AGMO

alkylglycerol monooxygenase, the group of Fatty acid hydroxylase domain containing

Basic information

Region (hg38): 7:15200317-15562015

Previous symbols: [ "TMEM195" ]

Links

ENSG00000187546 ∙ NCBI:392636 ∙ OMIM:613738 ∙ HGNC:33784 ∙ Uniprot:Q6ZNB7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

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

• not_specified (91 variants)
• not_provided (31 variants)
• AGMO-related_disorder (14 variants)
• AGMO-related_Neurodevelopmental_disorder (2 variants)
• See_cases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGMO gene is commonly pathogenic or not. These statistics are base on transcript: NM_001004320.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	2	4
missense			93	8	6	107
nonsense			3			3
start loss						0
frameshift	1	1	5		1	8
splice donor/acceptor (+/-2bp)		1	2			3
Total	1	2	103	10	9

Highest pathogenic variant AF is 0.0000316848

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGMO	protein_coding	protein_coding	ENST00000342526	13	361698

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.78e-26	0.0000140	124212	9	1526	125747	0.00612

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.56	339	230	1.48	0.0000111	2889
Missense in Polyphen		86	67.856	1.2674		835
Synonymous	-3.33	116	78.4	1.48	0.00000376	836
Loss of Function	-1.37	34	26.4	1.29	0.00000127	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00756	0.00754
Ashkenazi Jewish	0.0105	0.0106
East Asian	0.00120	0.00120
Finnish	0.0175	0.0175
European (Non-Finnish)	0.00678	0.00672
Middle Eastern	0.00120	0.00120
South Asian	0.00155	0.00154
Other	0.00776	0.00719

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glyceryl-ether monooxygenase that cleaves the O-alkyl bond of ether lipids. Ether lipids are essential components of brain membranes. {ECO:0000269|PubMed:20643956}.
• Pathway: Metabolism of lipids;Metabolism;Triglyceride biosynthesis;Triglyceride metabolism (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.45

Haploinsufficiency Scores

• pHI: 0.0571
• hipred: N
• hipred_score: 0.229
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Agmo

Gene ontology

• Biological process: membrane lipid metabolic process;triglyceride biosynthetic process;ether lipid metabolic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: iron ion binding;glyceryl-ether monooxygenase activity