SSNA1
protein-codingSS nuclear autoantigen 1
Gene summary
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. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SSNA1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003731.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 20 | 1 | 21 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 20 | 1 | 0 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003722.2 | 3 | MANE Select | |
| Ensembl | ENSP00000313752.5 | 3 | MANE Select | |
| Ensembl | ENSP00000479123.1 | 3 | Standard | |
| Ensembl | ENSP00000479123.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- miR-targeted genes in lymphocytes - TarBase
- miR-targeted genes in muscle cell - TarBase
- Regulation of PLK1 Activity at G2/M Transition
- Recruitment of mitotic centrosome proteins and complexes
- Loss of Nlp from mitotic centrosomes
Biological Process
- G2/M transition of mitotic cell cycle
- regulation of G2/M transition of mitotic cell cycle
- intraciliary transport
- ciliary receptor clustering involved in smoothened signaling pathway
- ciliary basal body-plasma membrane docking
Molecular Function
- protein binding
- identical protein binding
Cellular Component
- nucleus
- centrosome
- cytosol
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000322310
- Coding exons
- 3
- Length
- 1724
- Individuals with no LoFs
- 125267
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 142
- Defined
- 125409
- p
- 0.000566
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.601 | 81 | 67.2 | 1.21 | 0.00000319 | 769 |
| Missense (PolyPhen) | 12 | 14.04 | 0.85472 | 193 | ||
| Synonymous | -0.961 | 37 | 30.3 | 1.22 | 0.00000158 | 226 |
| Loss of Function | -0.104 | 5 | 4.76 | 1.05 | 2.01e-7 | 58 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.011 | 0.010 | notable |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00035 | 0.00032 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00071 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- LoFtool
- 0.352
- RVIS EVS
- -0.01
- RVIS percentile EVS
- 52.85
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |