ODAPH

odontogenesis associated phosphoprotein

Basic information

Region (hg38): 4:75556048-75565871

Previous symbols: [ "C4orf26" ]

Links

ENSG00000174792NCBI:152816OMIM:614829HGNC:26300Uniprot:Q17RF5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • amelogenesis imperfecta type 2 (Supportive), mode of inheritance: AR
  • amelogenesis imperfecta hypomaturation type 2A4 (Moderate), mode of inheritance: AR
  • amelogenesis imperfecta hypomaturation type 2A4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Amelogenesis imperfecta, hypomaturation type, IIA4ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingDental22901946

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ODAPH gene.

  • ODAPH-related_disorder (6 variants)
  • Amelogenesis_imperfecta_hypomaturation_type_2A4 (5 variants)
  • not_provided (2 variants)
  • not_specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODAPH gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178497.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
3
missense
1
clinvar
1
clinvar
1
clinvar
3
nonsense
2
clinvar
1
clinvar
3
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
Total 3 4 1 3 1

Highest pathogenic variant AF is 0.0000607199

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ODAPHprotein_codingprotein_codingENST00000435974 39838
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.04960.703125729011257300.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.21510296.11.060.000005421134
Missense in Polyphen94.8651.849952
Synonymous-0.09833837.21.020.00000218351
Loss of Function0.65523.280.6101.40e-736

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May promote nucleation of hydroxyapatite. {ECO:0000269|PubMed:22901946}.;

Intolerance Scores

loftool
rvis_EVS
0.97
rvis_percentile_EVS
90.23

Haploinsufficiency Scores

pHI
0.207
hipred
N
hipred_score
0.123
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Odaph
Phenotype

Gene ontology

Biological process
positive regulation of biomineral tissue development;positive regulation of enamel mineralization
Cellular component
extracellular region
Molecular function
protein binding