SPIN2A

Summary

SPIN2A (spindlin family member 2A, HGNC:20694) is a protein-coding gene on chromosome Xp11.21, encoding Spindlin-2A (Q99865). May be involved in the regulation of cell cycle progression.

This gene encodes one of three members of the DXF34 gene family, located in a 100-kb region of chromosome Xp11.21.

Source: NCBI Gene 54466 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_019003

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20694
Approved symbol	SPIN2A
Name	spindlin family member 2A
Location	Xp11.21
Locus type	gene with protein product
Status	Approved
Aliases	DXF34, TDRD25
Ensembl gene	ENSG00000147059
Ensembl biotype	protein_coding
OMIM	300621
Entrez	54466

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000374906, ENST00000374908, ENST00000614076, ENST00000907357, ENST00000930838, ENST00000930839, ENST00000930840, ENST00000930841

RefSeq mRNA: 1 — MANE Select: NM_019003 NM_019003

CCDS: CCDS35312

Canonical transcript exons

ENST00000374906 — 2 exons

Exon	Start	End
ENSE00001465083	57137260	57137397
ENSE00001908198	57135650	57136602

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 77.11.

Top tissues by expression

254 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	77.11	gold quality
tendon of biceps brachii	UBERON:0008188	69.89	gold quality
stromal cell of endometrium	CL:0002255	69.75	gold quality
cortical plate	UBERON:0005343	68.38	gold quality
apex of heart	UBERON:0002098	68.31	gold quality
right hemisphere of cerebellum	UBERON:0014890	68.01	gold quality
cerebellar hemisphere	UBERON:0002245	67.81	gold quality
cerebellar cortex	UBERON:0002129	67.70	gold quality
tibial nerve	UBERON:0001323	66.65	gold quality
tendon	UBERON:0000043	66.21	gold quality
right coronary artery	UBERON:0001625	65.74	gold quality
cerebellum	UBERON:0002037	65.74	gold quality
sural nerve	UBERON:0015488	65.61	gold quality
mucosa of transverse colon	UBERON:0004991	65.06	gold quality
ascending aorta	UBERON:0001496	65.05	gold quality
bone marrow cell	CL:0002092	65.01	silver quality
thoracic aorta	UBERON:0001515	64.93	gold quality
right frontal lobe	UBERON:0002810	64.82	gold quality
prefrontal cortex	UBERON:0000451	64.58	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	64.50	gold quality
left lobe of thyroid gland	UBERON:0001120	64.49	gold quality
calcaneal tendon	UBERON:0003701	64.44	gold quality
body of uterus	UBERON:0009853	64.31	gold quality
transverse colon	UBERON:0001157	64.25	gold quality
muscle layer of sigmoid colon	UBERON:0035805	64.25	gold quality
right lobe of thyroid gland	UBERON:0001119	64.24	gold quality
lower esophagus	UBERON:0013473	64.12	gold quality
lower esophagus muscularis layer	UBERON:0035833	64.11	gold quality
Brodmann (1909) area 9	UBERON:0013540	63.94	gold quality
lower esophagus mucosa	UBERON:0035834	63.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting SPIN2A, 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-3692-3P	99.98	70.27	2139
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-3618	99.69	68.57	1012
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-3149	98.77	67.13	1639
HSA-MIR-455-5P	98.74	67.31	795
HSA-MIR-4709-5P	98.51	67.25	1335
HSA-MIR-934	98.49	70.44	581
HSA-MIR-10395-3P	98.10	66.70	1726
HSA-MIR-6730-5P	98.03	68.12	1299
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-9851-5P	97.57	67.49	1067
HSA-MIR-1227-3P	97.36	66.94	834
HSA-MIR-101-5P	96.84	65.66	649
HSA-MIR-12128	96.67	66.98	1471

Literature-anchored findings (GeneRIF, showing 1)

• SPIN-2. SPIN-2 is a novel nuclear protein from HL-60 cells that functions to regulate cell cycle progression and this activity is related to the inhibition of apoptosis following the removal of essential growth factors (PMID:12145692)

Cross-species orthologs

112 orthologs

Organism	Symbol	Gene ID
danio_rerio	spinb	ENSDARG00000035697
danio_rerio	spina	ENSDARG00000058949
mus_musculus	Gm21719	ENSMUSG00000079806
mus_musculus	Gm21292	ENSMUSG00000091077
mus_musculus	Gm20865	ENSMUSG00000093848
mus_musculus	Gm20809	ENSMUSG00000093868
mus_musculus	Gm21454	ENSMUSG00000093903
mus_musculus	Gm20918	ENSMUSG00000093927
mus_musculus	Gm20823	ENSMUSG00000093950
mus_musculus	Gm21118	ENSMUSG00000094052
mus_musculus	Gm20826	ENSMUSG00000094081
mus_musculus	Gm20909	ENSMUSG00000094294
mus_musculus	Gm20831	ENSMUSG00000094325
mus_musculus	Gm21244	ENSMUSG00000094484
mus_musculus	Gm20821	ENSMUSG00000094556
mus_musculus	Gm20738	ENSMUSG00000094575
mus_musculus	Gm21394	ENSMUSG00000094660
mus_musculus	Gm21721	ENSMUSG00000094679
mus_musculus	Gm20747	ENSMUSG00000094729
mus_musculus	Gm20806	ENSMUSG00000094739
mus_musculus	Gm21812	ENSMUSG00000094773
mus_musculus	Gm20777	ENSMUSG00000094813
mus_musculus	Gm20828	ENSMUSG00000094838
mus_musculus	Gm21310	ENSMUSG00000095032
mus_musculus	Gm20873	ENSMUSG00000095148
mus_musculus	Gm20822	ENSMUSG00000095172
mus_musculus	Gm20834	ENSMUSG00000095242
mus_musculus	Ssty1	ENSMUSG00000095267
mus_musculus	Ssty2	ENSMUSG00000095302
mus_musculus	Gm20825	ENSMUSG00000095324
mus_musculus	Gm20795	ENSMUSG00000095452
mus_musculus	Gm20812	ENSMUSG00000095508
mus_musculus	Gm20877	ENSMUSG00000095520
mus_musculus	Gm20816	ENSMUSG00000095634
mus_musculus	Gm20854	ENSMUSG00000095650
mus_musculus	Gm20924	ENSMUSG00000095785
mus_musculus	Gm20917	ENSMUSG00000095867
mus_musculus	Gm20773	ENSMUSG00000095900
mus_musculus	Gm20737	ENSMUSG00000095950
mus_musculus	Gm21778	ENSMUSG00000096036
mus_musculus	Gm21943	ENSMUSG00000096122
mus_musculus	Gm21874	ENSMUSG00000096223
mus_musculus	Gm20914	ENSMUSG00000096268
mus_musculus	Gm20852	ENSMUSG00000096666
mus_musculus	Gm20830	ENSMUSG00000096686
mus_musculus	Gm21854	ENSMUSG00000096706
mus_musculus	Gm21425	ENSMUSG00000096820
mus_musculus	Gm20867	ENSMUSG00000096898
mus_musculus	Gm29049	ENSMUSG00000099861
mus_musculus	Gm29424	ENSMUSG00000099948
mus_musculus	Gm28171	ENSMUSG00000100634
mus_musculus	Gm20815	ENSMUSG00000101053
mus_musculus	Gm20772	ENSMUSG00000102739
mus_musculus	Gm21440	ENSMUSG00000103468
mus_musculus	Gm20807	ENSMUSG00000104267
rattus_norvegicus	LOC134486221	ENSRNOG00000048867
rattus_norvegicus	LOC134486240	ENSRNOG00000049619
rattus_norvegicus	LOC120099686	ENSRNOG00000064259
rattus_norvegicus		ENSRNOG00000065734
rattus_norvegicus	LOC134486234	ENSRNOG00000067676
rattus_norvegicus		ENSRNOG00000068289
rattus_norvegicus	LOC134484257	ENSRNOG00000069646
rattus_norvegicus	Ssty1-ps5	ENSRNOG00000070707
rattus_norvegicus		ENSRNOG00000072094
rattus_norvegicus		ENSRNOG00000072522
rattus_norvegicus		ENSRNOG00000072683
rattus_norvegicus		ENSRNOG00000072719
rattus_norvegicus		ENSRNOG00000073240
rattus_norvegicus		ENSRNOG00000073388
rattus_norvegicus		ENSRNOG00000073718
rattus_norvegicus		ENSRNOG00000074289
rattus_norvegicus		ENSRNOG00000074627
rattus_norvegicus		ENSRNOG00000075048
rattus_norvegicus		ENSRNOG00000075217
rattus_norvegicus		ENSRNOG00000075704
rattus_norvegicus		ENSRNOG00000075715
rattus_norvegicus		ENSRNOG00000076756
rattus_norvegicus		ENSRNOG00000076768
rattus_norvegicus		ENSRNOG00000077163
rattus_norvegicus		ENSRNOG00000077684
rattus_norvegicus		ENSRNOG00000077860
		ENSRNOG00000078153
rattus_norvegicus		ENSRNOG00000078247
rattus_norvegicus		ENSRNOG00000078425
rattus_norvegicus		ENSRNOG00000078859
rattus_norvegicus		ENSRNOG00000079273
rattus_norvegicus		ENSRNOG00000079973
rattus_norvegicus		ENSRNOG00000080258
rattus_norvegicus		ENSRNOG00000082759
rattus_norvegicus		ENSRNOG00000083031
rattus_norvegicus		ENSRNOG00000083094
rattus_norvegicus		ENSRNOG00000083348
rattus_norvegicus		ENSRNOG00000083477
		ENSRNOG00000084216
rattus_norvegicus		ENSRNOG00000084517
rattus_norvegicus		ENSRNOG00000084670
rattus_norvegicus		ENSRNOG00000084696
		ENSRNOG00000085197
rattus_norvegicus		ENSRNOG00000085381
rattus_norvegicus		ENSRNOG00000085696
rattus_norvegicus		ENSRNOG00000085874
rattus_norvegicus		ENSRNOG00000086556
rattus_norvegicus		ENSRNOG00000088152
rattus_norvegicus		ENSRNOG00000088255
rattus_norvegicus		ENSRNOG00000088275
rattus_norvegicus		ENSRNOG00000089025
rattus_norvegicus		ENSRNOG00000089042
rattus_norvegicus		ENSRNOG00000089633
rattus_norvegicus		ENSRNOG00000089769
rattus_norvegicus		ENSRNOG00000089859
rattus_norvegicus		ENSRNOG00000089969
rattus_norvegicus		ENSRNOG00000090248

