SPANXN3

Summary

SPANXN3 (SPANX family member N3, HGNC:33176) is a protein-coding gene on chromosome Xq27.3, encoding Sperm protein associated with the nucleus on the X chromosome N3 (Q5MJ09).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 17 total
• MANE Select transcript: NM_001009609

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33176
Approved symbol	SPANXN3
Name	SPANX family member N3
Location	Xq27.3
Locus type	gene with protein product
Status	Approved
Aliases	SPANX-N3, CT11.8
Ensembl gene	ENSG00000189252
Ensembl biotype	protein_coding
OMIM	300666
Entrez	139067

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000370503

RefSeq mRNA: 1 — MANE Select: NM_001009609 NM_001009609

CCDS: CCDS35418

Canonical transcript exons

ENST00000370503 — 2 exons

Exon	Start	End
ENSE00001452872	143508735	143509162
ENSE00001452873	143517314	143517475

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 93.25.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0909 / max 29.7716, expressed in 25 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200752	0.0909	25

Top tissues by expression

97 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	93.25	gold quality
right testis	UBERON:0004534	92.56	gold quality
left testis	UBERON:0004533	92.55	gold quality
testis	UBERON:0000473	92.26	gold quality
duodenum	UBERON:0002114	59.48	gold quality
bone marrow cell	CL:0002092	38.57	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
ganglionic eminence	UBERON:0004023	35.49	gold quality
left adrenal gland	UBERON:0001234	34.34	silver quality
right uterine tube	UBERON:0001302	33.76	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
left adrenal gland cortex	UBERON:0035825	33.38	gold quality
bone marrow	UBERON:0002371	32.97	gold quality
adrenal gland	UBERON:0002369	32.28	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
metanephros cortex	UBERON:0010533	31.78	silver quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
muscle of leg	UBERON:0001383	30.90	gold quality
gastrocnemius	UBERON:0001388	30.81	gold quality
right coronary artery	UBERON:0001625	30.27	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.71	gold quality
right adrenal gland	UBERON:0001233	28.53	gold quality
cortex of kidney	UBERON:0001225	28.04	silver quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.65

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (4): SPANXN4 (ENSG00000189326), SPANXN1 (ENSG00000203923), SPANXN5 (ENSG00000204363), SPANXN2 (ENSG00000268988)

Protein

Protein identifiers

Sperm protein associated with the nucleus on the X chromosome N3 — Q5MJ09 (reviewed: Q5MJ09)

Alternative names: Nuclear-associated protein SPAN-Xn3, SPANX family member N3

All UniProt accessions (1): Q5MJ09

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPAN-X family.

RefSeq proteins (1): NP_001009609* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010007	SPAN-X_fam	Family

Pfam: PF07458

UniProt features (10 total): compositionally biased region 5, region of interest 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5MJ09-F1	64.36	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 4 (showing top): chrXq27, DACH1_TARGET_GENES, DESCARTES_FETAL_INTESTINE_INTESTINAL_EPITHELIAL_CELLS, GSE40666_UNTREATED_VS_IFNA_STIM_EFFECTOR_CD8_TCELL_90MIN_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

394 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPANXN3	PSG3	Q16557	598
SPANXN3	SPANXD	Q9BXN6	583
SPANXN3	EOLA2	Q96DE9	570
SPANXN3	CXorf51A	A0A1B0GTR3	545
SPANXN3	ADH4	P08319	526
SPANXN3	SSX7	Q7RTT5	447
SPANXN3	EOLA1	Q8TE69	446
SPANXN3	RIBC1	Q8N443	436
SPANXN3	HSFX4	A0A1B0GTS1	417
SPANXN3	PER2	O15055	413
SPANXN3	ENO4	A6NNW6	411
SPANXN3	XAGE3	Q8WTP9	398
SPANXN3	FMR1NB	Q8N0W7	398
SPANXN3	CYLC1	P35663	390
SPANXN3	TENT5D	Q8NEK8	390

IntAct

51 interactions, top by confidence:

A	B	Type	Score
SPANXN3	SUOX	psi-mi:“MI:0914”(association)	0.640
SPANXN3	STAC3	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	CEP70	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
SP4	SPANXN3	psi-mi:“MI:0915”(physical association)	0.560
ZNF143	SPANXN3	psi-mi:“MI:0915”(physical association)	0.560
SDCBP	SPANXN3	psi-mi:“MI:0915”(physical association)	0.560
ZNF76	SPANXN3	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	ATP6V1C2	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	AARSD1	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	PBX4	psi-mi:“MI:0915”(physical association)	0.560
HAND2	SPANXN3	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	FAM217B	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	CAVIN1	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	YAF2	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	RAD23A	psi-mi:“MI:0914”(association)	0.530
SPANXN3	SRPRA	psi-mi:“MI:0915”(physical association)	0.400
SPANXN3	OGA	psi-mi:“MI:0914”(association)	0.350
SPANXN3	STAC3	psi-mi:“MI:0915”(physical association)	0.000
SPANXN3	CEP70	psi-mi:“MI:0915”(physical association)	0.000
SPANXN3	MEOX2	psi-mi:“MI:0915”(physical association)	0.000
SPANXN3	SP4	psi-mi:“MI:0915”(physical association)	0.000
SPANXN3	CAVIN1	psi-mi:“MI:0915”(physical association)	0.000
SPANXN3	ZNF143	psi-mi:“MI:0915”(physical association)	0.000
SPANXN3	SDCBP	psi-mi:“MI:0915”(physical association)	0.000
ATP6V1C2	SPANXN3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (40): CMSS1 (Affinity Capture-MS), EHD1 (Affinity Capture-MS), IMPDH1 (Affinity Capture-MS), FBXW11 (Affinity Capture-MS), BTRC (Affinity Capture-MS), FBXW2 (Affinity Capture-MS), SUOX (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), FBXW2 (Affinity Capture-MS), BTRC (Affinity Capture-MS), FBXW11 (Affinity Capture-MS), SUOX (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CUL1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQG5, A1L429, A4FU49, A6NDE8, A6NER3, A6NGK3, O75459, O76087, P0C2W7, P0C2X8, P0C671, P0C7A2, P0CL80, P0CL81, P0CL82, P0DSO3, P0DTW1, P49919, Q0ZNK1, Q13066, Q13069, Q13070, Q28181, Q4V321, Q4V326, Q5H9L2, Q5MJ09, Q5SS00, Q5VWK0, Q6IPX3, Q6NT46, Q6P6B1, Q6PGQ1, Q6SJ82, Q70KF4, Q8CCT4, Q8IYN2, Q8N660, Q8NDB6, Q8R0A5

Diamond homologs: Q0ZNK1, Q5MJ07, Q5MJ08, Q5MJ09, Q5MJ10, Q5VSR9, Q6SJ82, Q6SJ84, Q6SJ91, Q9BXN6, Q9NS26, Q9NY87, Q9NS25

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

243 predictions. Top by Δscore:

Variant	Effect	Δscore
X:143517310:TTA:T	donor_loss	1.0000
X:143517311:TA:T	donor_loss	1.0000
X:143517312:ACCTC:A	donor_loss	1.0000
X:143517313:CCT:C	donor_gain	1.0000
X:143517312:A:AC	donor_gain	0.9900
X:143517313:C:CC	donor_gain	0.9900
X:143509163:C:CC	acceptor_gain	0.9800
X:143517312:ACCT:A	donor_gain	0.9700
X:143517313:CCTC:C	donor_gain	0.9700
X:143509160:CATCT:C	acceptor_loss	0.9600
X:143509161:ATCTG:A	acceptor_loss	0.9600
X:143509162:TC:T	acceptor_loss	0.9600
X:143509163:CT:C	acceptor_loss	0.9600
X:143509164:T:A	acceptor_loss	0.9600
X:143509160:CAT:C	acceptor_gain	0.9500
X:143517313:CCTCA:C	donor_gain	0.9400
X:143517315:T:TA	donor_gain	0.9000
X:143509166:G:C	acceptor_gain	0.8800
X:143517311:TAC:T	donor_gain	0.8800
X:143517310:TTACC:T	donor_gain	0.8600
X:143517309:CTTA:C	donor_gain	0.8300
X:143517312:AC:A	donor_gain	0.8300
X:143517313:CC:C	donor_gain	0.8300
X:143517312:A:T	donor_gain	0.8200
X:143509161:AT:A	acceptor_gain	0.8100
X:143517006:T:A	donor_gain	0.8000
X:143510545:CTCTT:C	acceptor_gain	0.7900
X:143509159:GCAT:G	acceptor_gain	0.7600
X:143509160:CATC:C	acceptor_gain	0.7600
X:143517308:TCTTA:T	donor_gain	0.7600

AlphaMissense

928 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS111381212 (X:143509214 A>C,G,T), RS111851873 (X:143517726 G>A,C), RS111865676 (X:143514265 T>A,C), RS111877285 (X:143517627 T>C), RS112319223 (X:143517675 G>C,T), RS112435034 (X:143515587 C>T), RS112442093 (X:143517609 C>A,T), RS112719440 (X:143517804 C>T), RS112726334 (X:143517714 C>T), RS112896911 (X:143518342 A>G,T), RS113043096 (X:143508927 C>G,T), RS113076693 (X:143517861 T>C), RS113133860 (X:143517677 T>C), RS113490027 (X:143517106 T>C), RS113758209 (X:143509210 T>C,G)

Disease associations

OMIM: gene MIM:300666 | 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
GCST006014_32	Creatine kinase levels	7.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004534	creatine kinase measurement

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
2-methyl-4-isothiazolin-3-one	increases expression	1
sodium arsenite	increases expression	1
Acetaminophen	increases expression	1
Calcitriol	increases expression	1
Citrulline	increases expression	1
Malathion	decreases expression	1
Thiram	increases expression	1
Vanadates	increases expression	1

Clinical trials (associated diseases)

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