LMF1

lipase maturation factor 1

Basic information

Region (hg38): 16:853634-981318

Previous symbols: [ "C16orf26", "TMEM112" ]

Links

ENSG00000103227 ∙ NCBI:64788 ∙ OMIM:611761 ∙ HGNC:14154 ∙ Uniprot:Q96S06 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 18.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000262301.16	ENSP00000262301.12	11	yes	-
ENST00000543238.5	ENSP00000437418.1	7	-	-
ENST00000545827.6	ENSP00000443820.2	3	-	-
ENST00000562226.5	ENSP00000455833.1	4	-	-

Phenotypes

GenCC

Source: genCC

• lipase deficiency, combined (Moderate), mode of inheritance: AR
• lipase deficiency, combined (Strong), mode of inheritance: AR
• lipase deficiency, combined (Strong), mode of inheritance: AR
• lipase deficiency, combined (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined lipase deficiency	AR	Cardiovascular; Endocrine; Gastrointestinal	Individuals may present with severe hypertryglceridemia, with findings including gastrointestinal manifestations (abdominal pain, emesis, recurrent pancreatitis, hepatosplenomegaly), as well as eruptive xanthomata and lipemia retinalis, and dietary measures (fat restriction) and medical treatment (eg, gemfibrozil, omega-3 fatty acid supplementation) can be beneficial; Individuals may also manifest with diabetes mellitus, which can benefit from standard treatment (and which may also help with other manifestations)	Cardiovascular; Endocrine; Gastrointestinal	17994020; 19820022

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMF1 gene.

• Cardiovascular_phenotype (521 variants)
• not_provided (323 variants)
• Lipase_deficiency,_combined (36 variants)
• not_specified (34 variants)
• LMF1-related_disorder (31 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022773.4. 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			4	218	2	224
missense		3	300	42	6	351
nonsense	6	10	1			17
start loss						0
frameshift	7	5				12
splice donor/acceptor (+/-2bp)	1	2	3			6
Total	14	20	308	260	8

Highest pathogenic variant AF is 0.000060750102

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMF1	protein_coding	protein_coding	ENST00000262301	11	127685

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124553	0	113	124666	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.79	446	351	1.27	0.0000225	3630
Missense in Polyphen		170	139.91	1.2151		1431
Synonymous	-2.66	194	152	1.27	0.0000104	1140
Loss of Function	0.442	25	27.5	0.909	0.00000143	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000902	0.000889
Ashkenazi Jewish	0.00	0.00
East Asian	0.000671	0.000668
Finnish	0.000145	0.000139
European (Non-Finnish)	0.000451	0.000443
Middle Eastern	0.000671	0.000668
South Asian	0.000690	0.000686
Other	0.000906	0.000826

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maturation of specific proteins in the endoplasmic reticulum. Required for maturation and transport of active lipoprotein lipase (LPL) through the secretory pathway. Each LMF1 molecule chaperones 50 or more molecules of LPL. {ECO:0000250|UniProtKB:Q3U3R4, ECO:0000269|PubMed:24909692}.
• Disease: DISEASE: Combined lipase deficiency (CLD) [MIM:246650]: Characterized by repeated episodes of pancreatitis, tuberous xanthomas and lipodystrophy and is caused by deficiency of both lipoprotein lipase (LPL) and hepatic triglyceride lipase (HTGL). {ECO:0000269|PubMed:17994020}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Transport of small molecules;Assembly of active LPL and LIPC lipase complexes;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.865
• rvis_EVS: 1.23
• rvis_percentile_EVS: 93.26

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.444

Gene Damage Prediction

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

Gene ontology

• Biological process: triglyceride metabolic process;endoplasmic reticulum to Golgi vesicle-mediated transport;protein secretion;protein glycosylation in Golgi;chylomicron remnant clearance;regulation of lipoprotein lipase activity;positive regulation of lipoprotein lipase activity;protein maturation;regulation of cholesterol metabolic process;regulation of triglyceride metabolic process
• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane