AMELY

amelogenin Y-linked

Basic information

Region (hg38): Y:6865917-6911752

Previous symbols: [ "AMGL" ]

Links

ENSG00000099721

∙ NCBI:266 ∙ OMIM:410000 ∙ HGNC:462 ∙ Uniprot:Q99218 ∙ 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 AMELY gene.

Male infertility (1 variants)

Variants pathogenicity by type

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

Variants in AMELY

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

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

Position	Type	Phenotype	Significance	ClinVar
Y-6866079-C-T		Male infertility	Uncertain significance (-)	978002

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMELY	protein_coding	protein_coding	ENST00000215479	5	8110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000837	0.190	67818	17	0	67835	0.000125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.126	33	31.0	1.06	0.00000455	1249
Missense in Polyphen		9	10.075	0.89331		417
Synonymous	-0.364	13	11.4	1.14	0.00000169	388
Loss of Function	-1.12	5	2.94	1.70	3.97e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000463	0.000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000630	0.0000314
Middle Eastern	0.00	0.00
South Asian	0.00115	0.000569
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role in biomineralization. Seems to regulate the formation of crystallites during the secretory stage of tooth enamel development. Thought to play a major role in the structural organization and mineralization of developing enamel.;

Haploinsufficiency Scores

pHI: 0.142
hipred: N
hipred_score: 0.166
ghis: 0.401

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.00515

Gene Damage Prediction

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

Gene ontology

Biological process: biomineral tissue development
Cellular component: collagen-containing extracellular matrix
Molecular function: structural constituent of tooth enamel