AGMO

alkylglycerol monooxygenase, the group of Fatty acid hydroxylase domain containing

Basic information

Region (hg38): 7:15200316-15562015

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.

• Inborn genetic diseases (28 variants)
• not provided (20 variants)
• not specified (9 variants)
• AGMO-related condition (2 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.

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	3	4
missense			37	3	4	44
nonsense			2			2
start loss						0
frameshift			2		1	3
inframe indel			2			2
splice donor/acceptor (+/-2bp)		1	1			2
splice region			1			1
non coding						0
Total	0	1	44	4	8

Highest pathogenic variant AF is 0.0000197

Variants in AGMO

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

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

Position	Type	Phenotype	Significance	ClinVar
7-15201295-G-C		not specified	Uncertain significance (Sep 22, 2023)
7-15201316-A-G		not specified	Uncertain significance (Sep 16, 2021)
7-15201347-T-C		not specified	Uncertain significance (Nov 22, 2022)
7-15365505-AT-A		not specified • AGMO-related disorder	Conflicting classifications of pathogenicity (Jul 01, 2019)
7-15365512-A-AC		not specified	Uncertain significance (Jul 27, 2020)
7-15365519-A-C		not specified	Uncertain significance (Oct 10, 2023)
7-15365543-G-T		AGMO-related disorder	Uncertain significance (Jul 17, 2023)
7-15365553-G-A		AGMO-related disorder	Likely benign (Jul 12, 2019)
7-15365556-A-C			Benign (Dec 31, 2019)
7-15365563-C-T		not specified	Likely benign (Dec 07, 2017)
7-15365564-G-A			Conflicting classifications of pathogenicity (Aug 01, 2023)
7-15365590-C-T		not specified	Uncertain significance (Jan 02, 2024)
7-15365594-G-C		AGMO-related disorder	Benign (May 03, 2019)
7-15365596-G-C		AGMO-related disorder	Likely benign (May 10, 2022)
7-15366150-G-C		not specified	Uncertain significance (Dec 12, 2023)
7-15366160-A-C		not specified	Uncertain significance (Dec 27, 2023)
7-15366181-A-C		not specified	Uncertain significance (Mar 13, 2023)
7-15366196-CAGA-C		AGMO-related Neurodevelopmental disorder	Uncertain significance (Dec 19, 2021)
7-15366201-G-A		not specified	Uncertain significance (Oct 06, 2022)
7-15385436-T-C		AGMO-related disorder	Likely benign (May 30, 2019)
7-15385466-C-T		not specified	Uncertain significance (Sep 07, 2022)
7-15385471-T-C			Uncertain significance (Oct 21, 2021)
7-15385499-C-T		not specified	Uncertain significance (Dec 06, 2021)
7-15385502-CTG-C			Uncertain significance (Feb 08, 2023)
7-15385508-A-G		not specified	Uncertain significance (Dec 18, 2023)

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