SPANXN2

Summary

SPANXN2 (SPANX family member N2, HGNC:33175) is a protein-coding gene on chromosome Xq27.3, encoding Sperm protein associated with the nucleus on the X chromosome N2 (Q5MJ10).

At a glance

• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_001009615

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33175
Approved symbol	SPANXN2
Name	SPANX family member N2
Location	Xq27.3
Locus type	gene with protein product
Status	Approved
Aliases	SPANX-N2, CT11.7
Ensembl gene	ENSG00000268988
Ensembl biotype	protein_coding
OMIM	300665
Entrez	494119

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000598475

RefSeq mRNA: 1 — MANE Select: NM_001009615 NM_001009615

CCDS: CCDS35419

Canonical transcript exons

ENST00000598475 — 2 exons

Exon	Start	End
ENSE00003215181	143711955	143712499
ENSE00003978308	143720591	143720752

Expression profiles

Bgee: expression breadth tissue_specific, 10 present calls, max score 81.72.

Top tissues by expression

125 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	81.72	gold quality
testis	UBERON:0000473	60.69	gold quality
left testis	UBERON:0004533	60.65	gold quality
right testis	UBERON:0004534	58.67	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	52.28	gold quality
lower esophagus mucosa	UBERON:0035834	38.45	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
granulocyte	CL:0000094	36.18	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	35.76	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.92	gold quality
muscle tissue	UBERON:0002385	32.19	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
lymph node	UBERON:0000029	30.21	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
liver	UBERON:0002107	29.61	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
leukocyte	CL:0000738	28.51	gold quality
duodenum	UBERON:0002114	28.14	gold quality
monocyte	CL:0000576	28.00	gold quality
substantia nigra	UBERON:0002038	27.97	silver quality
placenta	UBERON:0001987	27.62	gold quality
right coronary artery	UBERON:0001625	27.18	gold quality
tonsil	UBERON:0002372	27.05	gold quality
superior frontal gyrus	UBERON:0002661	26.97	gold quality
blood	UBERON:0000178	26.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.14

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (4): SPANXN3 (ENSG00000189252), SPANXN4 (ENSG00000189326), SPANXN1 (ENSG00000203923), SPANXN5 (ENSG00000204363)

Protein

Protein identifiers

Sperm protein associated with the nucleus on the X chromosome N2 — Q5MJ10 (reviewed: Q5MJ10)

Alternative names: Nuclear-associated protein SPAN-Xn2, SPANX family member N2

All UniProt accessions (1): Q5MJ10

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPAN-X family.

RefSeq proteins (1): NP_001009615* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010007	SPAN-X_fam	Family

Pfam: PF07458

UniProt features (7 total): compositionally biased region 3, region of interest 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5MJ10-F1	59.10	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chrXq27

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

436 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPANXN2	EOLA2	Q96DE9	520
SPANXN2	CXorf51A	A0A1B0GTR3	511
SPANXN2	MUCL3	Q3MIW9	479
SPANXN2	PRB3	Q04118	478
SPANXN2	ZNF717	Q9BY31	432
SPANXN2	SSX7	Q7RTT5	430
SPANXN2	F2Z2I4	F2Z2I4	418
SPANXN2	EOLA1	Q8TE69	418
SPANXN2	HSFX4	A0A1B0GTS1	391
SPANXN2	MAST4	O15021	378
SPANXN2	FTHL17	Q9BXU8	376
SPANXN2	CT55	Q8WUE5	373
SPANXN2	XAGE3	Q8WTP9	371
SPANXN2	EPPIN	O95925	364
SPANXN2	MAGEB6	Q8N7X4	356

IntAct

151 interactions, top by confidence:

