YBX2

Chr 17

Y-box binding protein 2

Also known as: CONTRIN, CSDA3, DBPC, MSY2

NCBI Gene: 51087 ENSG00000006047 UniProt: Q9Y2T7

YBX2 encodes a nucleic acid binding protein that regulates mRNA stability and translation in germ cells and is a major component of messenger ribonucleoprotein particles. Mutations cause infertility in males due to defective sperm production, following an autosomal recessive inheritance pattern. The gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely pathogenic.

ResearchSummary from RefSeq, UniProt

This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15. [provided by RefSeq, Feb 2012]

ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.15

Clinical Summary— YBX2

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

44 VUS of 53 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?

0.15LOEUF

pLI 0.999

Z-score 4.14

OE 0.00 (0.00–0.15)

Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?

1.60Z-score

OE missense 0.68 (0.59–0.79)

138 obs / 202.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.15)

0≤0.351.4

Missense OE?0.68 (0.59–0.79)

0≤0.61.4

Synonymous OE?0.92

0≤1.21.6

LoF obs/exp: 0 / 19.9Missense obs/exp: 138 / 202.1Syn Z: 0.57

This gene — mechanism propensity

0.2599th %ile

GOF

0.3391th %ile

LOF

0.82top 5%

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

LOFprediction above median · LOEUF 0.15

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

53 submitted variants in ClinVar

ClinVar

Classification Summary

VUS44

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	44	44
Likely Benign	3	3
Benign	0	0
Total	47	47

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

View in ClinVar →

30 pathogenic / likely-pathogenic (of 39) ClinVar copy-number / structural variants overlap YBX2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →