YBX2

Y-box binding protein 2, the group of Y-box binding proteins

Basic information

Region (hg38): 17:7288263-7294639

Links

ENSG00000006047 ∙ NCBI:51087 ∙ OMIM:611447 ∙ HGNC:17948 ∙ Uniprot:Q9Y2T7 ∙ 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 YBX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YBX2 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			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	0

Variants in YBX2

This is a list of pathogenic ClinVar variants found in the YBX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7288808-T-C		not specified	Uncertain significance (Dec 13, 2021)
17-7289579-G-A		not specified	Uncertain significance (Nov 26, 2024)
17-7289583-G-C		not specified	Uncertain significance (Aug 01, 2024)
17-7289589-G-A		not specified	Uncertain significance (Apr 19, 2023)
17-7289598-G-C		not specified	Uncertain significance (Oct 04, 2024)
17-7289609-C-T		not specified	Uncertain significance (Sep 07, 2022)
17-7289610-G-A		not specified	Uncertain significance (May 31, 2023)
17-7289637-G-A		not specified	Uncertain significance (Jan 03, 2022)
17-7289675-C-T		not specified	Uncertain significance (Sep 22, 2023)
17-7289705-C-T		not specified	Uncertain significance (Nov 13, 2024)
17-7289998-G-C		not specified	Uncertain significance (Mar 29, 2022)
17-7290330-C-T		not specified	Uncertain significance (Oct 25, 2023)
17-7290340-G-A		not specified	Uncertain significance (Dec 07, 2023)
17-7290363-T-C		not specified	Uncertain significance (Jan 23, 2023)
17-7290393-G-A		not specified	Uncertain significance (Dec 09, 2024)
17-7290412-T-C		not specified	Uncertain significance (Feb 28, 2023)
17-7290481-G-C		not specified	Uncertain significance (Jun 26, 2024)
17-7291145-C-G		not specified	Uncertain significance (Oct 13, 2023)
17-7294332-T-A		not specified	Uncertain significance (Feb 23, 2023)
17-7294334-C-T		not specified	Uncertain significance (Nov 15, 2021)
17-7294347-C-T		not specified	Uncertain significance (Feb 08, 2022)
17-7294350-A-C		not specified	Uncertain significance (Jun 11, 2021)
17-7294384-T-G		not specified	Uncertain significance (Nov 12, 2021)
17-7294425-C-T		not specified	Uncertain significance (Sep 20, 2024)
17-7294478-G-A		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YBX2	protein_coding	protein_coding	ENST00000007699	8	6364

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00104	110462	0	1	110463	0.00000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	138	202	0.683	0.0000137	2237
Missense in Polyphen		4	15.086	0.26514		153
Synonymous	0.568	67	73.2	0.916	0.00000413	820
Loss of Function	4.14	0	19.9	0.00	0.00000148	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000106	0.0000106
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus promoter element. Binds to full-length mRNA with high affinity in a sequence-independent manner. Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0735

Intolerance Scores

• loftool: 0.315
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.646
• hipred: Y
• hipred_score: 0.549
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.643

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ybx2
• Phenotype: cellular phenotype; reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;spermatogenesis;translational attenuation;oocyte development;positive regulation of cold-induced thermogenesis
• Cellular component: fibrillar center;nucleus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;RNA binding