YBX1

Chr 1

Y-box binding protein 1

Also known as: BP-8, CBF-A, CSDA2, CSDB, DBPB, EFI-A, MDR-NF1, NSEP-1

NCBI Gene: 4904ENSG00000065978UniProt: P67809

Y-box binding protein 1 functions as a DNA- and RNA-binding protein that regulates transcription, translation, mRNA splicing and stability, and DNA repair. Mutations cause autosomal dominant cold-induced sweating syndrome with early childhood onset, characterized by profuse sweating triggered by cold temperatures and ambient temperature changes. This gene is highly constrained against loss-of-function variation (pLI 0.95, LOEUF 0.35), indicating that haploinsufficiency is likely not tolerated in the general population.

ResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.35
Clinical Summary— YBX1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.95). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
11 unique Pathogenic / Likely Pathogenic· 44 VUS of 73 total submissions
Explore recent and relevant literature in Research Assistant →
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.35LOEUF
pLI 0.946
Z-score 3.50
OE 0.11 (0.04–0.35)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
1.71Z-score
OE missense 0.64 (0.55–0.75)
118 obs / 183.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.11 (0.04–0.35)
0≤0.351.4
Missense OE0.64 (0.55–0.75)
0≤0.61.4
Synonymous OE0.95
0≤1.21.6
LoF obs/exp: 2 / 18.0Missense obs/exp: 118 / 183.3Syn Z: 0.29
DN
0.3991th %ile
GOF
0.3193th %ile
LOF
0.79top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.35

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

73 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic9
Likely Pathogenic2
VUS44
Likely Benign4
Benign1
9
Pathogenic
2
Likely Pathogenic
44
VUS
4
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
9
0
9
Likely Pathogenic
0
0
2
0
2
VUS
0
41
3
0
44
Likely Benign
0
0
0
4
4
Benign
0
1
0
0
1
Total04214460

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

YBX1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients