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 and phosphatidylinositol phosphate biosynthetic process. Acts upstream of or within lysosome organization. Located in Golgi membrane. Is active in cytoplasmic side of trans-Golgi network membrane. Implicated in autosomal dominant nonsyndromic deafness 87. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Deafness, autosomal dominant 87MIM #620281

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Deafness, autosomal dominant 87; no ClinGen or GenCC tier

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.34

LOEUF· LoF intol.

LOF

Mechanism· predicted

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

Background carrier burden — how many people carry a rare variant somewhere in PI4KB?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 89

774 rare PASS variants

Rare truncating (LoF)

1 in 2,300

79 rare PASS variants

Rare synonymous (reference)

1 in 120

408 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PI4KB. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 120	1 in 2,000
South Asian	~43k	1 in 110	1 in 2,600
Remaining (unassigned)	~30k	1 in 69	1 in 1,600
European (Finnish)	~27k	1 in 320	1 in 5,300
Admixed American	~22k	1 in 96	≈ 1 in 7,400
African / African American	~21k	1 in 120	≈ 1 in 4,200
East Asian	~20k	1 in 130	1 in 2,200
Ashkenazi Jewish	~13k	1 in 210	none seen
Middle Eastern	~2,884	1 in 94	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 10 of 11 coding exons well covered in gnomAD exomes; exon 3 marginal. Genomes: all 11.? see exons ↓