PACSIN2

Chr 22

protein kinase C and casein kinase substrate in neurons 2

Also known as: SDPII

NCBI Gene: 11252ENSG00000100266UniProt: Q9UNF0

This gene is a member of the protein kinase C and casein kinase substrate in neurons family. The encoded protein is involved in linking the actin cytoskeleton with vesicle formation by regulating tubulin polymerization. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

115
ClinVar variants
0
Pathogenic / LP
0.21
pLI score
0
Active trials
Clinical Summary— PACSIN2
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.24) despite low pLI — interpret in context.
📋
ClinVar Variants
115 total variants — no pathogenic classifications of 115 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.45LOEUF
pLI 0.213
Z-score 3.78
OE 0.24 (0.14–0.45)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.30Z-score
OE missense 0.79 (0.71–0.88)
248 obs / 312.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.24 (0.14–0.45)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.79 (0.71–0.88)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.04
0≤1.21.6
LoF obs/exp: 7 / 28.9Missense obs/exp: 248 / 312.8Syn Z: -0.35

ClinVar Variant Classifications

115 submitted variants in ClinVar

ClinVar

Classification Summary

Protein Context — Lollipop Plot

PACSIN2 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Reciprocal interactions among Cobll1, PACSIN2, and SH3BP1 regulate drug resistance in chronic myeloid leukemia.
Park K et al.·Cancer Med
2022
PACSIN2 rs2413739 influence on thiopurine pharmacokinetics: validation studies in pediatric patients.
Franca R et al.·Pharmacogenomics J
2020Clinical trial
PACSIN2-dependent apical endocytosis regulates the morphology of epithelial microvilli.
Postema MM et al.·Mol Biol Cell
2019
Proteome Analysis of Temporomandibular Joint with Disc Displacement.
Liu X et al.·J Dent Res
2022
Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals.
Eicher JD et al.·Am J Hum Genet
2016Meta-analysis
Childhood acute lymphoblastic leukemia mercaptopurine intolerance is associated with NUDT15 variants.
Wang DS et al.·Pediatr Res
2021
SLCO1B1 Polymorphisms are Associated With Drug Intolerance in Childhood Leukemia Maintenance Therapy.
Eldem İ et al.·J Pediatr Hematol Oncol
2018
A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases.
Rahman MH et al.·Int J Environ Res Public Health
2020
Genome-Wide Association Study of Osteoporosis Risk in Korean Pre-Menopausal Women: The Korean Genome and Epidemiology Study.
Kim SK et al.·Int J Mol Sci
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools