ODAPH

Chr 4AR

odontogenesis associated phosphoprotein

Also known as: AI2A4, C4orf26

NCBI Gene: 152816ENSG00000174792UniProt: Q17RF5OMIM: 614829

ODAPH encodes an extracellular matrix acidic phosphoprotein that promotes nucleation of hydroxyapatite during enamel mineralization. Mutations cause autosomal recessive amelogenesis imperfecta type IIA4, characterized by hypomineralized tooth enamel. The gene shows low constraint to loss-of-function variants (pLI 0.05, LOEUF 1.67), consistent with its recessive inheritance pattern and primary effect on dental development rather than essential cellular functions.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.671 OMIM phenotype
Clinical Summary— ODAPH
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.05) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
30 unique Pathogenic / Likely Pathogenic· 7 VUS of 54 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
1.67LOEUF
pLI 0.050
Z-score 0.66
OE 0.61 (0.24–1.67)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.21Z-score
OE missense 1.06 (0.90–1.25)
102 obs / 96.1 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.61 (0.24–1.67)
0≤0.351.4
Missense OE1.06 (0.90–1.25)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 2 / 3.3Missense obs/exp: 102 / 96.1Syn Z: -0.10
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateODAPH-related amyelogenesis imperfectaLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.84top 10%
GOF
0.4283th %ile
LOF
0.1697th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

54 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic26
Likely Pathogenic4
VUS7
Likely Benign5
Benign8
26
Pathogenic
4
Likely Pathogenic
7
VUS
5
Likely Benign
8
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
0
23
0
26
Likely Pathogenic
4
0
0
0
4
VUS
0
1
6
0
7
Likely Benign
0
2
1
2
5
Benign
0
3
5
0
8
Total7635250

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

View in ClinVar →

Protein Context — Lollipop Plot

ODAPH · 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 3 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