SPATA31D4

Summary

SPATA31D4 (SPATA31 subfamily D member 4, HGNC:38601) is a protein-coding gene on chromosome 9q21.32, encoding Spermatogenesis-associated protein 31D4 (Q6ZUB0). May play a role in spermatogenesis.

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

Source: NCBI Gene 389761 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001145197

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:38601
Approved symbol	SPATA31D4
Name	SPATA31 subfamily D member 4
Location	9q21.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ43859
Ensembl gene	ENSG00000189357
Ensembl biotype	protein_coding
Entrez	389761

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000419782

RefSeq mRNA: 1 — MANE Select: NM_001145197 NM_001145197

CCDS: CCDS83379

Canonical transcript exons

ENST00000419782 — 4 exons

Exon	Start	End
ENSE00002140906	81930455	81934998
ENSE00002159531	81930100	81930160
ENSE00002159930	81928428	81928699
ENSE00002200833	81929456	81929501

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 77.70.

Top tissues by expression

132 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	77.70	gold quality
left testis	UBERON:0004533	65.85	gold quality
right testis	UBERON:0004534	65.60	gold quality
testis	UBERON:0000473	65.12	gold quality
sural nerve	UBERON:0015488	39.44	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
granulocyte	CL:0000094	33.98	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	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
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.49	gold quality
vermiform appendix	UBERON:0001154	29.17	gold quality
liver	UBERON:0002107	29.14	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
islet of Langerhans	UBERON:0000006	27.53	gold quality
leukocyte	CL:0000738	27.45	gold quality
tonsil	UBERON:0002372	27.05	gold quality
monocyte	CL:0000576	26.92	gold quality
blood	UBERON:0000178	26.67	gold quality
urinary bladder	UBERON:0001255	26.67	gold quality
right coronary artery	UBERON:0001625	26.22	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

101 targeting SPATA31D4, 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-5196-5P	100.00	67.98	2761
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3120-5P	100.00	65.56	965
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-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
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-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-5010-3P	99.83	70.60	2357
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31f3	ENSMUSG00000050141
rattus_norvegicus		ENSRNOG00000089661

Paralogs (13): SPATA31C2 (ENSG00000177910), SPATA31E1 (ENSG00000177992), SPATA31A6 (ENSG00000185775), SPATA31D3 (ENSG00000186788), SPATA31F3 (ENSG00000187791), SPATA31A1 (ENSG00000204849), SPATA31F1 (ENSG00000205108), SPATA31D1 (ENSG00000214929), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A3 (ENSG00000275969), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Spermatogenesis-associated protein 31D4 — Q6ZUB0 (reviewed: Q6ZUB0)

Alternative names: Protein FAM75D4

All UniProt accessions (1): Q6ZUB0

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_001138669* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (12 total): compositionally biased region 4, sequence conflict 3, region of interest 3, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZUB0-F1	45.57	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr9q21, MIR4319, MIR5010_3P, MIR4447, MIR5196_5P, MIR4747_5P, MIR4303, MIR125B_5P, MIR125A_5P, MIR29A_5P, MIR877_3P, MIR4472, MIR3605_5P

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

262 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31D4	LRRC74A	Q0VAA2	609
SPATA31D4	DDX10	Q13206	527
SPATA31D4	SPANXN5	Q5MJ07	507
SPATA31D4	TSPYL6	Q8N831	504
SPATA31D4	TMPRSS12	Q86WS5	473
SPATA31D4	XAGE3	Q8WTP9	448
SPATA31D4	RGSL1	A5PLK6	432
SPATA31D4	OR4E2	Q8NGC2	407
SPATA31D4	CT47A11	Q5JQC4	405
SPATA31D4	THAP12	O43422	400
SPATA31D4	OR10Z1	Q8NGY1	399
SPATA31D4	VWA2	Q5GFL6	397
SPATA31D4	PCDHB6	Q9Y5E3	379
SPATA31D4	ARMC3	Q5W041	377
SPATA31D4	SPATA19	Q7Z5L4	377

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SPATA31D4		psi-mi:“MI:0915”(physical association)	0.370

BioGRID (1): SPATA31D4 (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

362 predictions. Top by Δscore:

