SPATA31A1

Summary

SPATA31A1 (SPATA31 subfamily A member 1, HGNC:23394) is a protein-coding gene on chromosome 9p12, encoding Spermatogenesis-associated protein 31A1 (Q5TZJ5). May play a role in spermatogenesis.

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

Source: NCBI Gene 647060 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 158 total
• MANE Select transcript: NM_001085452

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23394
Approved symbol	SPATA31A1
Name	SPATA31 subfamily A member 1
Location	9p12
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP434B204, C9orf36A
Ensembl gene	ENSG00000204849
Ensembl biotype	protein_coding
OMIM	621335
Entrez	647060

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000377647, ENST00000473440

RefSeq mRNA: 1 — MANE Select: NM_001085452 NM_001085452

CCDS: CCDS43808

Canonical transcript exons

ENST00000377647 — 4 exons

Exon	Start	End
ENSE00001669893	39357132	39357189
ENSE00001674055	39355669	39355919
ENSE00001869390	39358074	39361962
ENSE00003658890	39357758	39357818

Expression profiles

Bgee: expression breadth tissue_specific, 10 present calls, max score 71.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	71.20	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	70.88	gold quality
right testis	UBERON:0004534	70.88	gold quality
testis	UBERON:0000473	70.52	gold quality
cortical plate	UBERON:0005343	39.93	gold quality
sural nerve	UBERON:0015488	39.45	gold quality
bone marrow cell	CL:0002092	38.01	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
skeletal muscle tissue	UBERON:0001134	36.36	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	35.34	silver quality
muscle tissue	UBERON:0002385	33.25	gold quality
bone marrow	UBERON:0002371	32.69	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
urinary bladder	UBERON:0001255	30.85	silver quality
liver	UBERON:0002107	30.10	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.65	gold quality
monocyte	CL:0000576	29.46	gold quality
blood	UBERON:0000178	29.42	silver quality
leukocyte	CL:0000738	29.30	gold quality
lymph node	UBERON:0000029	28.73	gold quality
duodenum	UBERON:0002114	28.14	gold quality
right lobe of liver	UBERON:0001114	27.08	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
endocervix	UBERON:0000458	26.08	gold quality
gall bladder	UBERON:0002110	25.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting SPATA31A1, 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-519A-2-5P	98.78	71.74	1401
HSA-MIR-520B-5P	98.78	71.74	1401
HSA-MIR-4536-5P	98.47	64.39	657
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-5586-3P	95.51	67.00	805

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), SPATA31F1 (ENSG00000205108), SPATA31D1 (ENSG00000214929), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A3 (ENSG00000275969), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Spermatogenesis-associated protein 31A1 — Q5TZJ5 (reviewed: Q5TZJ5)

Alternative names: Protein FAM75A1

All UniProt accessions (1): Q5TZJ5

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_001078921* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain
IPR039509	SPATA31	Domain

Pfam: PF14650, PF15371

UniProt features (19 total): compositionally biased region 7, region of interest 6, sequence conflict 4, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TZJ5-F1	38.42	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr9p12, BRCA1_DN.V1_DN, MIR548D_3P, MIR548H_3P_MIR548Z, MIR548BB_3P, MIR548AC, MIR519A_2_5P_MIR520B_5P, MIR4684_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

120 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31A1	LRRC63	Q05C16	597
SPATA31A1	ANKRD60	Q9BZ19	571
SPATA31A1	CCDC74B	Q96LY2	541
SPATA31A1	FAM47C	Q5HY64	507
SPATA31A1	C12orf42	Q96LP6	506
SPATA31A1	TTLL8	A6PVC2	480
SPATA31A1	A6NGT6	A6NGT6	477
SPATA31A1	RBMY1J	Q15415	475
SPATA31A1	BAIAP2L2	Q6UXY1	374
SPATA31A1	CNTNAP3	Q9BZ76	371
SPATA31A1	INPP5F	Q9Y2H2	370
SPATA31A1	KRT78	Q8N1N4	350
SPATA31A1	KRT79	Q5XKE5	348
SPATA31A1	CTU1	Q7Z7A3	336
SPATA31A1	WDPCP	O95876	317

IntAct

0 interactions, top by confidence:

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	132
Likely benign	25
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1124 predictions. Top by Δscore:

