SSNA1

Summary

SSNA1 (SS nuclear autoantigen 1, HGNC:11321) is a protein-coding gene on chromosome 9q34.3, encoding Microtubule nucleation factor SSNA1 (O43805). Microtubule-binding protein which stabilizes dynamic microtubules by slowing growth and shrinkage at both plus and minus ends and serves as a sensor of microtubule damage, protecting microtubules from the microtubule-severing enzyme SPAST.

Enables identical protein binding activity and microtubule binding activity. Involved in axonogenesis; cell division; and microtubule nucleation. Located in several cellular components, including axoneme; microtubule organizing center; and midbody.

Source: NCBI Gene 8636 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_003731

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11321
Approved symbol	SSNA1
Name	SS nuclear autoantigen 1
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	NA14, N14
Ensembl gene	ENSG00000176101
Ensembl biotype	protein_coding
OMIM	610882
Entrez	8636

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 retained_intron

ENST00000322310, ENST00000459860, ENST00000463511, ENST00000464553, ENST00000915486

RefSeq mRNA: 1 — MANE Select: NM_003731 NM_003731

CCDS: CCDS7034

Canonical transcript exons

ENST00000322310 — 3 exons

Exon	Start	End
ENSE00001307942	137189066	137189265
ENSE00001329995	137188676	137188778
ENSE00003849396	137189807	137190366

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 98.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.9249 / max 120.2121, expressed in 1818 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99665	20.2842	1810
99666	8.7849	1767
99667	1.2343	652
99664	0.6215	349

Top tissues by expression

294 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.12	gold quality
right testis	UBERON:0004534	98.05	gold quality
apex of heart	UBERON:0002098	97.90	gold quality
lower esophagus mucosa	UBERON:0035834	96.61	gold quality
mucosa of transverse colon	UBERON:0004991	96.50	gold quality
body of stomach	UBERON:0001161	96.26	gold quality
granulocyte	CL:0000094	96.20	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.15	gold quality
testis	UBERON:0000473	96.12	gold quality
body of pancreas	UBERON:0001150	95.90	gold quality
esophagus mucosa	UBERON:0002469	95.70	gold quality
lower esophagus	UBERON:0013473	95.42	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.41	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.39	gold quality
skin of abdomen	UBERON:0001416	95.38	gold quality
esophagus	UBERON:0001043	95.37	gold quality
skin of leg	UBERON:0001511	95.31	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.23	gold quality
cerebellar hemisphere	UBERON:0002245	95.20	gold quality
heart left ventricle	UBERON:0002084	95.12	gold quality
cerebellar cortex	UBERON:0002129	95.09	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.00	gold quality
left coronary artery	UBERON:0001626	94.95	gold quality
transverse colon	UBERON:0001157	94.92	gold quality
monocyte	CL:0000576	94.87	gold quality
cardiac ventricle	UBERON:0002082	94.87	gold quality
gastrocnemius	UBERON:0001388	94.83	gold quality
metanephros cortex	UBERON:0010533	94.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.74	gold quality
spinal cord	UBERON:0002240	94.72	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.43
E-MTAB-7303	no	1681.51
E-ENAD-17	no	282.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting SSNA1, 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-3185	99.99	68.12	1959
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-3184-5P	98.56	67.13	1491
HSA-MIR-3173-5P	97.35	65.82	1282
HSA-MIR-6799-3P	97.35	65.60	1302
HSA-MIR-3126-5P	96.87	65.83	912
HSA-MIR-6875-5P	96.87	65.49	958
HSA-MIR-3907	96.76	65.04	662
HSA-MIR-769-5P	94.45	64.56	603

Literature-anchored findings (GeneRIF, showing 4)

• purification and characterization of NA14 and some variants; NA14 structure may be stabilized by two Glu-COO(-) ||| HO-Tyr H-bonds, highly conserved in NA14-like proteins in other species (PMID:22008182)
• NA14 may act as an adaptor protein regulating SPG4 localization to centrosomes, temporally and spatially regulating the microtubule-severing activity of SPG4 that is particularly critical during the cell cycle and neuronal development. (PMID:25390646)
• SSNA1 stabilizes dynamic microtubules and detects microtubule damage. (PMID:34970964)
• SSNA1 Promotes Hepatocellular Carcinoma Metastasis Via STAT3/EMT Induction. (PMID:37500134)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ssna1	ENSMUSG00000026966
rattus_norvegicus	Ssna1	ENSRNOG00000011093