Variant	Effect	Δscore
9:81930440:T:TA	acceptor_gain	1.0000
9:81930098:A:AG	acceptor_gain	0.9900
9:81930099:G:GG	acceptor_gain	0.9900
9:81930446:T:TA	acceptor_gain	0.9900
9:81928695:AAAAG:A	donor_loss	0.9800
9:81928700:GT:G	donor_loss	0.9800
9:81928701:T:A	donor_loss	0.9800
9:81930075:T:G	acceptor_gain	0.9800
9:81930590:G:GT	donor_gain	0.9800
9:81930646:GGGC:G	donor_gain	0.9800
9:81928557:GGC:G	donor_gain	0.9700
9:81930094:TTCCA:T	acceptor_loss	0.9700
9:81930095:TCCA:T	acceptor_loss	0.9700
9:81930097:CA:C	acceptor_loss	0.9700
9:81930098:AG:A	acceptor_loss	0.9700
9:81930098:AGACC:A	acceptor_gain	0.9700
9:81930099:GACCG:G	acceptor_gain	0.9700
9:81930647:GGC:G	donor_gain	0.9700
9:81930648:GC:G	donor_gain	0.9700
9:81930649:C:G	donor_gain	0.9700
9:81930099:GACC:G	acceptor_gain	0.9600
9:81930447:G:A	acceptor_gain	0.9600
9:81928611:G:GG	donor_gain	0.9500
9:81930090:T:TA	acceptor_gain	0.9500
9:81928610:A:AG	donor_gain	0.9400
9:81930099:GA:G	acceptor_gain	0.9400
9:81930156:AAAAG:A	donor_loss	0.9400
9:81930157:AAAG:A	donor_loss	0.9400
9:81930158:AAGG:A	donor_loss	0.9400
9:81930159:AGGT:A	donor_loss	0.9400

AlphaMissense

5990 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:81931662:T:C	F501L	0.926
9:81931664:C:A	F501L	0.926
9:81931664:C:G	F501L	0.926
9:81932250:T:A	W697R	0.899
9:81932250:T:C	W697R	0.899
9:81932181:T:C	F674L	0.895
9:81932183:T:A	F674L	0.895
9:81932183:T:G	F674L	0.895
9:81932252:G:C	W697C	0.861
9:81932252:G:T	W697C	0.861
9:81931746:T:C	F529L	0.858
9:81931748:C:A	F529L	0.858
9:81931748:C:G	F529L	0.858
9:81932880:T:C	F907L	0.856
9:81932882:C:A	F907L	0.856
9:81932882:C:G	F907L	0.856
9:81932044:A:T	K628I	0.835
9:81930540:T:C	C127R	0.833
9:81932045:A:C	K628N	0.826
9:81932045:A:T	K628N	0.826
9:81932061:T:A	W634R	0.821
9:81932061:T:C	W634R	0.821
9:81930525:T:C	C122R	0.816
9:81930542:T:G	C127W	0.814
9:81932832:T:C	F891L	0.812
9:81932834:C:A	F891L	0.812
9:81932834:C:G	F891L	0.812
9:81930540:T:A	C127S	0.808
9:81930541:G:C	C127S	0.808
9:81931668:G:C	G503R	0.806

dbSNP variants (sampled 300 via entrez): RS1000212170 (9:81932469 C>G), RS1000647777 (9:81930524 A>G), RS1001628552 (9:81934697 G>A), RS1005215195 (9:81933116 G>C), RS1006438937 (9:81933857 C>T), RS1010345281 (9:81932553 T>C), RS1011241875 (9:81934937 C>T), RS1011357668 (9:81934735 G>A,T), RS1015192160 (9:81933866 C>A), RS1016311408 (9:81935031 G>A), RS1016649023 (9:81933129 ATCATCC>A), RS1019113490 (9:81932555 TGA>T), RS1019134817 (9:81932261 C>G,T), RS1020114789 (9:81934742 A>G), RS1020145977 (9:81934250 T>C)

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

3 associations (top):

Study	Trait	p-value
GCST004521_104	Autism spectrum disorder or schizophrenia	2.000000e-08
GCST006106_5	Forehead morphology	7.000000e-06
GCST008180_13	Spontaneous preterm birth with premature rupture of membranes	6.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006917	spontaneous preterm birth

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases methylation	1

Clinical trials (associated diseases)

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