PI4KB

Chr 1AD

phosphatidylinositol 4-kinase beta

Also known as: DFNA87, NPIK, PI4K-BETA, PI4K92, PI4KBETA, PI4KIII, PI4KIIIBETA, PIK4CB

NCBI Gene: 5298 ENSG00000143393 UniProt: Q9UBF8 OMIM: 602758

Enables 1-phosphatidylinositol 4-kinase activity and 14-3-3 protein binding activity. Involved in inner ear development. Acts upstream of or within lysosome organization. Located in Golgi membrane. Implicated in autosomal dominant nonsyndromic deafness 87. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismADLOEUF 0.341 OMIM phenotype

Clinical Summary— PI4KB

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.87) — some intolerance to loss-of-function variants.

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ClinVar Variants

4 unique Pathogenic / Likely Pathogenic· 65 VUS of 97 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.34LOEUF

pLI 0.866

Z-score 4.85

OE 0.19 (0.11–0.34)

Highly constrained

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

Missense Constraint?

3.55Z-score

OE missense 0.55 (0.49–0.61)

268 obs / 489.0 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.19 (0.11–0.34)

0≤0.351.4

Missense OE?0.55 (0.49–0.61)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 8 / 41.8Missense obs/exp: 268 / 489.0Syn Z: 0.47

This gene — mechanism propensity

0.4487th %ile

GOF

0.5464th %ile

LOF

0.66top 25%

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

LOFprediction above median · LOEUF 0.34

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

97 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4

VUS65

Likely Benign3

Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	4	0	4
Likely Pathogenic	0	0	0
VUS	65	0	65
Likely Benign	0	3	3
Benign	0	0	0
Total	69	3	72

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

View in ClinVar →

14 pathogenic / likely-pathogenic (of 19) ClinVar copy-number / structural variants overlap PI4KB — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →