SPEM3

Summary

SPEM3 (SPEM family member 3, HGNC:53651) is a protein-coding gene on chromosome 17p13.1, encoding Uncharacterized protein SPEM3 (A0A1B0GUW6).

Predicted to be involved in flagellated sperm motility and sperm individualization. Predicted to be located in membrane. Predicted to be active in cytoplasm.

Source: NCBI Gene 107983988 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001364708

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53651
Approved symbol	SPEM3
Name	SPEM family member 3
Location	17p13.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283439
Ensembl biotype	protein_coding
Entrez	107983988

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000636696, ENST00000651079

RefSeq mRNA: 2 — MANE Select: NM_001364708 NM_001364672, NM_001364708

CCDS: CCDS92248

Canonical transcript exons

ENST00000636696 — 3 exons

Exon	Start	End
ENSE00003797191	7428857	7429040
ENSE00003799709	7429368	7432820
ENSE00003800242	7429190	7429247

Expression profiles

Bgee: expression breadth broad, 22 present calls, max score 92.19.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0815 / max 82.9996, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159188	0.0677	3
159189	0.0137	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	92.19	gold quality
right testis	UBERON:0004534	92.08	gold quality
testis	UBERON:0000473	91.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.17	gold quality
sural nerve	UBERON:0015488	44.47	gold quality
bone marrow cell	CL:0002092	41.08	gold quality
colonic epithelium	UBERON:0000397	41.00	gold quality
skeletal muscle tissue	UBERON:0001134	39.43	gold quality
gastrocnemius	UBERON:0001388	37.41	gold quality
ganglionic eminence	UBERON:0004023	37.16	gold quality
muscle of leg	UBERON:0001383	36.62	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
muscle tissue	UBERON:0002385	35.51	gold quality
right coronary artery	UBERON:0001625	35.37	gold quality
bone marrow	UBERON:0002371	35.33	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.31	gold quality
mucosa of transverse colon	UBERON:0004991	33.80	gold quality
monocyte	CL:0000576	33.08	gold quality
tonsil	UBERON:0002372	32.98	gold quality
leukocyte	CL:0000738	32.59	gold quality
metanephros cortex	UBERON:0010533	32.21	gold quality
prefrontal cortex	UBERON:0000451	31.10	silver quality
urinary bladder	UBERON:0001255	30.45	gold quality
lymph node	UBERON:0000029	29.92	gold quality
blood	UBERON:0000178	29.91	gold quality
right hemisphere of cerebellum	UBERON:0014890	29.88	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
cortex of kidney	UBERON:0001225	29.83	gold quality
adrenal gland	UBERON:0002369	29.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.16

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spem3	ENSMUSG00000109737
rattus_norvegicus	Spem3	ENSRNOG00000069891

Protein

Protein identifiers

Uncharacterized protein SPEM3 — A0A1B0GUW6 (reviewed: A0A1B0GUW6)

All UniProt accessions (2): A0A1B0GUW6, A0A494C095

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (2): NP_001351601, NP_001351637* (*=MANE)

Domains & families (InterPro)

UniProt features (19 total): compositionally biased region 10, region of interest 7, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GUW6-F1	39.73	0.03

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MICROTUBULE_BASED_MOVEMENT, GOBP_SEXUAL_REPRODUCTION, GOBP_CELL_MOTILITY, GOBP_MICROTUBULE_BASED_PROCESS, GOBP_REPRODUCTIVE_PROCESS, GOBP_MULTICELLULAR_ORGANISMAL_REPRODUCTIVE_PROCESS, GOBP_SPERMATID_DIFFERENTIATION, GOBP_ANATOMICAL_STRUCTURE_FORMATION_INVOLVED_IN_MORPHOGENESIS, chr17p13

GO Biological Process (2): sperm individualization (GO:0007291), flagellated sperm motility (GO:0030317)

GO Molecular Function (0):

GO Cellular Component (2): cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
developmental process involved in reproduction	1
spermatid development	1
cellularization	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

236 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPEM3	SPEM2	Q0P670	625
SPEM3	SPATA31F1	Q6ZU69	583
SPEM3	GARIN3	Q8TC56	576
SPEM3	SPATA3	Q8NHX4	505
SPEM3	PROCA1	Q8NCQ7	487
SPEM3	NT5C1B	Q96P26	448
SPEM3	TMEM202	A6NGA9	445
SPEM3	CCDC136	Q96JN2	432
SPEM3	SUN5	Q8TC36	419
SPEM3	SPACA1	Q9HBV2	417
SPEM3	ODAD3	A5D8V7	415
SPEM3	ROPN1	Q9HAT0	393
SPEM3	FSIP2	Q5CZC0	378
SPEM3	DEPP1	Q9NTK1	368
SPEM3	ST6GALNAC2	Q9UJ37	366

IntAct

0 interactions, top by confidence:

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: A0A1B0GUW6, Q32LJ5, Q5F289, Q8N4L4, Q0P670, Q68FV4

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

0 predictions. Top by Δscore:

AlphaMissense

7789 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:7428999:A:C	S33R	0.969
17:7429001:C:A	S33R	0.969
17:7429001:C:G	S33R	0.969
17:7429006:T:A	I35N	0.945
17:7429016:C:A	N38K	0.942
17:7429016:C:G	N38K	0.942
17:7429006:T:C	I35T	0.932
17:7432445:T:C	F1092L	0.929
17:7432447:C:A	F1092L	0.929
17:7432447:C:G	F1092L	0.929
17:7429028:T:A	N42K	0.925
17:7429028:T:G	N42K	0.925
17:7428996:G:C	G32R	0.924
17:7429203:T:C	L51P	0.923
17:7429193:T:A	W48R	0.920
17:7429193:T:C	W48R	0.920
17:7429020:T:A	W40R	0.919
17:7429020:T:C	W40R	0.919
17:7428997:G:A	G32D	0.913
17:7428982:T:C	I27T	0.902
17:7429207:G:C	K52N	0.893
17:7429207:G:T	K52N	0.893
17:7429006:T:G	I35S	0.887
17:7429191:T:C	L47P	0.884
17:7429195:G:C	W48C	0.883
17:7429195:G:T	W48C	0.883
17:7428982:T:A	I27N	0.882
17:7429002:T:C	F34L	0.881
17:7429004:C:A	F34L	0.881
17:7429004:C:G	F34L	0.881

dbSNP variants (sampled 300 via entrez): RS1000353858 (17:7432198 G>A), RS1000553876 (17:7433163 C>T), RS1001349540 (17:7430454 CT>C), RS1001380373 (17:7430202 C>T), RS1002435431 (17:7430052 C>A,G), RS1002466485 (17:7429853 C>T), RS1003108036 (17:7432792 G>A,C), RS1003139330 (17:7432536 C>T), RS1003361594 (17:7427783 C>T), RS1003439028 (17:7431503 C>T), RS1003935329 (17:7428216 G>T), RS1004370704 (17:7428033 G>A), RS1004637530 (17:7432245 C>T), RS1005057405 (17:7432292 C>G), RS1006308209 (17:7429485 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

0 associations (top):

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
aristolochic acid I	increases expression	1

Clinical trials (associated diseases)

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