AMTN

amelotin

Basic information

Region (hg38): 4:70518569-70532743

Links

ENSG00000187689

∙ NCBI:401138 ∙ OMIM:610912 ∙ HGNC:33188 ∙ Uniprot:Q6UX39 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

amelogenesis imperfecta, type 3A (Supportive), mode of inheritance: AD
amelogenesis imperfecta type 3B (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, type IIIB	AD	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	27412008

ClinVar

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

not_specified (18 variants)
AMTN-related_disorder (4 variants)
not_provided (1 variants)
Amelogenesis_imperfecta,_type_3A (1 variants)
Amelogenesis_imperfecta_type_3B (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMTN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000212557.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar					1
missense			17 clinvar	3 clinvar	2 clinvar	22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	17	3	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMTN	protein_coding	protein_coding	ENST00000339336	8	14203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.13e-11	0.0215	125714	0	16	125730	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.380	99	110	0.898	0.00000539	1301
Missense in Polyphen		20	20.657	0.96818		260
Synonymous	-0.489	48	43.9	1.09	0.00000226	453
Loss of Function	-0.704	14	11.4	1.22	4.85e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Is a promoter of calcium phosphate mineralization, playing a critical role in the formation of the compact, mineralized, aprismatic enamel surface layer during the maturation stage of amelogenesis. {ECO:0000269|PubMed:25407797}.;
Disease: DISEASE: Amelogenesis imperfecta 3B (AI3B) [MIM:617607]: An autosomal dominant form of amelogenesis imperfecta, a defect of enamel formation. AI3B is characterized by hypomineralized enamel that has reduced tickness and exhibits structural defects. {ECO:0000269|PubMed:27412008}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

pRec: 0.0547

Intolerance Scores

loftool: 0.763
rvis_EVS: 1.3
rvis_percentile_EVS: 93.95

Haploinsufficiency Scores

pHI: 0.0448
hipred: N
hipred_score: 0.123
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0517

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Amtn
Phenotype: skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype;

Gene ontology

Biological process: cell adhesion;biomineral tissue development;odontogenesis of dentin-containing tooth;post-translational protein modification;cellular protein metabolic process;positive regulation of biomineral tissue development;positive regulation of enamel mineralization
Cellular component: basement membrane;endoplasmic reticulum lumen;cell-cell junction;extracellular matrix
Molecular function: molecular_function;protein binding