A	B	Type	Score
SPANXN2	CAVIN1	psi-mi:“MI:0915”(physical association)	0.670
SPANXN2		psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	ZNF84	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	FAM193B	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	ZNF75A	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	RRP1	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	CDCA8	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	SYTL4	psi-mi:“MI:0915”(physical association)	0.560
SMN1	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
BEND7	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
COIL	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	GPRASP3	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	ANKRD11	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	L3MBTL3	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	BANP	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	PICK1	psi-mi:“MI:0915”(physical association)	0.560
ZBTB48	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
SP4	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	STAC3	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	THAP1	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	DPPA4	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	YAF2	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	SFMBT1	psi-mi:“MI:0915”(physical association)	0.560
SP3	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	BIVM	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (95): SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid), SPANXN2 (Two-hybrid)

ESM2 similar proteins: A0A1D9BZF0, A6QL64, B4DH59, B5DUH6, D3YZV8, E9Q6E9, O43493, O46383, O77733, P06916, P08116, P0C758, P0DKJ7, P0DKJ8, P0DPF3, P31568, P62521, Q01033, Q01042, Q1HVF7, Q2W8Q7, Q3BBV2, Q42626, Q42627, Q4ZJZ1, Q4ZJZ3, Q5JPF3, Q5MJ10, Q6AXX0, Q6GX35, Q6IC83, Q6P3W6, Q6PGQ1, Q7M4S9, Q7M732, Q86T75, Q8BP27, Q8IZU1, Q8N2N9, Q96QF7

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

328 predictions. Top by Δscore:

Variant	Effect	Δscore
X:143720629:T:TA	donor_gain	0.9300
X:143720585:TCTTA:T	donor_loss	0.9200
X:143720586:CTTAC:C	donor_loss	0.9200
X:143720587:TTACC:T	donor_loss	0.9200
X:143720588:TACCT:T	donor_loss	0.9200
X:143720589:AC:A	donor_loss	0.9200
X:143720590:CC:C	donor_loss	0.9200
X:143720590:CCT:C	donor_gain	0.7600
X:143720000:C:G	acceptor_gain	0.7400
X:143712498:ATCTG:A	acceptor_gain	0.7300
X:143720283:T:A	donor_gain	0.7300
X:143720234:G:A	donor_gain	0.7100
X:143720148:C:CT	donor_gain	0.7000
X:143712405:C:CC	acceptor_gain	0.6700
X:143712500:C:CA	acceptor_loss	0.6700
X:143712512:C:CT	acceptor_loss	0.6600
X:143712513:A:T	acceptor_loss	0.6600
X:143720589:A:AC	donor_gain	0.6500
X:143720590:C:CC	donor_gain	0.6500
X:143712503:A:AC	acceptor_loss	0.6400
X:143712502:G:C	acceptor_loss	0.6300
X:143720180:G:T	donor_gain	0.6200
X:143720591:C:A	donor_loss	0.6200
X:143712500:C:CC	acceptor_gain	0.6100
X:143720584:ATCTT:A	donor_loss	0.6100
X:143712497:CATCT:C	acceptor_gain	0.5900
X:143712531:CAT:C	acceptor_loss	0.5900
X:143712507:GAAAA:G	acceptor_loss	0.5800
X:143712418:C:CA	acceptor_gain	0.5600
X:143712296:T:TA	acceptor_gain	0.5500

AlphaMissense

1166 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS111276881 (X:143720076 C>G), RS111298314 (X:143712837 T>C), RS111372484 (X:143719684 C>T), RS111386622 (X:143712430 G>A,C), RS111562170 (X:143715627 C>T), RS112471346 (X:143718519 G>C), RS112546832 (X:143720505 G>A), RS11284051 (X:143722512 GA>G,GAA,GAAA), RS112899274 (X:143717154 C>A), RS113009891 (X:143722521 A>C,T), RS113286912 (X:143719549 A>G,T), RS113547916 (X:143720859 C>G), RS113771480 (X:143719126 A>C), RS113891615 (X:143721310 G>A), RS113926261 (X:143720920 C>A,G,T)

Disease associations

OMIM: gene MIM:300665 | 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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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