SPANXN1

Summary

SPANXN1 (SPANX family member N1, HGNC:33174) is a protein-coding gene on chromosome Xq27.3, encoding Sperm protein associated with the nucleus on the X chromosome N1 (Q5VSR9).

This gene represents one of several duplicated family members that are located on chromosome X. This gene family encodes proteins that play a role in spermiogenesis. These proteins represent a specific subgroup of cancer/testis-associated antigens, and they may be candidates for tumor vaccines. This family member belongs to a subgroup of related genes that are present in all primates and rats and mice, and thus, it represents one of the ancestral family members.

Source: NCBI Gene 494118 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_001009614

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33174
Approved symbol	SPANXN1
Name	SPANX family member N1
Location	Xq27.3
Locus type	gene with protein product
Status	Approved
Aliases	SPANX-N1, CT11.6
Ensembl gene	ENSG00000203923
Ensembl biotype	protein_coding
OMIM	300664
Entrez	494118

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000370493

RefSeq mRNA: 1 — MANE Select: NM_001009614 NM_001009614

CCDS: CCDS35421

Canonical transcript exons

ENST00000370493 — 2 exons

Exon	Start	End
ENSE00001452857	145255671	145256208
ENSE00001842908	145247503	145247661

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 90.91.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0718 / max 6.9555, expressed in 51 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197897	0.0718	51

Top tissues by expression

124 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	90.91	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.31	gold quality
right testis	UBERON:0004534	60.60	gold quality
testis	UBERON:0000473	57.85	gold quality
left testis	UBERON:0004533	57.42	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
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.26	gold quality
liver	UBERON:0002107	28.37	gold quality
monocyte	CL:0000576	28.29	gold quality
leukocyte	CL:0000738	28.23	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
urinary bladder	UBERON:0001255	26.96	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
blood	UBERON:0000178	25.83	gold quality
placenta	UBERON:0001987	25.81	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)

25 targeting SPANXN1, 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-5193	100.00	67.26	1744
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-149-5P	99.25	67.16	1315
HSA-MIR-4699-5P	98.99	67.50	1210
HSA-MIR-1245B-5P	98.88	66.55	576
HSA-MIR-3142	98.88	66.09	529
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-11399	98.71	65.69	869
HSA-MIR-9903	98.47	66.70	748
HSA-MIR-8078	98.32	65.73	361
HSA-MIR-660-3P	98.14	66.04	1434
HSA-MIR-6893-3P	97.79	64.91	1238
HSA-MIR-5196-3P	97.57	65.98	979
HSA-MIR-370-3P	97.09	64.92	1221
HSA-MIR-4793-5P	96.88	65.90	872
HSA-MIR-1288-3P	96.86	66.95	536
HSA-MIR-4740-5P	96.25	67.96	726
HSA-MIR-4515	95.70	65.73	716
HSA-MIR-1269A	92.75	64.61	542
HSA-MIR-1269B	92.75	64.73	538

Cross-species orthologs

0 orthologs

Paralogs (4): SPANXN3 (ENSG00000189252), SPANXN4 (ENSG00000189326), SPANXN5 (ENSG00000204363), SPANXN2 (ENSG00000268988)

Protein

Protein identifiers

Sperm protein associated with the nucleus on the X chromosome N1 — Q5VSR9 (reviewed: Q5VSR9)

Alternative names: Nuclear-associated protein SPAN-Xn1, SPANX family member N1

All UniProt accessions (1): Q5VSR9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPAN-X family.

RefSeq proteins (1): NP_001009614* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010007	SPAN-X_fam	Family

Pfam: PF07458

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VSR9-F1	68.68	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): chrXq27, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MIR4531, MIR205_5P, MIR5193, MIR660_3P, MIR4793_5P, MIR5196_3P, MIR4515, FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP, FLORIO_HUMAN_NEOCORTEX

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

450 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPANXN1	EOLA2	Q96DE9	513
SPANXN1	CXorf51A	A0A1B0GTR3	507
SPANXN1	FTHL17	Q9BXU8	450
SPANXN1	CT55	Q8WUE5	447
SPANXN1	SSX7	Q7RTT5	419
SPANXN1	EOLA1	Q8TE69	417
SPANXN1	PPP1R2C	O14990	416
SPANXN1	C5orf22	Q49AR2	397
SPANXN1	SLITRK2	Q9H156	397
SPANXN1	SPATA25	Q9BR10	393
SPANXN1	C1orf174	Q8IYL3	390
SPANXN1	NUP35	Q8NFH5	387
SPANXN1	HSFX4	A0A1B0GTS1	379
SPANXN1	ATP5F1E	P56381	374
SPANXN1	NDUFAF2	Q8N183	370
SPANXN1	XAGE3	Q8WTP9	370

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A097SRV6, A0A0J1BDH3, O41801, P04605, P0C1K3, P0C766, P0CG34, P0CG35, P0DX04, P12692, P15633, P15835, P18758, P20065, P21113, P21117, P21752, P21753, P26351, P26352, P33248, P33735, P33736, P33737, P34338, P34493, P53768, P60743, P75605, Q12026, Q4UKT5, Q54CC7, Q55GR5, Q5MJ07, Q5MJ08, Q5VSR9, Q66H17, Q6I7R5, Q6SJ84, Q6SJ91

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

296 predictions. Top by Δscore:

Variant	Effect	Δscore
X:145255667:ACAG:A	acceptor_loss	0.9900
X:145255668:CAG:C	acceptor_loss	0.9900
X:145255669:A:AG	acceptor_gain	0.9900
X:145255669:AG:A	acceptor_loss	0.9900
X:145255670:G:GA	acceptor_loss	0.9900
X:145255670:G:GG	acceptor_gain	0.9900
X:145255670:GAT:G	acceptor_gain	0.9800
X:145247660:AGGT:A	donor_loss	0.9500
X:145247661:GGTA:G	donor_loss	0.9500
X:145247662:GT:G	donor_loss	0.9500
X:145247663:T:G	donor_loss	0.9500
X:145254376:G:C	acceptor_gain	0.9500
X:145255670:GATGC:G	acceptor_gain	0.9500
X:145255666:A:AG	acceptor_gain	0.9400
X:145255669:AGAT:A	acceptor_gain	0.9400
X:145255670:GATG:G	acceptor_gain	0.9400
X:145255667:A:G	acceptor_gain	0.9200
X:145255670:GA:G	acceptor_gain	0.9200
X:145247625:G:GT	donor_gain	0.9000
X:145247659:GAG:G	donor_gain	0.8800
X:145255657:T:TA	acceptor_gain	0.8800
X:145247969:A:T	donor_gain	0.8300
X:145247662:G:GG	donor_gain	0.8100
X:145254371:T:TA	acceptor_gain	0.8100
X:145255666:AACAG:A	acceptor_gain	0.7700
X:145255667:ACAGA:A	acceptor_gain	0.7700
X:145255665:TAACA:T	acceptor_gain	0.7600
X:145255668:CAGAT:C	acceptor_gain	0.7500
X:145255669:AGATG:A	acceptor_gain	0.7400
X:145254375:AGAGG:A	acceptor_gain	0.7200

AlphaMissense

479 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1002717106 (X:145256209 T>C,G), RS1006685943 (X:145246670 G>A), RS1009878570 (X:145256122 G>A), RS1036600131 (X:145246596 C>A,G), RS11094465 (X:145248541 C>A,G), RS111267976 (X:145251756 G>A,T), RS111387995 (X:145247996 G>A), RS111590533 (X:145251243 G>A), RS111798586 (X:145248919 A>G), RS111807226 (X:145255539 A>C), RS112007025 (X:145255497 T>C), RS112036181 (X:145247800 C>G), RS112268595 (X:145256403 A>G), RS112290576 (X:145249653 TG>T), RS112375266 (X:145252452 G>T)

Disease associations

OMIM: gene MIM:300664 | disease phenotypes: MIM:300815

GenCC curated gene-disease

Mondo (1): chromosome Xq28 duplication syndrome (MONDO:0010436)

Orphanet (1): Proximal Xq28 duplication syndrome (Orphanet:1762)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002642_6	Response to simvastatin treatment (PCSK9 protein level change)	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006899	PCSK9 protein measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C567580	Chromosome Xq28 Duplication Syndrome (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
2-methyl-4-isothiazolin-3-one	increases expression	1
sodium arsenite	increases expression	1
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Copper	affects binding, decreases expression	1
Disulfiram	affects binding, decreases expression	1
Thiram	increases expression	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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