Protein

Protein identifiers

Microtubule nucleation factor SSNA1 — O43805 (reviewed: O43805)

Alternative names: Nuclear autoantigen of 14 kDa, Sjoegren syndrome nuclear autoantigen 1

All UniProt accessions (2): A0A087WV26, O43805

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule-binding protein which stabilizes dynamic microtubules by slowing growth and shrinkage at both plus and minus ends and serves as a sensor of microtubule damage, protecting microtubules from the microtubule-severing enzyme SPAST. Induces microtubule branching which is mediated by the formation of long SSNA1 fibrils which guide microtubule protofilaments to split apart from the mother microtubule and form daughter microtubules. Plays a role in axon outgrowth and branching. Required for cell division.

Subunit / interactions. Self-associates to form fibrils. Also forms dimers as well as monomers. Interacts with SPAST.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole. Midbody. Flagellum basal body. Flagellum axoneme. Cell projection. Axon.

Tissue specificity. Widely expressed.

Similarity. Belongs to the SSNA1 family.

RefSeq proteins (1): NP_003722* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR033362	SSNA1_fam	Family

UniProt features (11 total): mutagenesis site 3, sequence conflict 2, initiator methionine 1, chain 1, region of interest 1, coiled-coil region 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43805-F1	93.69	0.86

Functional residue map

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

Post-translational modifications (1): 2

Mutagenesis-validated functional residues (3):

Position	Phenotype
18	does not affect oligomer formation; when associated with s-23 and s-30.
23	does not affect oligomer formation; when associated with s-18 and s-30.
30	does not affect oligomer formation; when associated with s-18 and s-23.

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

ID	Pathway
R-HSA-2565942	Regulation of PLK1 Activity at G2/M Transition
R-HSA-380259	Loss of Nlp from mitotic centrosomes
R-HSA-380270	Recruitment of mitotic centrosome proteins and complexes
R-HSA-380284	Loss of proteins required for interphase microtubule organization from the centrosome
R-HSA-380320	Recruitment of NuMA to mitotic centrosomes
R-HSA-5620912	Anchoring of the basal body to the plasma membrane
R-HSA-8854518	AURKA Activation by TPX2
R-HSA-1640170	Cell Cycle
R-HSA-1852241	Organelle biogenesis and maintenance
R-HSA-380287	Centrosome maturation
R-HSA-453274	Mitotic G2-G2/M phases
R-HSA-5617833	Cilium Assembly
R-HSA-68877	Mitotic Prometaphase
R-HSA-68886	M Phase
R-HSA-69275	G2/M Transition
R-HSA-69278	Cell Cycle, Mitotic

MSigDB gene sets: 170 (showing top): GOBP_NEURON_PROJECTION_EXTENSION, CMYB_01, GOBP_GROWTH, GOBP_NEUROGENESIS, RIZKI_TUMOR_INVASIVENESS_3D_DN, GOBP_MICROTUBULE_NUCLEATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, AMIT_EGF_RESPONSE_480_MCF10A, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, GOBP_DEVELOPMENTAL_CELL_GROWTH, GOCC_NEURON_PROJECTION, GOBP_CELL_PROJECTION_ORGANIZATION

GO Biological Process (10): microtubule cytoskeleton organization (GO:0000226), microtubule nucleation (GO:0007020), smoothened signaling pathway (GO:0007224), axonogenesis (GO:0007409), intraciliary transport (GO:0042073), receptor clustering (GO:0043113), axon extension (GO:0048675), cell division (GO:0051301), axon arborization (GO:0140060), nervous system development (GO:0007399)

GO Molecular Function (3): microtubule binding (GO:0008017), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (15): nucleus (GO:0005634), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), plasma membrane (GO:0005886), axoneme (GO:0005930), axon (GO:0030424), midbody (GO:0030496), ciliary basal body (GO:0036064), supramolecular fiber (GO:0099512), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-10 pathways:

