SPATA31G1

Summary

SPATA31G1 (SPATA31 subfamily G member 1, HGNC:31418) is a protein-coding gene on chromosome 9p13.3, encoding Spermatogenesis-associated protein 31G1 (Q5VYM1). Dispensable for normal development and fertility.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 13 total
• MANE Select transcript: NM_203299

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31418
Approved symbol	SPATA31G1
Name	SPATA31 subfamily G member 1
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC41945
Ensembl gene	ENSG00000174038
Ensembl biotype	protein_coding
Entrez	138724

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 nonsense_mediated_decay

ENST00000312292, ENST00000354479, ENST00000378745, ENST00000416537, ENST00000421362, ENST00000534880, ENST00000537671

RefSeq mRNA: 5 — MANE Select: NM_203299 NM_001040410, NM_001040411, NM_001040412, NM_001287391, NM_203299

CCDS: CCDS47961, CCDS47962, CCDS6572

Canonical transcript exons

ENST00000312292 — 2 exons

Exon	Start	End
ENSE00002219787	35042240	35042485
ENSE00002241803	35042861	35045986

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 91.20.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0746 / max 69.4671, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96559	0.0746	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	91.20	gold quality
cardiac muscle of right atrium	UBERON:0003379	89.81	gold quality
left ventricle myocardium	UBERON:0006566	89.19	gold quality
left testis	UBERON:0004533	87.99	gold quality
right testis	UBERON:0004534	86.98	gold quality
testis	UBERON:0000473	85.63	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.26	gold quality
upper arm skin	UBERON:0004263	83.64	gold quality
vena cava	UBERON:0004087	82.73	gold quality
cerebellar vermis	UBERON:0004720	81.75	gold quality
myocardium	UBERON:0002349	80.52	gold quality
sperm	CL:0000019	80.03	silver quality
nasal cavity epithelium	UBERON:0005384	79.02	gold quality
epithelial cell of pancreas	CL:0000083	77.10	gold quality
cardia of stomach	UBERON:0001162	76.88	silver quality
adult organism	UBERON:0007023	75.39	gold quality
sural nerve	UBERON:0015488	75.14	gold quality
vastus lateralis	UBERON:0001379	75.01	gold quality
body of tongue	UBERON:0011876	74.96	gold quality
bone marrow cell	CL:0002092	74.95	gold quality
quadriceps femoris	UBERON:0001377	74.88	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	74.48	gold quality
pharyngeal mucosa	UBERON:0000355	73.90	gold quality
lateral nuclear group of thalamus	UBERON:0002736	73.81	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	73.22	gold quality
heart right ventricle	UBERON:0002080	73.20	gold quality
substantia nigra pars compacta	UBERON:0001965	72.30	gold quality
substantia nigra pars reticulata	UBERON:0001966	72.30	gold quality
trachea	UBERON:0003126	72.16	gold quality
pylorus	UBERON:0001166	71.87	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

1 targeting SPATA31G1, 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-11399	98.71	65.69	869

Literature-anchored findings (GeneRIF, showing 1)

• C9orf131 and C10orf120 are not essential for male fertility in humans or mice. (PMID:36871790)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata31g1	ENSMUSG00000028451
rattus_norvegicus	Spata31g1	ENSRNOG00000022601

Protein

Protein identifiers

Spermatogenesis-associated protein 31G1 — Q5VYM1 (reviewed: Q5VYM1)

All UniProt accessions (5): Q5VYM1, A0A1D5RMQ0, F5H224, F5H4E3, F8W7H5

UniProt curated annotations — full annotation on UniProt →

Function. Dispensable for normal development and fertility.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5VYM1-1	1	yes
Q5VYM1-2	2, D
Q5VYM1-3	3

RefSeq proteins (5): NP_001035500, NP_001035501, NP_001035502, NP_001274320, NP_976044* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026677	Spata31g1-like	Family

UniProt features (25 total): region of interest 8, compositionally biased region 7, sequence variant 6, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VYM1-F1	39.71	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): TGACCTY_ERR1_Q2, chr9p13, AR_03, SUPT16H_TARGET_GENES, BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_DN, GSE29614_CTRL_VS_TIV_FLU_VACCINE_PBMC_2007_UP, PR_02, GR_Q6, ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP, GSE25502_WT_VS_KLF13_KO_THYMIC_MEMORY_LIKE_CD8_TCELL_UP, GR_01

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

804 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31G1	REDIC1	Q86WS4	667
SPATA31G1	FAM209A	Q5JX71	647
SPATA31G1	C9orf43	Q8TAL5	646
SPATA31G1	TULP2	O00295	627
SPATA31G1	C20orf173	Q96LM9	608
SPATA31G1	SPATA16	Q9BXB7	598
SPATA31G1	MAGEB16	A2A368	595
SPATA31G1	TMCO5A	Q8N6Q1	584
SPATA31G1	ZFAND4	Q86XD8	561
SPATA31G1	PKDREJ	Q9NTG1	534
SPATA31G1	PLCZ1	Q86YW0	513
SPATA31G1	CABS1	Q96KC9	507
SPATA31G1	GARIN2	Q8N9W8	480
SPATA31G1	CXorf65	A6NEN9	479
SPATA31G1	CCDC187	A0A096LP49	476
SPATA31G1	CATSPER1	Q8NEC5	476

IntAct

3 interactions, top by confidence:

A	B	Type	Score
rpoH	SPATA31G1	psi-mi:“MI:0915”(physical association)	0.000
SPATA31G1	thiD2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): C9orf131 (Affinity Capture-MS), C9orf131 (Affinity Capture-MS), C9orf131 (Affinity Capture-MS), C9orf131 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTH6, A0A1B0GUW6, A0A1D5RMD1, A2AQH4, A4FU49, A6NJ88, C4P6S0, D3YU32, E9PAV3, F1QU13, I3L273, J3KML8, P70670, Q32L62, Q3V0E1, Q3V3Q4, Q4R729, Q5H9F3, Q5QJ38, Q5SWP3, Q5U4C1, Q5VWK0, Q5VYM1, Q68DN1, Q6AZ54, Q7TSG5, Q810T2, Q8CH19, Q8K4E0, Q8N3K9, Q8N5Q1, Q8NDH2, Q8TCU4, Q8WNU4, Q8WWL7, Q920R4, Q921B4, Q923B3, Q96JA4, Q96M34

Diamond homologs: Q3V0E1, Q5VYM1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

344 predictions. Top by Δscore:

Variant	Effect	Δscore
9:35042384:A:AG	donor_gain	0.9500
9:35042482:C:T	donor_gain	0.9400
9:35042855:TCCCA:T	acceptor_loss	0.9300
9:35042856:CCCA:C	acceptor_loss	0.9300
9:35042857:CCAG:C	acceptor_loss	0.9300
9:35042858:CAGGA:C	acceptor_loss	0.9300
9:35042859:A:AG	acceptor_gain	0.9300
9:35042860:G:GG	acceptor_gain	0.9300
9:35042374:A:T	donor_gain	0.9200
9:35042373:G:GT	donor_gain	0.9100
9:35042245:GC:G	donor_gain	0.9000
9:35042859:AG:A	acceptor_gain	0.8900
9:35042860:GG:G	acceptor_gain	0.8900
9:35042791:AGTG:A	donor_gain	0.8800
9:35042860:GGAA:G	acceptor_gain	0.8700
9:35042285:GC:G	donor_gain	0.8600
9:35042291:GGGGA:G	donor_gain	0.8600
9:35042385:C:G	donor_gain	0.8600
9:35042284:GGC:G	donor_gain	0.8500
9:35042475:TGC:T	donor_gain	0.8400
9:35042283:GGGC:G	donor_gain	0.8300
9:35042860:GGA:G	acceptor_gain	0.8100
9:35042860:GGAAC:G	acceptor_gain	0.8100
9:35042252:G:T	donor_gain	0.8000
9:35042804:AAAC:A	donor_loss	0.8000
9:35042805:AACC:A	donor_loss	0.8000
9:35042806:ACCTT:A	donor_loss	0.8000
9:35042807:C:G	donor_loss	0.8000
9:35042544:ATTG:A	donor_gain	0.7900
9:35042803:CAAA:C	donor_loss	0.7900

