MBOAT7

membrane bound O-acyltransferase domain containing 7, the group of Membrane bound O-acyltransferase family

Basic information

Region (hg38): 19:54173412-54189882

Previous symbols: [ "LENG4" ]

Links

ENSG00000125505 ∙ NCBI:79143 ∙ OMIM:606048 ∙ HGNC:15505 ∙ Uniprot:Q96N66 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal recessive 57 (Moderate), mode of inheritance: AR
• intellectual disability, autosomal recessive 57 (Strong), mode of inheritance: AR
• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual disability, autosomal recessive 57 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 57	AR	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	Neurologic	27616480

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MBOAT7 gene.

• not provided (4 variants)
• Intellectual disability, autosomal recessive 57 (3 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBOAT7 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	12	1	14
missense			66	3		69
nonsense	1	4				5
start loss			2			2
frameshift	5	3	4			12
inframe indel	1		2			3
splice donor/acceptor (+/-2bp)		1				1
splice region			1	3		4
non coding			1			1
Total	7	8	76	15	1

Highest pathogenic variant AF is 0.00000711

Variants in MBOAT7

This is a list of pathogenic ClinVar variants found in the MBOAT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54174048-T-C		Inborn genetic diseases	Uncertain significance (Mar 17, 2023)
19-54174055-G-A		Inborn genetic diseases	Uncertain significance (Mar 04, 2024)
19-54174059-C-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
19-54174060-T-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
19-54174061-T-G		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
19-54174063-T-C		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
19-54174063-T-TC			Uncertain significance (Jun 20, 2019)
19-54174080-GGGCTGGGATGCTGCCTTCCGCC-G		Intellectual disability, autosomal recessive 57	Uncertain significance (Apr 14, 2020)
19-54174091-C-A		Inborn genetic diseases	Uncertain significance (May 04, 2022)
19-54174097-T-C		Intellectual disability, autosomal recessive 57 • Inborn genetic diseases	Uncertain significance (Jan 08, 2021)
19-54174099-C-T			Benign/Likely benign (Jul 01, 2024)
19-54174100-G-A		Inborn genetic diseases	Uncertain significance (May 10, 2022)
19-54174102-C-T			Uncertain significance (Jul 01, 2023)
19-54174107-G-GGGGCTGCCCCCACCTAAAGCCAGCCCCAGCCCCA			Uncertain significance (Mar 26, 2021)
19-54174113-G-T			Likely benign (Jun 01, 2022)
19-54174126-G-GCCAGCC			Uncertain significance (Jan 01, 2019)
19-54174138-C-A		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
19-54174170-G-T		Inborn genetic diseases	Uncertain significance (Nov 19, 2022)
19-54174173-G-T		Intellectual disability, autosomal recessive 57	Likely pathogenic (-)
19-54174203-G-A			Benign (Nov 16, 2018)
19-54174220-C-T		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
19-54174234-A-G		Intellectual disability, autosomal recessive 57	Uncertain significance (Feb 26, 2018)
19-54174243-T-C		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
19-54174247-C-A		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
19-54174249-C-T		Inborn genetic diseases	Uncertain significance (Mar 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBOAT7	protein_coding	protein_coding	ENST00000245615	7	16627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.113	0.886	125731	0	15	125746	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.441	274	295	0.928	0.0000203	2959
Missense in Polyphen		74	92.4	0.80087		959
Synonymous	-1.51	156	134	1.17	0.00000949	1020
Loss of Function	2.85	5	18.1	0.276	8.58e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000513	0.0000462
European (Non-Finnish)	0.0000484	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyltransferase which contributes to the regulation of free arachidonic acid (AA) in the cell through the remodeling of phospholipids. Mediates the conversion of lysophosphatidylinositol (1-acylglycerophosphatidylinositol or LPI) into phosphatidylinositol (1,2-diacyl-sn-glycero-3-phosphoinositol or PI) (LPIAT activity). Prefers arachidonoyl-CoA as the acyl donor. Lysophospholipid acyltransferases (LPLATs) catalyze the reacylation step of the phospholipid remodeling pathway also known as the Lands cycle. Required for cortical lamination during brain development (By similarity). {ECO:0000250|UniProtKB:Q8CHK3, ECO:0000269|PubMed:18094042, ECO:0000269|PubMed:18772128}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Acyl chain remodelling of PI;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.690
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.267
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mboat7
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: phospholipid biosynthetic process;ventricular system development;layer formation in cerebral cortex;phosphatidylinositol acyl-chain remodeling
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane
• Molecular function: 1-acylglycerol-3-phosphate O-acyltransferase activity;protein binding;2-acylglycerol-3-phosphate O-acyltransferase activity;lysophospholipid acyltransferase activity