Variant	Effect	Δscore
9:39357081:A:C	acceptor_gain	1.0000
9:39357083:T:G	acceptor_gain	1.0000
9:39357086:T:A	acceptor_gain	1.0000
9:39357076:A:AG	acceptor_gain	0.9900
9:39357076:A:T	acceptor_gain	0.9900
9:39357077:C:CT	acceptor_gain	0.9900
9:39357077:T:G	acceptor_gain	0.9900
9:39357078:T:A	acceptor_gain	0.9900
9:39357082:A:AG	acceptor_gain	0.9900
9:39357082:ATCTT:A	acceptor_gain	0.9900
9:39357084:A:T	acceptor_gain	0.9900
9:39357093:C:CT	acceptor_gain	0.9900
9:39357094:C:CA	acceptor_gain	0.9900
9:39357095:C:CT	acceptor_gain	0.9900
9:39357096:C:CA	acceptor_gain	0.9900
9:39357112:G:C	acceptor_gain	0.9900
9:39357114:C:G	acceptor_gain	0.9900
9:39357755:C:CC	acceptor_gain	0.9900
9:39357756:A:AG	acceptor_gain	0.9900
9:39357757:G:GG	acceptor_gain	0.9900
9:39355918:C:G	donor_loss	0.9800
9:39355918:CCTTT:C	donor_gain	0.9800
9:39355919:ACCTT:A	donor_loss	0.9800
9:39355920:TA:T	donor_loss	0.9800
9:39355921:TTACC:T	donor_loss	0.9800
9:39355922:CTTAC:C	donor_loss	0.9800
9:39355923:CCTTA:C	donor_loss	0.9800
9:39357075:A:AC	acceptor_gain	0.9800
9:39357075:A:C	acceptor_gain	0.9800
9:39357076:ATT:A	acceptor_gain	0.9800

AlphaMissense

8805 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:39359011:T:C	F416L	0.975
9:39359013:C:A	F416L	0.975
9:39359013:C:G	F416L	0.975
9:39359039:A:T	E425V	0.933
9:39359017:G:C	G418R	0.931
9:39359104:T:C	F447L	0.914
9:39359106:C:A	F447L	0.914
9:39359106:C:G	F447L	0.914
9:39359040:G:C	E425D	0.912
9:39359040:G:T	E425D	0.912
9:39359041:T:C	S426P	0.897
9:39359014:T:A	W417R	0.892
9:39359014:T:C	W417R	0.892
9:39360136:T:C	F791L	0.890
9:39360138:C:A	F791L	0.890
9:39360138:C:G	F791L	0.890
9:39360202:T:A	W813R	0.878
9:39360202:T:C	W813R	0.878
9:39359035:A:C	S424R	0.861
9:39359037:C:A	S424R	0.861
9:39359037:C:G	S424R	0.861
9:39360204:G:C	W813C	0.854
9:39360204:G:T	W813C	0.854
9:39359039:A:G	E425G	0.849
9:39359012:T:C	F416S	0.848
9:39359034:C:A	H423Q	0.840
9:39359034:C:G	H423Q	0.840
9:39359017:G:T	G418C	0.835
9:39359039:A:C	E425A	0.827
9:39359470:T:C	F569L	0.822

dbSNP variants (sampled 300 via entrez): RS1001159299 (9:39361363 T>C,G), RS1001507197 (9:39361110 G>A), RS1002223515 (9:39359187 T>C), RS1003280555 (9:39355379 C>T), RS1004672962 (9:39361994 G>A,C,T), RS1005516442 (9:39358747 G>A,T), RS1006089296 (9:39357628 G>A,T), RS1007460772 (9:39355529 T>A,C), RS1007517291 (9:39356702 C>T), RS1010169108 (9:39361355 C>G), RS1010755315 (9:39356455 G>A,C), RS10125162 (9:39358957 C>T), RS1016130585 (9:39361676 G>A), RS1016391066 (9:39362012 A>G), RS1017446429 (9:39359075 C>A,T)

Disease associations

OMIM: gene MIM:621335 | 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
GCST007637_13	Diffusing capacity of carbon monoxide	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009369	diffusing capacity of the lung for carbon monoxide

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
Valproic Acid	increases expression	1

Clinical trials (associated diseases)

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