AlphaMissense

6979 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:35042366:A:C	S38R	0.930
9:35042368:T:A	S38R	0.930
9:35042368:T:G	S38R	0.930
9:35042396:T:C	F48L	0.914
9:35042398:C:A	F48L	0.914
9:35042398:C:G	F48L	0.914
9:35042888:T:C	F87L	0.896
9:35042890:C:A	F87L	0.896
9:35042890:C:G	F87L	0.896
9:35043215:T:C	F196L	0.889
9:35043217:C:A	F196L	0.889
9:35043217:C:G	F196L	0.889
9:35044976:T:A	W783R	0.884
9:35044976:T:C	W783R	0.884
9:35043137:T:C	F170L	0.870
9:35043139:C:A	F170L	0.870
9:35043139:C:G	F170L	0.870
9:35043128:T:C	F167L	0.867
9:35043130:C:A	F167L	0.867
9:35043130:C:G	F167L	0.867
9:35044978:G:C	W783C	0.854
9:35044978:G:T	W783C	0.854
9:35042405:T:A	W51R	0.848
9:35042405:T:C	W51R	0.848
9:35042409:A:C	Q52P	0.835
9:35042359:C:G	C35W	0.834
9:35042357:T:C	C35R	0.831
9:35044989:T:C	L787P	0.830
9:35042345:T:A	C31S	0.819
9:35042346:G:C	C31S	0.819

dbSNP variants (sampled 300 via entrez): RS1000865706 (9:35046385 C>T), RS1002776281 (9:35042002 T>C,G), RS1004398847 (9:35040828 T>C), RS1004451330 (9:35040501 A>C), RS1004710569 (9:35046031 A>G), RS1005885581 (9:35042014 G>A), RS1007878836 (9:35045406 T>C), RS1008745446 (9:35040091 C>G,T), RS1008820092 (9:35041551 G>A,C), RS1008939970 (9:35040028 A>C,G,T), RS1009117345 (9:35040331 T>C), RS1009531273 (9:35046172 T>C), RS1010562041 (9:35043415 T>A), RS1010891569 (9:35046315 C>A), RS1011170199 (9:35039944 T>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:167320, MIM:605726, MIM:613954, MIM:614373

GenCC curated gene-disease

Mondo (4): inclusion body myopathy with Paget disease of bone and frontotemporal dementia (MONDO:0000507), autosomal recessive distal spinal muscular atrophy 2 (MONDO:0011585), frontotemporal dementia and/or amyotrophic lateral sclerosis 6 (MONDO:0013501), amyotrophic lateral sclerosis type 16 (MONDO:0013715)

Orphanet (5): Distal hereditary motor neuropathy, Jerash type (Orphanet:139552), Frontotemporal dementia with motor neuron disease (Orphanet:275872), Juvenile amyotrophic lateral sclerosis (Orphanet:300605), Inclusion body myopathy with Paget disease of bone and frontotemporal dementia (Orphanet:52430), Amyotrophic lateral sclerosis (Orphanet:803)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006295_2	Response to quetiapine in schizophrenia	8.000000e-07
GCST90002393_374	Monocyte count	6.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005091	monocyte count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C535715	Spinal muscular atrophy, Jerash type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases mutagenesis, affects methylation	2
aristolochic acid I	increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
Folic Acid	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01353430	Not specified	RECRUITING	Characterization of Inclusion Body Myopathy Associated With Paget’s Disease of Bone and Frontotemporal Dementia (IBMPFD)
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT04823143	Not specified	COMPLETED	Natural History Study of Patients With VCP-related Disease