SSB

small RNA binding exonuclease protection factor La, the group of La ribonucleoproteins|RNA binding motif containing

Basic information

Region (hg38): 2:169791933-169812064

Links

ENSG00000138385 ∙ NCBI:6741 ∙ OMIM:109090 ∙ HGNC:11316 ∙ Uniprot:P05455 ∙ 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 SSB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSB 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					1	1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	1

Variants in SSB

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

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

Position	Type	Phenotype	Significance	ClinVar
2-169800972-T-C			Benign (Dec 31, 2019)
2-169800995-C-T		not specified	Uncertain significance (Nov 13, 2024)
2-169805523-A-G		not specified	Uncertain significance (Jun 09, 2022)
2-169805534-G-C		not specified	Uncertain significance (Jan 31, 2024)
2-169805734-G-C		not specified	Uncertain significance (Feb 02, 2024)
2-169805774-A-T		not specified	Uncertain significance (Aug 16, 2022)
2-169805837-A-G		not specified	Uncertain significance (May 03, 2023)
2-169806801-A-C		not specified	Uncertain significance (Dec 03, 2021)
2-169806818-A-C		not specified	Uncertain significance (Oct 27, 2023)
2-169808486-G-A		not specified	Uncertain significance (Sep 28, 2022)
2-169808887-A-C		not specified	Uncertain significance (Sep 27, 2021)
2-169808890-A-T		not specified	Uncertain significance (Feb 27, 2024)
2-169808892-A-C		not specified	Uncertain significance (Feb 27, 2024)
2-169810297-A-C		not specified	Uncertain significance (Jul 12, 2023)
2-169810323-C-T		not specified	Uncertain significance (Nov 15, 2021)
2-169810406-G-A		not specified	Uncertain significance (Nov 29, 2023)
2-169810912-G-A		not specified	Uncertain significance (Nov 07, 2022)
2-169811185-C-G		not specified	Uncertain significance (Mar 01, 2023)
2-169811185-C-T		not specified	Uncertain significance (Nov 10, 2024)
2-169811186-G-T		not specified	Uncertain significance (Oct 12, 2024)
2-169811270-C-T		not specified	Uncertain significance (May 03, 2023)
2-169811284-GATGATGAAC-G			Likely benign (Sep 01, 2024)
2-169811288-A-G		not specified	Uncertain significance (Sep 09, 2024)
2-169811293-C-A		not specified	Uncertain significance (Mar 18, 2024)
2-169811299-G-C		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSB	protein_coding	protein_coding	ENST00000409333	11	20132

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0896	0.910	125720	0	24	125744	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	141	201	0.703	0.00000944	2733
Missense in Polyphen		16	48.167	0.33218		735
Synonymous	0.785	60	68.3	0.879	0.00000335	685
Loss of Function	3.14	6	21.8	0.275	9.17e-7	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000433	0.000431
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000619	0.0000527
Middle Eastern	0.000111	0.000109
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the 3' poly(U) terminus of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation (PubMed:3192525, PubMed:2470590). In case of Coxsackievirus B3 infection, binds to the viral internal ribosome entry site (IRES) and stimulates the IRES-mediated translation (PubMed:12384597). {ECO:0000269|PubMed:12384597, ECO:0000269|PubMed:2470590, ECO:0000269|PubMed:3192525}.
• Pathway: Systemic lupus erythematosus - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase III Transcription Termination;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

• pRec: 0.393

Intolerance Scores

• loftool: 0.611
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.977
• hipred: Y
• hipred_score: 0.825
• ghis: 0.665

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssb
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; embryo phenotype; immune system phenotype

Gene ontology

• Biological process: tRNA 5'-leader removal;tRNA modification;tRNA export from nucleus;tRNA processing;histone mRNA metabolic process;tRNA 3'-end processing;nuclear histone mRNA catabolic process;IRES-dependent viral translational initiation;protein localization to cytoplasmic stress granule
• Cellular component: nuclear chromosome, telomeric region;nucleus;cytoplasm;ribonucleoprotein complex
• Molecular function: tRNA binding;RNA binding;mRNA binding;protein binding;poly(U) RNA binding;protein homodimerization activity;sequence-specific mRNA binding