PHF24

Chr 9

PHD finger protein 24

Also known as: GINIP

NCBI Gene: 23349ENSG00000122733UniProt: Q9UPV7OMIM: 619928

PHF24 encodes a transcriptional corepressor that negatively regulates gene transcription and is predicted to be involved in GABAergic synaptic transmission and pain perception pathways. The gene is highly constrained against loss-of-function variants (LOEUF 0.56), but no definitive human disease associations have been established for PHF24 mutations. Additional clinical and molecular studies are needed to determine the inheritance pattern and phenotypic spectrum associated with this gene.

OMIMResearchSummary from RefSeq
GOFmechanismLOEUF 0.56
Clinical Summary— PHF24
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.28) despite low pLI — interpret in context.
📋
ClinVar Variants
71 unique Pathogenic / Likely Pathogenic· 281 VUS of 396 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.56LOEUF
pLI 0.070
Z-score 3.05
OE 0.28 (0.15–0.56)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.72Z-score
OE missense 0.88 (0.79–0.98)
231 obs / 264.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.28 (0.15–0.56)
0≤0.351.4
Missense OE0.88 (0.79–0.98)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 6 / 21.1Missense obs/exp: 231 / 264.0Syn Z: 0.19
DN
0.4289th %ile
GOF
0.6444th %ile
LOF
0.4233th %ile

The highest-scoring mechanism for this gene is gain-of-function.

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

396 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic63
Likely Pathogenic8
VUS281
Likely Benign29
Benign9
63
Pathogenic
8
Likely Pathogenic
281
VUS
29
Likely Benign
9
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
63
0
63
Likely Pathogenic
0
0
8
0
8
VUS
0
269
12
0
281
Likely Benign
0
24
2
3
29
Benign
0
8
0
1
9
Total0301854390

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

View in ClinVar →

Protein Context — Lollipop Plot

PHF24 · 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