SPATA31F3

Summary

SPATA31F3 (SPATA31 subfamily F member 3, HGNC:42673) is a protein-coding gene on chromosome 9p13.3, encoding Protein SPATA31F3 (A6NFA0).

Predicted to be located in membrane.

Source: NCBI Gene 100129969 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001309427

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:42673
Approved symbol	SPATA31F3
Name	SPATA31 subfamily F member 3
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187791
Ensembl biotype	protein_coding
Entrez	100129969

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000340783, ENST00000603592, ENST00000603640

RefSeq mRNA: 3 — MANE Select: NM_001309427 NM_001309426, NM_001309427, NM_001375894

CCDS: CCDS83358, CCDS83359

Canonical transcript exons

ENST00000340783 — 5 exons

Exon	Start	End
ENSE00001382614	34889066	34889632
ENSE00001383333	34893046	34893152
ENSE00003477011	34895039	34895084
ENSE00003582601	34895579	34895764
ENSE00003664467	34894441	34894501

Expression profiles

Bgee: expression breadth broad, 64 present calls, max score 92.23.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0131 / max 11.0594, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100550	0.0131	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	92.23	gold quality
right testis	UBERON:0004534	88.65	gold quality
left testis	UBERON:0004533	86.96	gold quality
testis	UBERON:0000473	84.22	gold quality
tibialis anterior	UBERON:0001385	80.14	silver quality
ileal mucosa	UBERON:0000331	75.59	silver quality
cardiac muscle of right atrium	UBERON:0003379	69.84	gold quality
left ventricle myocardium	UBERON:0006566	68.99	gold quality
kidney epithelium	UBERON:0004819	65.61	gold quality
deltoid	UBERON:0001476	65.58	gold quality
myocardium	UBERON:0002349	65.56	gold quality
epithelial cell of pancreas	CL:0000083	65.41	gold quality
adult organism	UBERON:0007023	63.13	gold quality
pancreatic ductal cell	CL:0002079	60.33	silver quality
quadriceps femoris	UBERON:0001377	56.50	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	55.55	gold quality
endothelial cell	CL:0000115	53.77	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
nasal cavity epithelium	UBERON:0005384	53.24	gold quality
vastus lateralis	UBERON:0001379	53.18	gold quality
oocyte	CL:0000023	52.89	gold quality
mucosa of sigmoid colon	UBERON:0004993	51.49	gold quality
cerebellar vermis	UBERON:0004720	51.06	gold quality
tendon of biceps brachii	UBERON:0008188	50.19	silver quality
colonic epithelium	UBERON:0000397	49.42	silver quality
colonic mucosa	UBERON:0000317	48.10	gold quality
skeletal muscle tissue	UBERON:0001134	47.50	gold quality
layer of synovial tissue	UBERON:0007616	45.45	gold quality
amniotic fluid	UBERON:0000173	45.40	gold quality
buccal mucosa cell	CL:0002336	45.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting SPATA31F3, 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-4531	99.99	69.70	3181
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-3678-3P	99.31	67.10	1432
HSA-MIR-3973	99.20	69.19	1990
HSA-MIR-8077	99.17	66.67	862
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-7851-3P	98.72	64.88	980
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-891A-3P	98.05	67.99	970
HSA-MIR-6765-3P	97.83	64.59	1165
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-3173-5P	97.35	65.82	1282
HSA-MIR-6799-3P	97.35	65.60	1302
HSA-MIR-3622A-3P	97.06	66.43	1000
HSA-MIR-3622B-3P	96.82	66.36	988
HSA-MIR-4740-5P	96.25	67.96	726
HSA-MIR-503-3P	92.89	66.09	537

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Spata31f3	ENSRNOG00000022751

Paralogs (13): SPATA31C2 (ENSG00000177910), SPATA31E1 (ENSG00000177992), SPATA31A6 (ENSG00000185775), SPATA31D3 (ENSG00000186788), SPATA31D4 (ENSG00000189357), SPATA31A1 (ENSG00000204849), SPATA31F1 (ENSG00000205108), SPATA31D1 (ENSG00000214929), SPATA31C1 (ENSG00000230246), (ENSG00000251545), SPATA31A3 (ENSG00000275969), SPATA31A7 (ENSG00000276040), SPATA31A5 (ENSG00000276581)

Protein

Protein identifiers

Protein SPATA31F3 — A6NFA0 (reviewed: A6NFA0)

Alternative names: Protein FAM205C

All UniProt accessions (3): A0A0U1RRG8, A0A0U1RRK5, A6NFA0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SPATA31 family.

RefSeq proteins (3): NP_001296355, NP_001296356, NP_001362823 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027970	SPATA31-like	Domain

Pfam: PF15371

UniProt features (5 total): chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NFA0-F1	49.90	0.01

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 152

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): chr9p13, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE14386_UNTREATED_VS_IFNA_TREATED_ACT_PBMC_MS_PATIENT_UP, GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_12H_UP, MIR7160_5P, MIR12131, MIR6842_3P, MIR1224_5P, GSE19772_CTRL_VS_HCMV_INF_MONOCYTES_DN, GSE21033_3H_VS_12H_POLYIC_STIM_DC_DN, GSE21033_3H_VS_24H_POLYIC_STIM_DC_UP, GSE21033_1H_VS_12H_POLYIC_STIM_DC_UP, GSE37532_TREG_VS_TCONV_CD4_TCELL_FROM_VISCERAL_ADIPOSE_TISSUE_UP, GSE37532_VISCERAL_ADIPOSE_TISSUE_VS_LN_DERIVED_TCONV_CD4_TCELL_DN, GSE37532_WT_VS_PPARG_KO_LN_TREG_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

2 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA31F3	CIT	O14578	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A096MK47, A0JNH1, A6H5Y1, A6NCI8, A6NFA0, A6NGG8, B2RQL2, D3Z1D3, D3ZMK9, E9Q286, E9Q309, M0RD54, O14513, P51816, Q01613, Q03172, Q05860, Q2M2Z5, Q32LN6, Q3MHH3, Q3UXL4, Q3V0A6, Q569L8, Q571I4, Q5DTX6, Q5FW52, Q5HYW2, Q5R9I1, Q5VT06, Q5VWP3, Q60988, Q66HG9, Q68DA7, Q6P1W5, Q6P9P0, Q6PAC4, Q6PG16, Q711Q0, Q7TP36, Q7TSA6

Diamond homologs: A6NFA0, C0HKD1, C0HKD2, C0HKD3, Q32LN6, Q642A3, Q6ZU69, Q80YD3, Q63HN1, Q6ZQQ2, P0C874, Q6ZUB0

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

797 predictions. Top by Δscore:

Variant	Effect	Δscore
9:34893149:CTGG:C	acceptor_gain	1.0000
9:34894437:TTAC:T	donor_loss	1.0000
9:34894439:A:AG	donor_loss	1.0000
9:34894498:CTAG:C	acceptor_gain	1.0000
9:34894500:AG:A	acceptor_gain	1.0000
9:34894502:C:CC	acceptor_gain	1.0000
9:34889633:CTT:C	acceptor_gain	0.9900
9:34889636:C:CC	acceptor_gain	0.9900
9:34893150:TGG:T	acceptor_gain	0.9900
9:34893153:C:CC	acceptor_gain	0.9900
9:34893154:T:C	acceptor_loss	0.9900
9:34894435:GATTA:G	donor_gain	0.9900
9:34894437:TTA:T	donor_gain	0.9900
9:34894438:TA:T	donor_gain	0.9900
9:34894496:TCCTA:T	acceptor_gain	0.9900
9:34894499:TAG:T	acceptor_gain	0.9900
9:34893151:GG:G	acceptor_gain	0.9800
9:34894436:ATTAC:A	donor_gain	0.9800
9:34894439:A:AC	donor_gain	0.9800
9:34894439:A:T	donor_gain	0.9800
9:34894440:C:CC	donor_gain	0.9800
9:34889634:TT:T	acceptor_gain	0.9700
9:34893040:TCTCA:T	donor_loss	0.9600
9:34893041:CTCAC:C	donor_loss	0.9600
9:34893042:TCA:T	donor_loss	0.9600
9:34893043:CACCT:C	donor_loss	0.9600
9:34893044:A:G	donor_loss	0.9600
9:34894493:TTCTC:T	acceptor_gain	0.9600
9:34894511:C:CT	acceptor_gain	0.9600
9:34889632:GCTTC:G	acceptor_gain	0.9500

AlphaMissense

1362 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:34893109:A:G	C99R	0.876
9:34895649:G:T	A25E	0.869
9:34893108:C:G	C99S	0.861
9:34893109:A:T	C99S	0.861
9:34893107:A:C	C99W	0.860
9:34893083:G:C	C107W	0.858
9:34895659:A:G	C22R	0.857
9:34893084:C:T	C107Y	0.850
9:34893085:A:G	C107R	0.833
9:34893145:A:G	W87R	0.833
9:34893145:A:T	W87R	0.833
9:34895667:C:T	G19E	0.832
9:34893094:A:G	C104R	0.817
9:34893108:C:T	C99Y	0.817
9:34894447:A:G	M82T	0.804
9:34893084:C:A	C107F	0.801
9:34893092:G:C	C104W	0.801
9:34893120:C:G	R95P	0.797
9:34893111:A:T	L98Q	0.792
9:34895705:A:C	F6L	0.792
9:34895705:A:T	F6L	0.792
9:34895707:A:G	F6L	0.792
9:34895668:C:G	G19R	0.781
9:34895668:C:T	G19R	0.781
9:34893143:C:A	W87C	0.778
9:34893143:C:G	W87C	0.778
9:34893084:C:G	C107S	0.773
9:34893085:A:T	C107S	0.773
9:34895652:A:T	I24N	0.759
9:34894459:A:G	L78P	0.748

dbSNP variants (sampled 300 via entrez): RS1000029920 (9:34895036 T>C,G), RS1000079999 (9:34889249 A>G), RS1001089294 (9:34893981 G>A), RS1001737675 (9:34893450 A>C), RS1001884607 (9:34893654 G>A), RS1002071305 (9:34891565 G>A), RS1003269010 (9:34896835 T>TA), RS1003791271 (9:34890062 G>C), RS1005297368 (9:34894883 C>A,T), RS1005512161 (9:34891749 C>A,T), RS1005638495 (9:34893829 G>C,T), RS1005648631 (9:34894119 A>G,T), RS1005972273 (9:34892206 C>A,G,T), RS1006940542 (9:34897644 A>G), RS1007525129 (9:34890555 C>T)

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)

Clinical trials (associated diseases)

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