HDLBP

Chr 2

high density lipoprotein binding protein

Also known as: HBP, PRO2900, VGL

The encoded protein binds high density lipoprotein (HDL) to regulate cellular cholesterol levels and also binds RNA to induce heterochromatin formation. Mutations cause neurodevelopmental disorders with intellectual disability, developmental delay, and behavioral abnormalities, typically with childhood onset. This gene follows autosomal dominant inheritance and is highly constrained against loss-of-function variants.

Summary from RefSeq, UniProt
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0
Active trials
7
Pubs (1 yr)
0
P/LP submissions
P/LP missense
0.15
LOEUF· LoF intol.
LOF
Mechanism· predicted
Clinical SummaryHDLBP
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.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.15LOEUF
pLI 1.000
Z-score 6.67
OE 0.07 (0.030.15)
Highly constrained

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

Missense Constraint
4.10Z-score
OE missense 0.58 (0.540.63)
451 obs / 771.3 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.07 (0.030.15)
00.351.4
Missense OE0.58 (0.540.63)
00.61.4
Synonymous OE1.04
01.21.6
LoF obs/exp: 4 / 59.5Missense obs/exp: 451 / 771.3Syn Z: -0.49
DN
0.4289th %ile
GOF
0.3689th %ile
LOF
0.67top 25%

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

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

HDLBP · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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