AMELY

protein-coding

amelogenin Y-linked

Gene summary

This gene encodes a member of the amelogenin family of extracellular matrix proteins. Amelogenins are involved in biomineralization during tooth enamel development. Mutations in a related gene on chromosome X cause X-linked amelogenesis imperfecta. [provided by RefSeq, Jul 2008]

Previous symbols:

AMGL

MANE transcript

NM_001143.2

Inheritance

—

ClinVar variants

U:3

Top phenotype

Male infertility

gnomAD constraint

pLI —, LoF o/e 1.7

Max pathogenic AF

—

Genomic locus

chrY:6,865,918-6,911,752

External References & Databases

Ensembl (ENSG00000099721)

Transcript & Mutation Effects

hg38 • Region Span ~45.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AMELY variants in ClinVar

1 Conditions Cataloged

Male infertilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001143.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

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

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001143.2	RefSeq	NP_001134.1	5	MANE Select
ENST00000651267.2	Ensembl	ENSP00000498344.1	5	MANE Select
NM_001364814.1	RefSeq	NP_001351743.1	6	Standard
ENST00000383036.1	Ensembl	ENSP00000372505.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biomineral tissue development

Molecular Function

structural constituent of tooth enamel

Cellular Component

collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000215479
Coding exons: 5
Length: 8110
Individuals with no LoFs: 67818
Homozygous LoFs: 17
Heterozygous LoFs: 0
Defined: 67835
p: 0.000125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.126	33	31.0	1.06	0.00000455	1249
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00016	rare
Latino/Admixed American	0.00014	0.000070	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000031	rare
South Asian	0.0011	0.00057	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.00515

Gene Damage Prediction

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