Category	Pathways
G2/M Transition	3
Centrosome maturation	2
Cell Cycle, Mitotic	2
Loss of proteins required for interphase microtubule organization from the centrosome	1
Mitotic Prometaphase	1
Assembly of the 9+0 primary cilium	1
Organelle biogenesis and maintenance	1
M Phase	1
Mitotic G2-G2/M phases	1
Cell Cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cilium	3
microtubule organizing center	3
axonogenesis	2
intracellular membraneless organelle	2
cytoskeleton organization	1
microtubule-based process	1
microtubule cytoskeleton organization	1
microtubule polymerization	1
cell surface receptor signaling pathway	1
cell morphogenesis involved in neuron differentiation	1
neuron projection morphogenesis	1
axon development	1
transport along microtubule	1
cilium organization	1
plasma membrane	1
protein localization to membrane	1
neuron projection extension	1
cellular process	1
neuron projection arborization	1
system development	1
tubulin binding	1
protein binding	1
binding	1
intracellular membrane-bounded organelle	1
centriole	1
cytoplasm	1
membrane	1
cell periphery	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
neuron projection	1
supramolecular polymer	1
intracellular anatomical structure	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

1090 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSNA1	SPAST	Q9UBP0	881
SSNA1	ATL2	Q8NHH9	828
SSNA1	ATL3	Q6DD88	821
SSNA1	CNTLN	Q9NXG0	770
SSNA1	CHMP1B	Q7LBR1	769
SSNA1	ATL1	Q8WXF7	749
SSNA1	TUBG1	P23258	712
SSNA1	SPART	Q8N0X7	639
SSNA1	RTN1	Q16799	635
SSNA1	MTRNR2L11	S4R3Y5	571
SSNA1	DRAP1	Q14919	556
SSNA1	CFAP99	D6REC4	547
SSNA1	EIF3M	Q7L2H7	507
SSNA1	MTRNR2L13	S4R3P1	507
SSNA1	PFDN6	O15212	496

IntAct

100 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:0914”(association)	0.900
SSNA1	SSNA1	psi-mi:“MI:0915”(physical association)	0.840
LNX1	SSNA1	psi-mi:“MI:0915”(physical association)	0.780
TBC1D7	SSNA1	psi-mi:“MI:0915”(physical association)	0.780
SSNA1	LNX1	psi-mi:“MI:0915”(physical association)	0.780
SSNA1	TBC1D7	psi-mi:“MI:0915”(physical association)	0.780
PSMC5	PSMD11	psi-mi:“MI:0914”(association)	0.730
SDCBP	SSNA1	psi-mi:“MI:0915”(physical association)	0.720
TXN2	SSNA1	psi-mi:“MI:0915”(physical association)	0.720
SSNA1	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
SSNA1	TXN2	psi-mi:“MI:0915”(physical association)	0.720
LCA5	SSNA1	psi-mi:“MI:0914”(association)	0.700
SSNA1	LCA5	psi-mi:“MI:0915”(physical association)	0.700

BioGRID (60): SSNA1 (Two-hybrid), SSNA1 (Two-hybrid), SSNA1 (Two-hybrid), TXN2 (Two-hybrid), TBC1D7 (Two-hybrid), GOPC (Two-hybrid), LNX1 (Two-hybrid), TCEANC (Two-hybrid), SSNA1 (Affinity Capture-MS), SSNA1 (Co-fractionation), SSNA1 (Co-fractionation), SSNA1 (Co-fractionation), SSNA1 (Co-fractionation), SSNA1 (Co-fractionation), SSNA1 (Affinity Capture-MS)

ESM2 similar proteins: A0PJP4, A2VDP1, A5D7M3, B2RW38, D3ZUQ0, F1QNW4, O00291, O14645, O43805, O75146, O75150, O95995, Q17QG3, Q26630, Q3U319, Q499U4, Q4FZV3, Q4R3K5, Q4R7K7, Q4R7Y8, Q4V328, Q5DTM8, Q5E9C3, Q5EBL4, Q5RAU7, Q5T655, Q5VTR2, Q5ZLS3, Q60779, Q68CZ1, Q6DGZ3, Q6GN86, Q7XJ96, Q7Z3E2, Q8BKE9, Q8BR07, Q8BVN8, Q8C9S4, Q8CG73, Q8CJB9

Diamond homologs: O43805, Q5E9C3, Q9JJ94, Q9XF62

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

309 predictions. Top by Δscore:

