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.

not_specified (38 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000003142.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			38 clinvar			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	0	1

Loading clinvar variants...

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