SPATA31D3

Summary

SPATA31D3 (SPATA31 subfamily D member 3, HGNC:38603) is a protein-coding gene on chromosome 9q21.32, encoding Spermatogenesis-associated protein 31D3 (P0C874). May play a role in spermatogenesis.

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

Source: NCBI Gene 389762 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• MANE Select transcript: NM_207416

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:38603
Approved symbol	SPATA31D3
Name	SPATA31 subfamily D member 3
Location	9q21.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ44082
Ensembl gene	ENSG00000186788
Ensembl biotype	protein_coding
Entrez	389762

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000445385

RefSeq mRNA: 1 — MANE Select: NM_207416 NM_207416

CCDS: CCDS83380

Canonical transcript exons

ENST00000445385 — 4 exons

Exon	Start	End
ENSE00002148406	81943500	81943771
ENSE00002148717	81945547	81950093
ENSE00002156829	81944528	81944573
ENSE00002182453	81945172	81945232

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 84.03.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.03	gold quality
right testis	UBERON:0004534	71.73	gold quality
left testis	UBERON:0004533	70.96	gold quality
testis	UBERON:0000473	70.50	gold quality
sural nerve	UBERON:0015488	39.59	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ganglionic eminence	UBERON:0004023	37.13	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
skeletal muscle tissue	UBERON:0001134	34.82	gold quality
mucosa of transverse colon	UBERON:0004991	33.74	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
muscle tissue	UBERON:0002385	32.12	gold quality
monocyte	CL:0000576	32.02	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
leukocyte	CL:0000738	31.62	gold quality
liver	UBERON:0002107	30.14	gold quality
tonsil	UBERON:0002372	29.88	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.49	gold quality
vermiform appendix	UBERON:0001154	29.16	gold quality
right uterine tube	UBERON:0001302	28.69	gold quality
duodenum	UBERON:0002114	28.14	gold quality
urinary bladder	UBERON:0001255	27.91	gold quality
lymph node	UBERON:0000029	27.57	gold quality
islet of Langerhans	UBERON:0000006	27.54	gold quality
blood	UBERON:0000178	27.36	gold quality
right lobe of liver	UBERON:0001114	27.18	gold quality
muscle of leg	UBERON:0001383	26.74	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

112 targeting SPATA31D3, 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-7110-3P	100.00	73.18	2486
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-6825-5P	99.96	69.81	3431
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-539-5P	99.93	70.30	2855
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-4319	99.76	69.83	2586

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31f3	ENSMUSG00000050141
rattus_norvegicus		ENSRNOG00000089661

Paralogs (13): SPATA31C2 (ENSG00000177910), SPATA31E1 (ENSG00000177992), SPATA31A6 (ENSG00000185775), 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 31D3 — P0C874 (reviewed: P0C874)

Alternative names: Protein FAM75D3

All UniProt accessions (1): P0C874

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_997299* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (11 total): compositionally biased region 4, region of interest 3, sequence conflict 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C874-F1	45.58	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr9q21, MIR6825_5P, MIR4319, MIR4303, MIR125B_5P, MIR125A_5P, MIR29A_5P, MIR877_3P, MIR629_5P, MIR6763_5P, MIR3605_5P, MIR3150A_3P, MIR7113_3P

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

238 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31D3	LRRC74A	Q0VAA2	664
SPATA31D3	OR4E2	Q8NGC2	448
SPATA31D3	THAP12	O43422	447
SPATA31D3	OR10Z1	Q8NGY1	447
SPATA31D3	VWA2	Q5GFL6	446
SPATA31D3	PCDHB6	Q9Y5E3	433
SPATA31D3	GLYCTK	Q8IVS8	419
SPATA31D3	OR6K6	Q8NGW6	404
SPATA31D3	OR5C1	Q8NGR4	403
SPATA31D3	KRTAP12-3	P60328	400
SPATA31D3	OR51I2	Q9H344	399
SPATA31D3	AKAP17A	Q02040	396
SPATA31D3	OR51I1	Q9H343	394
SPATA31D3	OR1I1	O60431	394
SPATA31D3	OR10G3	Q8NGC4	391

IntAct

2 interactions, top by confidence:

A	B	Type	Score
MICA	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): SPATA31D3 (Affinity Capture-MS), SPATA31D3 (Protein-peptide)

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, Q63HN1, Q6ZU69, Q642A3, A6NFA0, Q32LN6, Q80YD3

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

365 predictions. Top by Δscore:

Variant	Effect	Δscore
9:81945532:T:TA	acceptor_gain	1.0000
9:81943629:GGC:G	donor_gain	0.9800
9:81945147:T:G	acceptor_gain	0.9800
9:81945170:A:AG	acceptor_gain	0.9800
9:81945171:G:GG	acceptor_gain	0.9800
9:81945538:T:TA	acceptor_gain	0.9800
9:81945682:G:GT	donor_gain	0.9800
9:81945738:GGGC:G	donor_gain	0.9700
9:81945739:GGC:G	donor_gain	0.9700
9:81945740:GC:G	donor_gain	0.9700
9:81945741:C:G	donor_gain	0.9700
9:81945166:TTCCA:T	acceptor_loss	0.9600
9:81945167:TCCAG:T	acceptor_loss	0.9600
9:81945168:CCA:C	acceptor_loss	0.9600
9:81945169:CA:C	acceptor_loss	0.9600
9:81945170:A:AT	acceptor_loss	0.9600
9:81945171:G:GA	acceptor_loss	0.9600
9:81945539:G:A	acceptor_gain	0.9600
9:81945170:AGACC:A	acceptor_gain	0.9400
9:81945171:GACCG:G	acceptor_gain	0.9400
9:81943530:T:G	donor_gain	0.9200
9:81943683:G:GG	donor_gain	0.9200
9:81945162:T:TA	acceptor_gain	0.9200
9:81945171:GACC:G	acceptor_gain	0.9200
9:81943566:GCAGC:G	donor_gain	0.9100
9:81943682:A:AG	donor_gain	0.9100
9:81944526:A:AG	acceptor_gain	0.9100
9:81944527:G:GG	acceptor_gain	0.9100
9:81945228:AAAAG:A	donor_loss	0.9100
9:81945229:AAAGG:A	donor_loss	0.9100

AlphaMissense

5989 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:81946754:T:C	F501L	0.971
9:81946756:C:A	F501L	0.971
9:81946756:C:G	F501L	0.971
9:81947342:T:A	W697R	0.950
9:81947342:T:C	W697R	0.950
9:81946760:G:C	G503R	0.928
9:81947344:G:C	W697C	0.913
9:81947344:G:T	W697C	0.913
9:81947273:T:C	F674L	0.905
9:81947275:T:A	F674L	0.905
9:81947275:T:G	F674L	0.905
9:81946778:A:C	S509R	0.887
9:81946780:C:A	S509R	0.887
9:81946780:C:G	S509R	0.887
9:81945632:T:C	C127R	0.882
9:81946757:T:A	W502R	0.880
9:81946757:T:C	W502R	0.880
9:81945617:T:C	C122R	0.870
9:81947323:G:C	K690N	0.869
9:81947323:G:T	K690N	0.869
9:81946838:T:C	F529L	0.865
9:81946840:C:A	F529L	0.865
9:81946840:C:G	F529L	0.865
9:81946777:C:A	H508Q	0.862
9:81946777:C:G	H508Q	0.862
9:81947060:T:C	F603L	0.861
9:81947062:T:A	F603L	0.861
9:81947062:T:G	F603L	0.861
9:81945634:T:G	C127W	0.858
9:81947314:C:A	H687Q	0.857

dbSNP variants (sampled 300 via entrez): RS1000341889 (9:81950303 A>G), RS1000678337 (9:81949596 G>T), RS1003565473 (9:81948012 G>A), RS1008227229 (9:81949672 C>A,T), RS1008980376 (9:81948343 C>G), RS1009644334 (9:81950328 G>A,C), RS1011918986 (9:81949587 C>G), RS1012025276 (9:81949449 G>A,T), RS1014261016 (9:81950274 T>C), RS1014836635 (9:81950087 A>G), RS1016195302 (9:81945347 G>A), RS1016735292 (9:81950535 G>A), RS1017234038 (9:81948459 C>T), RS1018551203 (9:81949116 G>A,T), RS1019540748 (9:81949818 A>G)

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

1 associations (top):

Study	Trait	p-value
GCST004521_104	Autism spectrum disorder or schizophrenia	2.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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