Paralogs (4): SPIN1 (ENSG00000106723), SPIN4 (ENSG00000186767), SPIN2B (ENSG00000186787), SPIN3 (ENSG00000204271)

Protein

Protein identifiers

Spindlin-2A — Q99865 (reviewed: Q99865)

Alternative names: Protein DXF34, Spindlin-like protein 2A

All UniProt accessions (2): Q99865, A0A087X074

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the regulation of cell cycle progression. Exhibits H3K4me3-binding activity.

Subunit / interactions. Interacts with C11orf84/SPINDOC.

Subcellular location. Nucleus.

Similarity. Belongs to the SPIN/STSY family.

RefSeq proteins (1): NP_061876* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003671	SPIN/Ssty	Family
IPR042567	SPIN/Ssty_sf	Homologous_superfamily

Pfam: PF02513

UniProt features (13 total): region of interest 6, site 3, compositionally biased region 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99865-F1	81.67	0.67

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 176 (histone h3k4me3 and h3r8me2a binding); 180 (histone h3k4me3 and h3r8me2a binding); 169 (histone h3k4me3 and h3r8me2a binding)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, CAGCTG_AP4_Q5, WGTTNNNNNAAA_UNKNOWN, CHEN_METABOLIC_SYNDROM_NETWORK, DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP, chrXp11, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, DCA_UP.V1_UP, GSE14386_UNTREATED_VS_IFNA_TREATED_ACT_PBMC_MS_PATIENT_DN, ZNF618_TARGET_GENES, MIR9983_3P, MIR4719, MIR1283, MIR10395_3P, MIR9851_5P

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), gamete generation (GO:0007276), chromatin organization (GO:0006325)

GO Molecular Function (2): histone H3K4me3 reader activity (GO:0140002), protein binding (GO:0005515)

GO Cellular Component (3): nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
sexual reproduction	1
multicellular organismal reproductive process	1
cellular component organization	1
histone H3 reader activity	1
binding	1
nuclear lumen	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

162 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPIN2A	IL3	P08700	497
SPIN2A	SPINDOC	Q9BUA3	446
SPIN2A	LUZP6	Q538Z0	433
SPIN2A	PCDHGB3	Q9Y5G1	394
SPIN2A	TERF1	P54274	387
SPIN2A	RGPD5	Q99666	370
SPIN2A	SPNS1	Q9H2V7	351
SPIN2A	RPP40	O75818	321
SPIN2A	SPATA4	Q8NEY3	311
SPIN2A	PIGY	Q3MUY2	294
SPIN2A	ACY3	Q96HD9	290
SPIN2A	ELMOD1	Q8N336	290
SPIN2A	GARIN1A	Q6NXP2	280
SPIN2A	OR51A4	Q8NGJ6	248
SPIN2A	PTRH2	Q9Y3E5	248

IntAct

8 interactions, top by confidence:

A	B	Type	Score
sseJ	AGPS	psi-mi:“MI:0914”(association)	0.460
PRDM7	SNRPD2	psi-mi:“MI:0914”(association)	0.350
SCRIB	CHD2	psi-mi:“MI:0914”(association)	0.350
UBA52	FUOM	psi-mi:“MI:0914”(association)	0.350
SIPA1L3	SIPA1L1	psi-mi:“MI:0914”(association)	0.350
PRKACG	HNRNPCL1	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350

BioGRID (16): SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (PCA), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), PRDM7 (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS), SPIN2A (Affinity Capture-MS)

ESM2 similar proteins: A2Z4C5, A7X680, B8AJL9, F4HVW5, F4I933, F4IV66, F4JR57, K4DF01, P0C7Q8, P13675, Q0WPN7, Q10PL5, Q1ECE0, Q2KI39, Q33BI9, Q4V8J7, Q56A73, Q5JUX0, Q5R997, Q5RA80, Q5RAW7, Q61142, Q6NVE3, Q6YZM6, Q8GVE5, Q8K1L2, Q8L7G0, Q8LJW3, Q8RWD9, Q8RWY4, Q8RY82, Q8W4F0, Q90WG1, Q90WG2, Q93VH2, Q93XX4, Q93YR9, Q944S3, Q94BM7, Q99865

Diamond homologs: P13675, Q2KI39, Q4V8J7, Q56A73, Q5JUX0, Q5R997, Q5RA80, Q5RAW7, Q61142, Q6NVE3, Q8K1L2, Q90WG1, Q90WG2, Q99865, Q9BPZ2, Q9Y657

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

126 predictions. Top by Δscore:

