SSNA1

SS nuclear autoantigen 1

Basic information

Region (hg38): 9:137188660-137190370

Links

ENSG00000176101 ∙ NCBI:8636 ∙ OMIM:610882 ∙ HGNC:11321 ∙ Uniprot:O43805 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SSNA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSNA1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in SSNA1

This is a list of pathogenic ClinVar variants found in the SSNA1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-137188772-G-T		not specified	Uncertain significance (Nov 09, 2024)
9-137188776-A-C		not specified	Uncertain significance (May 24, 2024)
9-137189129-A-G		not specified	Uncertain significance (Oct 04, 2024)
9-137189131-A-C		not specified	Uncertain significance (Feb 24, 2025)
9-137189185-A-G		not specified	Uncertain significance (Jul 26, 2023)
9-137189210-C-T		not specified	Uncertain significance (Apr 06, 2022)
9-137189233-A-T		not specified	Uncertain significance (Jun 29, 2022)
9-137189237-T-C		not specified	Uncertain significance (Dec 05, 2022)
9-137189246-C-T		not specified	Uncertain significance (Dec 12, 2023)
9-137189251-G-A		not specified	Uncertain significance (Mar 16, 2022)
9-137189260-C-T		not specified	Uncertain significance (Jun 21, 2022)
9-137189818-C-G		not specified	Uncertain significance (Dec 06, 2021)
9-137189826-C-G		not specified	Uncertain significance (Jun 07, 2024)
9-137189850-A-G		not specified	Uncertain significance (Mar 12, 2024)
9-137189865-C-G		not specified	Uncertain significance (Nov 09, 2024)
9-137189871-C-T		not specified	Uncertain significance (Mar 20, 2023)
9-137189900-G-A		not specified	Uncertain significance (Jun 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSNA1	protein_coding	protein_coding	ENST00000322310	3	1724

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000334	0.384	125267	0	142	125409	0.000566

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.601	81	67.2	1.21	0.00000319	769
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0107	0.0101
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000349	0.000318
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.000715	0.000653

dbNSFP

Source: dbNSFP

• Pathway: 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;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.352
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.217
• hipred: Y
• hipred_score: 0.514
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ssna1

Gene ontology

• 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
• Cellular component: nucleus;centrosome;cytosol;ciliary basal body
• Molecular function: protein binding;identical protein binding