PIP5KL1

Chr 9

phosphatidylinositol-4-phosphate 5-kinase like 1

Also known as: PIPKH

NCBI Gene: 138429ENSG00000167103UniProt: Q5T9C9OMIM: 612865

The protein acts as a scaffold to localize and regulate type I PI(4)P 5-kinases to specific cellular compartments, where they generate PI(4,5)P2 for actin nucleation, signaling and scaffold protein recruitment. PIP5KL1 mutations cause disease through a predicted gain-of-function mechanism, though the specific associated disorder and inheritance pattern are not provided in the available data.

OMIMResearchSummary from RefSeq, UniProt, Mechanism
MultiplemechanismLOEUF 0.95
Clinical Summary— PIP5KL1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
42 unique Pathogenic / Likely Pathogenic· 57 VUS of 110 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.95LOEUF
pLI 0.000
Z-score 1.73
OE 0.56 (0.34–0.95)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.79Z-score
OE missense 0.85 (0.76–0.96)
194 obs / 227.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.56 (0.34–0.95)
0≤0.351.4
Missense OE0.85 (0.76–0.96)
0≤0.61.4
Synonymous OE0.84
0≤1.21.6
LoF obs/exp: 10 / 17.9Missense obs/exp: 194 / 227.4Syn Z: 1.25
DN
0.6550th %ile
GOF
0.6443th %ile
LOF
0.2678th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

110 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic41
Likely Pathogenic1
VUS57
Likely Benign2
41
Pathogenic
1
Likely Pathogenic
57
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
41
0
41
Likely Pathogenic
0
0
1
0
1
VUS
0
55
2
0
57
Likely Benign
0
2
0
0
2
Benign
0
0
0
0
0
Total057440101

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

View in ClinVar →

Protein Context — Lollipop Plot

PIP5KL1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients