ODAM

odontogenic, ameloblast associated

Basic information

Region (hg38): 4:70195725-70204576

Links

ENSG00000109205 ∙ NCBI:54959 ∙ OMIM:614843 ∙ HGNC:26043 ∙ Uniprot:A1E959 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODAM 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
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	13	0	2

Variants in ODAM

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

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

Position	Type	Phenotype	Significance	ClinVar
4-70196539-C-T			Benign (Nov 16, 2021)
4-70196591-C-A			Benign (Nov 16, 2021)
4-70197293-A-G		not specified	Uncertain significance (Nov 13, 2023)
4-70197934-A-G		not specified	Uncertain significance (Oct 07, 2022)
4-70198084-A-G		not specified	Uncertain significance (Jan 09, 2024)
4-70198111-C-A		not specified	Uncertain significance (Jun 13, 2024)
4-70200499-G-A		not specified	Uncertain significance (Nov 07, 2023)
4-70200504-A-G		not specified	Uncertain significance (Apr 12, 2024)
4-70200521-A-G		not specified	Uncertain significance (Oct 26, 2021)
4-70200569-C-A		not specified	Uncertain significance (Nov 05, 2021)
4-70201464-A-C		not specified	Uncertain significance (Mar 23, 2022)
4-70202278-G-C		not specified	Uncertain significance (Dec 08, 2023)
4-70202303-G-C		not specified	Uncertain significance (Jun 06, 2023)
4-70202765-G-A		not specified	Uncertain significance (Dec 03, 2021)
4-70202789-G-A		not specified	Uncertain significance (Jun 26, 2023)
4-70202876-G-T		not specified	Uncertain significance (Jan 02, 2024)
4-70202895-C-A		not specified	Uncertain significance (Dec 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODAM	protein_coding	protein_coding	ENST00000396094	10	8081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-15	0.00670	125570	0	102	125672	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.470	154	138	1.11	0.00000622	1792
Missense in Polyphen		39	31.511	1.2377		365
Synonymous	-1.06	56	46.7	1.20	0.00000215	533
Loss of Function	-0.264	22	20.7	1.06	9.82e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00187	0.00186
Ashkenazi Jewish	0.00	0.00
East Asian	0.00207	0.00202
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000206	0.000202
Middle Eastern	0.00207	0.00202
South Asian	0.0000662	0.0000653
Other	0.000340	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tooth-associated epithelia protein that probably plays a role in odontogenesis, the complex process that results in the initiation and generation of the tooth. May be incorporated in the enamel matrix at the end of mineralization process. Involved in the induction of RHOA activity via interaction with ARHGEF and expression of downstream factors such as ROCK. Plays a role in attachment of the junctional epithelium to the tooth surface. {ECO:0000269|PubMed:25911094}.

Intolerance Scores

• loftool: 0.841
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.0980
• hipred: N
• hipred_score: 0.123
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.292

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Odam

Gene ontology

• Biological process: positive regulation of protein phosphorylation;inflammatory response;positive regulation of gene expression;biomineral tissue development;regulation of actin cytoskeleton organization;odontogenesis of dentin-containing tooth;positive regulation of GTPase activity;cellular protein metabolic process;positive regulation of epithelial cell proliferation involved in wound healing
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;cell periphery;supramolecular fiber
• Molecular function: protein binding