Variant	Effect	Δscore
X:57136954:T:A	donor_gain	0.9000
X:57136948:C:CT	donor_gain	0.8900
X:57136949:T:TT	donor_gain	0.8900
X:57136951:C:A	donor_gain	0.7700
X:57136944:CCCA:C	donor_gain	0.7600
X:57136945:CCAC:C	donor_gain	0.7600
X:57136709:AGGAG:A	donor_gain	0.7500
X:57136947:ACTAC:A	donor_gain	0.7400
X:57136948:CTACC:C	donor_gain	0.7400
X:57136767:AAGTT:A	donor_gain	0.6900
X:57136959:C:A	donor_gain	0.6700
X:57136967:G:A	donor_gain	0.6200
X:57136912:C:CA	donor_gain	0.5800
X:57136935:TG:T	donor_gain	0.5700
X:57136947:A:AC	donor_gain	0.5600
X:57136958:G:A	donor_gain	0.5400
X:57136919:C:A	donor_gain	0.5300
X:57136600:CTG:C	acceptor_gain	0.5200
X:57136598:GCCTG:G	acceptor_gain	0.5100
X:57136599:CCTGC:C	acceptor_gain	0.5100
X:57136760:C:CA	donor_gain	0.5000
X:57136368:G:C	donor_gain	0.4900
X:57136771:T:TA	donor_gain	0.4900
X:57136995:G:GA	donor_gain	0.4900
X:57136603:C:CC	acceptor_gain	0.4800
X:57136940:A:AC	donor_gain	0.4800
X:57136938:CCA:C	donor_gain	0.4700
X:57136953:C:T	donor_gain	0.4700
X:57136950:ACCCT:A	donor_gain	0.4600
X:57136951:CCCTC:C	donor_gain	0.4600

AlphaMissense

1701 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:57136187:A:C	F137L	0.997
X:57136187:A:T	F137L	0.997
X:57136189:A:G	F137L	0.997
X:57135869:A:C	F243L	0.995
X:57135869:A:T	F243L	0.995
X:57135871:A:G	F243L	0.995
X:57136339:A:G	Y87H	0.995
X:57136112:A:C	F162L	0.994
X:57136112:A:T	F162L	0.994
X:57136114:A:G	F162L	0.994
X:57136383:A:T	V72D	0.994
X:57136396:A:G	W68R	0.992
X:57136396:A:T	W68R	0.992
X:57136083:A:G	L172S	0.991
X:57136188:A:C	F137C	0.991
X:57136320:A:T	V93D	0.991
X:57136193:G:C	H135Q	0.989
X:57136193:G:T	H135Q	0.989
X:57136340:T:A	K86N	0.989
X:57136340:T:G	K86N	0.989
X:57136394:C:A	W68C	0.989
X:57136394:C:G	W68C	0.989
X:57136102:A:G	Y166H	0.988
X:57136143:A:G	L152S	0.988
X:57136424:C:A	W58C	0.988
X:57136424:C:G	W58C	0.988
X:57136426:A:G	W58R	0.988
X:57136426:A:T	W58R	0.988
X:57136153:C:A	G149W	0.987
X:57136390:C:G	G70R	0.987

dbSNP variants (sampled 300 via entrez): RS1001121776 (X:57142059 T>C), RS1001234172 (X:57142879 A>C), RS1001281171 (X:57142763 T>G), RS1002049027 (X:57143646 C>A), RS1002080432 (X:57143028 G>C,T), RS1002333266 (X:57143411 C>A), RS1002621421 (X:57133802 T>C), RS1002715603 (X:57139245 G>C), RS1003125649 (X:57137431 G>A), RS1003198912 (X:57138645 T>C), RS1003725464 (X:57141550 C>T), RS1003892517 (X:57138539 C>T), RS1004098161 (X:57147406 C>T), RS1004346711 (X:57138397 A>G), RS1004367511 (X:57138204 T>C)

Disease associations

OMIM: gene MIM:300621 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST006661_145	Male-pattern baldness	6.000000e-19
GCST007847_104	Type 2 diabetes	5.000000e-09
GCST90002385_591	High light scatter reticulocyte count	3.000000e-32
GCST90002386_502	High light scatter reticulocyte percentage of red cells	3.000000e-35
GCST90002405_429	Reticulocyte count	9.000000e-30
GCST90002406_580	Reticulocyte fraction of red cells	9.000000e-34

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ferrous chloride	increases expression	1
tetrachlorodian	decreases expression	1
Zoledronic Acid	increases expression, affects cotreatment	1
Fluvastatin	increases expression, affects cotreatment	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Methotrexate	increases expression	1
Smoke	decreases expression	1
Triclosan	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases abundance, increases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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