YBX3

Y-box binding protein 3, the group of Y-box binding proteins

Basic information

Region (hg38): 12:10699089-10723323

Previous symbols: [ "CSDA" ]

Links

ENSG00000060138 ∙ NCBI:8531 ∙ OMIM:603437 ∙ HGNC:2428 ∙ Uniprot:P16989 ∙ 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 YBX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YBX3 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			53	1		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	1	0

Variants in YBX3

This is a list of pathogenic ClinVar variants found in the YBX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10701994-C-T		not specified	Uncertain significance (Apr 25, 2022)
12-10702004-G-A		not specified	Uncertain significance (Nov 10, 2022)
12-10702006-C-T		not specified	Uncertain significance (Jun 30, 2023)
12-10702007-G-A		not specified	Uncertain significance (Jul 31, 2024)
12-10702021-C-T		not specified	Uncertain significance (Jun 18, 2021)
12-10702034-G-A		not specified	Uncertain significance (Nov 15, 2023)
12-10702045-G-A		not specified	Uncertain significance (Aug 08, 2022)
12-10702061-T-G		not specified	Uncertain significance (Apr 04, 2023)
12-10702071-C-G		not specified	Uncertain significance (May 17, 2023)
12-10702084-T-G		not specified	Uncertain significance (Jan 08, 2024)
12-10702111-G-A		not specified	Uncertain significance (Jan 08, 2024)
12-10702120-C-T		not specified	Uncertain significance (Oct 16, 2024)
12-10702121-G-C		not specified	Uncertain significance (Jan 30, 2024)
12-10704066-C-A		not specified	Uncertain significance (Jul 20, 2021)
12-10704066-C-T		not specified	Uncertain significance (Sep 13, 2023)
12-10704073-T-G		not specified	Uncertain significance (Dec 22, 2023)
12-10704076-G-C		not specified	Uncertain significance (Oct 06, 2024)
12-10704084-T-C		not specified	Uncertain significance (Jun 11, 2021)
12-10704090-G-A		not specified	Uncertain significance (Jun 27, 2022)
12-10704090-G-T		not specified	Uncertain significance (Oct 05, 2023)
12-10709925-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-10709940-A-G		not specified	Uncertain significance (Dec 20, 2023)
12-10709987-T-C		not specified	Uncertain significance (Feb 27, 2024)
12-10709991-G-A		not specified	Uncertain significance (Sep 04, 2024)
12-10709995-C-G		not specified	Uncertain significance (Nov 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YBX3	protein_coding	protein_coding	ENST00000228251	9	24229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000806	0.924	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.112	222	227	0.979	0.0000162	2339
Missense in Polyphen		101	98.093	1.0296		773
Synonymous	-0.831	79	70.1	1.13	0.00000389	798
Loss of Function	1.68	11	18.9	0.582	0.00000103	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000983	0.0000980
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full-length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression (By similarity). {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human);RalA downstream regulated genes;Apoptosis-related network due to altered Notch3 in ovarian cancer (Consensus)

Recessive Scores

• pRec: 0.188

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• pHI: 0.834
• hipred: Y
• hipred_score: 0.504
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ybx3
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo 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); reproductive system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;in utero embryonic development;spermatogenesis;male gonad development;response to cold;fertilization;positive regulation of organ growth;negative regulation of skeletal muscle tissue development;negative regulation of necroptotic process;3'-UTR-mediated mRNA stabilization;cellular response to tumor necrosis factor;cellular hyperosmotic response;negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress;positive regulation of cytoplasmic translation
• Cellular component: nucleus;cytoplasm;cytosol;bicellular tight junction;perinuclear region of cytoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;double-stranded DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;RNA binding;mRNA 3'-UTR binding;protein binding;Rho GTPase binding;polysome binding