17	gold quality
duodenum	UBERON:0002114	28.14	gold quality
leukocyte	CL:0000738	28.11	gold quality
fallopian tube	UBERON:0003889	27.93	silver quality
blood	UBERON:0000178	27.86	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
uterine cervix	UBERON:0000002	26.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting SPATA31A3, 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-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

Literature-anchored findings (GeneRIF, showing 1)

• Novel biomarkers for primary biliary cholangitis to improve diagnosis and understand underlying regulatory mechanisms. (PMID:31033124)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31	ENSMUSG00000056223
rattus_norvegicus	Spata31	ENSRNOG00000018202

Paralogs (13): SPATA31C2 (ENSG00000177910), SPATA31E1 (ENSG00000177992), SPATA31A6 (ENSG00000185775), SPATA31D3 (ENSG00000186788), SPATA31F3 (ENSG00000187791), SPATA31D4 (ENSG00000189357), SPATA31A1 (ENSG00000204849), SPATA31F1 (ENSG00000205108), SPATA31D1 (ENSG00000214929), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Spermatogenesis-associated protein 31A3 — Q5VYP0 (reviewed: Q5VYP0)

Alternative names: Protein FAM75A3

All UniProt accessions (1): Q5VYP0

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_001076593* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (18 total): region of interest 8, compositionally biased region 7, chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VYP0-F1	38.73	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, chr9q21, 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

36 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31A3	CNTNAP3B	Q96NU0	621
SPATA31A3	DLAT	P10515	348
SPATA31A3	TDRD7	Q8NHU6	220
SPATA31A3	FOXE3	Q13461	203
SPATA31A3	ALDH1B1	P30837	202
SPATA31A3	CRYGS	P22914	201
SPATA31A3	FYCO1	Q9BQS8	182
SPATA31A3	TRPM6	Q9BX84	178
SPATA31A3	TRPV3	Q8NET8	164
SPATA31A3	TRPM3	Q9HCF6	164
SPATA31A3	PKD1	P98161	153
SPATA31A3	TRPM4	Q8TD43	152
SPATA31A3	MCOLN1	Q9GZU1	151
SPATA31A3	SPATA31A6	Q5VVP1	0
SPATA31A3	RELA	Q04206	0
SPATA31A3	PRAMEF11	O60813	0
SPATA31A3	PPP1R2C	O14990	0

IntAct

0 interactions, top by confidence:

BioGRID (2): SPATA31A3 (Affinity Capture-MS), SPATA31A3 (Negative Genetic)

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, C0HKD1, C0HKD2, C0HKD3, Q642A3, A6NFR6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	223
Likely benign	29
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

728 predictions. Top by Δscore:

Variant	Effect	Δscore
9:66991178:T:G	acceptor_gain	1.0000
9:66990504:G:GG	acceptor_gain	0.9900
9:66990504:GCTG:G	acceptor_gain	0.9900
9:66990505:A:AG	acceptor_gain	0.9900
9:66990505:AGCT:A	acceptor_gain	0.9900
9:66991147:C:G	acceptor_gain	0.9900
9:66991165:C:CA	acceptor_gain	0.9900
9:66991167:C:CA	acceptor_gain	0.9900
9:66991175:T:A	acceptor_gain	0.9900
9:66991179:A:AG	acceptor_gain	0.9900
9:66991179:ATCTT:A	acceptor_gain	0.9900
9:66991183:T:A	acceptor_gain	0.9900
9:66991184:T:G	acceptor_gain	0.9900
9:66991185:A:AG	acceptor_gain	0.9900
9:66992330:GTAAG:G	donor_loss	0.9900
9:66992331:GGTA:G	donor_loss	0.9900
9:66992332:AGGT:A	donor_loss	0.9900
9:66992333:AAGG:A	donor_loss	0.9900
9:66990445:GAG:G	donor_gain	0.9800
9:66990504:GCT:G	acceptor_gain	0.9800
9:66991149:G:C	acceptor_gain	0.9800
9:66991166:C:CT	acceptor_gain	0.9800
9:66991185:A:T	acceptor_gain	0.9800
9:66991185:ATT:A	acceptor_gain	0.9800
9:66992329:T:A	donor_loss	0.9800
9:66992335:GAAAG:G	donor_gain	0.9800
9:66989652:C:A	acceptor_gain	0.9700
9:66990441:T:G	donor_loss	0.9700
9:66990442:GTGAG:G	donor_loss	0.9700
9:66990443:GGT:G	donor_loss	0.9700

AlphaMissense

8802 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:66989250:G:C	F416L	0.959
9:66989250:G:T	F416L	0.959
9:66989252:A:G	F416L	0.959
9:66989157:G:C	F447L	0.925
9:66989157:G:T	F447L	0.925
9:66989159:A:G	F447L	0.925
9:66988125:G:C	F791L	0.911
9:66988125:G:T	F791L	0.911
9:66988127:A:G	F791L	0.911
9:66989246:C:G	G418R	0.896
9:66988061:A:G	W813R	0.876
9:66988061:A:T	W813R	0.876
9:66989249:A:G	W417R	0.870
9:66989249:A:T	W417R	0.870
9:66988791:A:C	F569L	0.856
9:66988791:A:T	F569L	0.856
9:66988793:A:G	F569L	0.856
9:66988059:C:A	W813C	0.849
9:66988059:C:G	W813C	0.849
9:66989229:G:C	H423Q	0.849
9:66989229:G:T	H423Q	0.849
9:66987459:A:C	F1013L	0.848
9:66987459:A:T	F1013L	0.848
9:66987461:A:G	F1013L	0.848
9:66989226:G:C	S424R	0.848
9:66989226:G:T	S424R	0.848
9:66989228:T:G	S424R	0.848
9:66989163:G:C	F445L	0.826
9:66989163:G:T	F445L	0.826
9:66989165:A:G	F445L	0.826

dbSNP variants (sampled 300 via entrez): RS1000516310 (9:66989957 G>A,C), RS1000547418 (9:66989625 G>A,C), RS1001391971 (9:66987473 C>A,T), RS1001424591 (9:66987028 G>A,C), RS1003401000 (9:66991830 G>A), RS1003433883 (9:66991242 C>G), RS1004777608 (9:66987895 C>A), RS1005214011 (9:66987503 C>G), RS1005784309 (9:66990345 C>A), RS1005816856 (9:66990196 G>A), RS1006899059 (9:66990862 C>T), RS1007874326 (9:66993964 T>G), RS1007905375 (9:66993626 T>C), RS1007936409 (9:66992899 G>A), RS1010188769 (9:66989665 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
Methapyrilene	increases methylation	1

Clinical trials (associated diseases)

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