ODAPH

odontogenesis associated phosphoprotein

Basic information

Region (hg38): 4:75556048-75565871

Previous symbols: [ "C4orf26" ]

Links

ENSG00000174792 ∙ NCBI:152816 ∙ OMIM:614829 ∙ HGNC:26300 ∙ Uniprot:Q17RF5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, hypomaturation type, IIA4	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dental	22901946

ClinVar

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

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	1		2
missense				1	3	4
nonsense		1				1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	3	5
Total	0	2	1	4	6

Variants in ODAPH

This is a list of pathogenic ClinVar variants found in the ODAPH region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-75556133-GGTAAC-ATGCTGGTTACTGGTA		Amelogenesis imperfecta hypomaturation type 2A4 • ODAPH-related disorder	Likely pathogenic (Jan 23, 2023)
4-75556136-A-T		ODAPH-related disorder	Likely benign (Jul 18, 2023)
4-75556287-A-G			Benign (Jun 18, 2021)
4-75556365-A-C			Benign (Jun 18, 2021)
4-75556418-A-C			Benign (Jun 18, 2021)
4-75556594-T-G		ODAPH-related disorder	Likely benign (Mar 30, 2020)
4-75564112-A-G		ODAPH-related disorder	Likely pathogenic (Jun 25, 2024)
4-75564112-A-T		Amelogenesis imperfecta hypomaturation type 2A4	Pathogenic (Sep 07, 2012)
4-75564135-C-T		not specified	Benign (Nov 10, 2018)
4-75564164-G-T		ODAPH-related disorder	Likely benign (May 31, 2022)
4-75564175-C-A		Amelogenesis imperfecta hypomaturation type 2A4	Pathogenic (Sep 07, 2012)
4-75564238-C-T		not specified	Uncertain significance (Sep 01, 2021)
4-75564275-C-T		Amelogenesis imperfecta hypomaturation type 2A4	Pathogenic (Apr 17, 2023)
4-75564323-T-C			Benign (Dec 31, 2019)
4-75564364-G-A		Amelogenesis imperfecta hypomaturation type 2A4 • ODAPH-related disorder	Likely pathogenic (Sep 02, 2022)
4-75564372-G-A			Benign (Nov 10, 2018)
4-75564512-C-T		ODAPH-related disorder	Likely benign (Jan 20, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODAPH	protein_coding	protein_coding	ENST00000435974	3	9838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0496	0.703	125729	0	1	125730	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.215	102	96.1	1.06	0.00000542	1134
Missense in Polyphen		9	4.865	1.8499		52
Synonymous	-0.0983	38	37.2	1.02	0.00000218	351
Loss of Function	0.655	2	3.28	0.610	1.40e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.23

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Odaph

Gene ontology

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