Variant	Effect	Δscore
9:137188777:GT:G	donor_gain	1.0000
9:137189248:G:GT	donor_gain	1.0000
9:137189297:GGGA:G	donor_gain	1.0000
9:137188779:G:GG	donor_gain	0.9900
9:137188802:G:GT	donor_gain	0.9900
9:137188802:G:T	donor_gain	0.9900
9:137189276:G:GT	donor_gain	0.9900
9:137189277:G:T	donor_gain	0.9900
9:137189305:C:T	donor_gain	0.9900
9:137188773:TC:T	donor_gain	0.9800
9:137189261:TCAAG:T	donor_loss	0.9800
9:137189262:CAAG:C	donor_loss	0.9800
9:137189263:AAGGT:A	donor_loss	0.9800
9:137189264:AG:A	donor_loss	0.9800
9:137189265:GG:G	donor_loss	0.9800
9:137189266:GTGG:G	donor_loss	0.9800
9:137189267:T:G	donor_loss	0.9800
9:137189277:G:GT	donor_gain	0.9800
9:137189298:G:T	donor_gain	0.9800
9:137189798:T:TA	acceptor_gain	0.9800
9:137189801:CCCCA:C	acceptor_loss	0.9800
9:137189802:CCCA:C	acceptor_loss	0.9800
9:137189803:CCA:C	acceptor_loss	0.9800
9:137189804:CAGA:C	acceptor_loss	0.9800
9:137189805:A:AG	acceptor_gain	0.9800
9:137189805:AGA:A	acceptor_loss	0.9800
9:137189806:G:GC	acceptor_loss	0.9800
9:137189806:G:GG	acceptor_gain	0.9800
9:137188774:CA:C	donor_gain	0.9700
9:137188775:AA:A	donor_gain	0.9700

AlphaMissense

778 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:137188739:G:C	G5R	0.999
9:137188749:T:C	L8P	0.999
9:137188762:C:A	N12K	0.999
9:137188762:C:G	N12K	0.999
9:137188770:T:C	L15P	0.999
9:137189078:T:C	L22P	0.999
9:137189174:T:C	L54P	0.999
9:137189216:G:C	R68P	0.999
9:137189257:T:G	Y82D	0.999
9:137189808:T:C	I85T	0.999
9:137189811:T:C	L86P	0.999
9:137189819:T:C	S89P	0.999
9:137189829:T:C	L92S	0.999
9:137189829:T:G	L92W	0.999
9:137189832:T:C	L93P	0.999
9:137189841:T:A	L96H	0.999
9:137188739:G:T	G5C	0.998
9:137188740:G:A	G5D	0.998
9:137188770:T:A	L15Q	0.998
9:137189090:G:C	R26P	0.998
9:137189141:T:C	L43P	0.998
9:137189195:T:C	L61P	0.998
9:137189237:T:A	I75N	0.998
9:137189251:G:C	A80P	0.998
9:137189254:G:C	A81P	0.998
9:137189257:T:C	Y82H	0.998
9:137189816:A:C	S88R	0.998
9:137189818:C:A	S88R	0.998
9:137189818:C:G	S88R	0.998
9:137189841:T:C	L96P	0.998

dbSNP variants (sampled 300 via entrez): RS1000411549 (9:137190156 G>A), RS1001970198 (9:137189410 C>A,G), RS1002272841 (9:137188340 C>A,G,T), RS1002816602 (9:137190674 C>G,T), RS1003544064 (9:137187167 G>A,C), RS1003905986 (9:137188876 C>A,G,T), RS1003984875 (9:137187319 T>C), RS1004367881 (9:137188249 G>A), RS1004662853 (9:137186945 C>T), RS1004695626 (9:137187127 G>A,C), RS1004710290 (9:137190228 C>A,T), RS1004908214 (9:137190031 C>T), RS1005382937 (9:137188242 T>C), RS1005581115 (9:137188073 G>A), RS1005611454 (9:137190409 G>A)

Disease associations

OMIM: gene MIM:610882 | 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

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
triphenyl phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
abrine	decreases expression	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Ozone	affects expression, increases abundance	1
Selenium	increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Thiram	decreases expression	1
Valproic Acid	increases methylation	1
Asbestos, Crocidolite	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B3IB	Abcam HEK293T SSNA1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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