PHF24

Chr 9

PHD finger protein 24

Also known as: GINIP

NCBI Gene: 23349 ENSG00000122733 UniProt: Q9UPV7 OMIM: 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.

OMIM ResearchSummary from RefSeq

Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Clinical highlights

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

0.56

LOEUF

GOF

Mechanism· predicted

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 OE?0.28 (0.15–0.56)

0≤0.351.4

Missense OE?0.88 (0.79–0.98)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 6 / 21.1Missense obs/exp: 231 / 264.0Syn Z: 0.19

Background carrier burden — how many people carry a rare variant somewhere in PHF24?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 100

500 rare PASS variants

Rare truncating (LoF)

1 in 6,200

42 rare PASS variants

Rare synonymous (reference)

1 in 270

195 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PHF24. 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 6,300
South Asian	~43k	1 in 110	≈ 1 in 11,000
Remaining (unassigned)	~30k	1 in 100	1 in 870
European (Finnish)	~27k	1 in 190	≈ 1 in 13,000
Admixed American	~22k	1 in 110	≈ 1 in 11,000
African / African American	~21k	1 in 110	≈ 1 in 17,000
East Asian	~20k	1 in 120	≈ 1 in 5,000
Ashkenazi Jewish	~13k	1 in 450	none seen
Middle Eastern	~2,884	1 in 56	≈ 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): All 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