SPANXN5

Summary

SPANXN5 (SPANX family member N5, HGNC:33178) is a protein-coding gene on chromosome Xp11.22, encoding Sperm protein associated with the nucleus on the X chromosome N5 (Q5MJ07).

At a glance

• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_001009616

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33178
Approved symbol	SPANXN5
Name	SPANX family member N5
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	SPANX-N5, CT11.10
Ensembl gene	ENSG00000204363
Ensembl biotype	protein_coding
OMIM	300668
Entrez	494197

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000375511

RefSeq mRNA: 1 — MANE Select: NM_001009616 NM_001009616

CCDS: CCDS35295

Canonical transcript exons

ENST00000375511 — 2 exons

Exon	Start	End
ENSE00001467292	52796144	52796631
ENSE00001891852	52797274	52797427

Expression profiles

Bgee: expression breadth broad, 23 present calls, max score 92.66.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0303 / max 12.1793, expressed in 11 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199311	0.0303	11

Top tissues by expression

111 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	92.66	gold quality
right testis	UBERON:0004534	90.00	gold quality
left testis	UBERON:0004533	89.61	gold quality
testis	UBERON:0000473	89.19	gold quality
placenta	UBERON:0001987	39.63	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
duodenum	UBERON:0002114	34.36	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	29.04	gold quality
liver	UBERON:0002107	28.42	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	26.75	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
muscle of leg	UBERON:0001383	26.04	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
pancreas	UBERON:0001264	25.43	silver quality
gastrocnemius	UBERON:0001388	25.08	gold quality
leukocyte	CL:0000738	24.80	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting SPANXN5, 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-205-5P	99.81	70.05	1557
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-4699-5P	98.99	67.50	1210
HSA-MIR-4716-5P	98.82	68.57	1168
HSA-MIR-3611	98.76	68.76	1290
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-4691-5P	98.41	66.77	1343
HSA-MIR-6792-3P	98.41	66.86	1359
HSA-MIR-660-3P	98.14	66.04	1434
HSA-MIR-1245B-3P	98.01	68.91	1387
HSA-MIR-5196-3P	97.57	65.98	979
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-627-5P	95.51	66.80	509
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), SPANXN1 (ENSG00000203923), SPANXN2 (ENSG00000268988)

Protein

Protein identifiers

Sperm protein associated with the nucleus on the X chromosome N5 — Q5MJ07 (reviewed: Q5MJ07)

Alternative names: Nuclear-associated protein SPAN-Xn5, SPANX family member N5

All UniProt accessions (1): Q5MJ07

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPAN-X family.

RefSeq proteins (1): NP_001009616* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010007	SPAN-X_fam	Family

Pfam: PF07458

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5MJ07-F1	65.73	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): chrXp11, MIR205_5P, MIR5193, MIR371A_5P, MIR660_3P, MIR4710, MIR4793_5P, MIR5196_3P, MIR4515

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

390 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPANXN5	TRIM49B	A6NDI0	507
SPANXN5	SPATA31D4	Q6ZUB0	507
SPANXN5	WFDC11	Q8NEX6	476
SPANXN5	C16orf90	A8MZG2	476
SPANXN5	F5GXT2	F5GXT2	447
SPANXN5	IQCF3	P0C7M6	446
SPANXN5	FAM86C1P	Q9NVL1	445
SPANXN5	RIBC1	Q8N443	416
SPANXN5	TSPYL6	Q8N831	413
SPANXN5	RGPD4	Q7Z3J3	405
SPANXN5	TRIM73	Q86UV7	404
SPANXN5	DEFB112	Q30KQ8	396
SPANXN5	TMPRSS12	Q86WS5	391
SPANXN5	KRTAP7-1	Q8IUC3	379
SPANXN5	XAGE3	Q8WTP9	378

IntAct

3 interactions, top by confidence:

A	B	Type	Score
PLEKHG1	ARPC1B	psi-mi:“MI:0914”(association)	0.350
SPANXN5	USP1	psi-mi:“MI:0914”(association)	0.350

BioGRID (16): SPANXN5 (Affinity Capture-MS), KLHL18 (Affinity Capture-MS), LIG1 (Affinity Capture-MS), USP1 (Affinity Capture-MS), BPGM (Affinity Capture-MS), EHD4 (Affinity Capture-MS), BANP (Affinity Capture-MS), METTL3 (Affinity Capture-MS), VWA9 (Affinity Capture-MS), TRIM11 (Affinity Capture-MS), GPD1L (Affinity Capture-MS), PRUNE (Affinity Capture-MS), DESI1 (Affinity Capture-MS), EHD1 (Affinity Capture-MS), C17orf75 (Affinity Capture-MS)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

88 predictions. Top by Δscore:

Variant	Effect	Δscore
X:52796629:CAT:C	acceptor_gain	0.9900
X:52796630:ATC:A	acceptor_loss	0.9900
X:52796631:TC:T	acceptor_loss	0.9900
X:52796632:C:A	acceptor_loss	0.9900
X:52796632:C:CC	acceptor_gain	0.9900
X:52796627:TGCAT:T	acceptor_gain	0.9800
X:52796628:GCAT:G	acceptor_gain	0.9700
X:52796629:CATC:C	acceptor_gain	0.9700
X:52797268:TCTTA:T	donor_loss	0.9600
X:52797269:CTTA:C	donor_loss	0.9600
X:52797270:TTACC:T	donor_loss	0.9600
X:52797271:TA:T	donor_loss	0.9600
X:52797272:A:C	donor_loss	0.9600
X:52797273:C:CA	donor_loss	0.9600
X:52796630:AT:A	acceptor_gain	0.9500
X:52796635:T:TC	acceptor_gain	0.9400
X:52796644:C:CT	acceptor_gain	0.9400
X:52796635:T:C	acceptor_gain	0.9200
X:52796645:A:T	acceptor_gain	0.9200
X:52797273:CCT:C	donor_gain	0.9000
X:52797272:A:AC	donor_gain	0.8100
X:52797273:C:CC	donor_gain	0.8100
X:52796634:G:GC	acceptor_gain	0.7800
X:52796630:ATCTG:A	acceptor_gain	0.7700
X:52796631:TCTGT:T	acceptor_gain	0.7700
X:52796628:GCATC:G	acceptor_gain	0.7600
X:52796629:CATCT:C	acceptor_gain	0.7600
X:52796632:CTGTT:C	acceptor_gain	0.7600
X:52797309:T:TA	donor_gain	0.7600
X:52796633:T:G	acceptor_gain	0.7100

AlphaMissense

478 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1003287662 (X:52795803 T>A), RS1022194585 (X:52795849 T>C), RS1038571165 (X:52795711 C>A), RS1047476817 (X:52795791 T>C), RS1047885944 (X:52795970 T>A), RS1054868882 (X:52796034 A>G), RS111848053 (X:52796745 T>C,G), RS113926707 (X:52796484 T>C), RS1156857512 (X:52798766 A>C), RS1157099380 (X:52797124 C>T), RS1159141053 (X:52799427 C>A,T), RS1159319802 (X:52797898 A>T), RS1160680961 (X:52795859 A>G), RS1163640123 (X:52799225 G>C,T), RS1164217705 (X:52796963 C>T)

Disease associations

OMIM: gene MIM:300668 | 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

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	increases expression	2
propionaldehyde	increases expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
15-acetyldeoxynivalenol	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	affects methylation	1
Copper	affects binding, decreases expression	1
Disulfiram	affects binding, decreases expression	1
Thiram	increases expression	1

Clinical trials (associated diseases)

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