PHF3

Chr 6

PHD finger protein 3

NCBI Gene: 23469ENSG00000118482UniProt: Q92576
581
ClinVar variants
77
Pathogenic / LP
0.99
pLI score· haploinsufficient
1
Active trials
Clinical Summary— PHF3
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
77 Pathogenic / Likely Pathogenic· 332 VUS of 581 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.29LOEUF
pLI 0.993
Z-score 6.78
OE 0.19 (0.12–0.29)
Highly constrained

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

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.76Z-score
OE missense 0.93 (0.89–0.98)
972 obs / 1040.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.19 (0.12–0.29)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.93 (0.89–0.98)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.07
0≤1.21.6
LoF obs/exp: 15 / 80.8Missense obs/exp: 972 / 1040.6Syn Z: -1.04

ClinVar Variant Classifications

581 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic47
Likely Pathogenic30
VUS332
Likely Benign153
Benign9
Conflicting10
47
Pathogenic
30
Likely Pathogenic
332
VUS
153
Likely Benign
9
Benign
10
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
28
0
19
0
47
Likely Pathogenic
23
2
5
0
30
VUS
6
319
6
1
332
Likely Benign
0
26
12
115
153
Benign
0
5
2
2
9
Conflicting
—10
Total5735244118581

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

View in ClinVar →

Protein Context — Lollipop Plot

PHF3 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Polyacylated Delphinidin Biosynthesis Catalysed by PhF3'5'H-PhBGLU12-PhSCPL2 Determines the Blue Pigmentation in Cineraria (Pericallis hybrida).
Cui Y et al.·Plant Biotechnol J
2025🔓 Open Access
Lnc-PHF3-3 aggravates the chemoresistance of osteosarcoma cells to doxorubicin via the miR-142-3p/HMGB1 axis.
Zhou J et al.·Transl Oncol
2025🔓 Open Access
The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.
Benedum J et al.·Nat Commun
2023🔓 Open Access
PhCHS5 and PhF3'5'H Genes Over-Expression in Petunia (Petunia hybrida) and Phalaenopsis (Phalaenopsis aphrodite) Regulate Flower Color and Branch Number.
Lou Y et al.·Plants (Basel)
2023🔓 Open Access
PHF3 Technique: A Pyramid Hybrid Feature Fusion Framework for Severity Classification of Ulcerative Colitis Using Endoscopic Images.
Qi J et al.·Bioengineering (Basel)
2022🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
16P11.2 Deletion Syndrome16p11.2 Duplications1Q21.1 Deletion

Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight

RECRUITING
NCT01238250Simons SearchlightStarted 2010-10

External Resources

Links to major genomics databases and tools