LMF1

lipase maturation factor 1

Basic information

Region (hg38): 16:853634-981318

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

Links

ENSG00000103227NCBI:64788OMIM:611761HGNC:14154Uniprot:Q96S06AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Combined lipase deficiencyARCardiovascular; Endocrine; GastrointestinalIndividuals 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; Gastrointestinal17994020; 19820022

ClinVar

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

  • Cardiovascular_phenotype (502 variants)
  • not_provided (276 variants)
  • Lipase_deficiency,_combined (36 variants)
  • not_specified (33 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
204
clinvar
3
clinvar
208
missense
2
clinvar
285
clinvar
40
clinvar
7
clinvar
334
nonsense
5
clinvar
10
clinvar
1
clinvar
16
start loss
0
frameshift
6
clinvar
5
clinvar
11
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
1
clinvar
4
Total 12 19 288 244 10

Highest pathogenic variant AF is 0.000060750102

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LMF1protein_codingprotein_codingENST00000262301 11127685
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.14e-160.025112455301131246660.000453
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.794463511.270.00002253630
Missense in Polyphen170139.911.21511431
Synonymous-2.661941521.270.00001041140
Loss of Function0.4422527.50.9090.00000143259

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009020.000889
Ashkenazi Jewish0.000.00
East Asian0.0006710.000668
Finnish0.0001450.000139
European (Non-Finnish)0.0004510.000443
Middle Eastern0.0006710.000668
South Asian0.0006900.000686
Other0.0009060.000826

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

Haploinsufficiency Scores

pHI
0.107
hipred
N
hipred_score
0.229
ghis
0.477

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lmf1
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype;

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
Molecular function