LMF2

lipase maturation factor 2

Basic information

Region (hg38): 22:50502949-50507702

Previous symbols: [ "TMEM153", "TMEM112B" ]

Links

ENSG00000100258 ∙ NCBI:91289 ∙ ∙ HGNC:25096 ∙ Uniprot:Q9BU23 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMF2 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				4		4
missense			84	8		92
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	84	12	0

Variants in LMF2

This is a list of pathogenic ClinVar variants found in the LMF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50503395-T-C		not specified	Uncertain significance (Sep 28, 2022)
22-50503399-T-G		not specified	Uncertain significance (Nov 30, 2022)
22-50503401-C-T		not specified	Uncertain significance (Apr 27, 2023)
22-50503405-G-A		not specified	Uncertain significance (May 16, 2022)
22-50503407-G-T		not specified	Uncertain significance (May 16, 2022)
22-50503411-T-G		not specified	Uncertain significance (Jan 23, 2023)
22-50503423-T-C		not specified	Uncertain significance (Mar 02, 2023)
22-50503444-C-T		not specified	Uncertain significance (Aug 02, 2023)
22-50503468-C-T		not specified	Uncertain significance (Mar 16, 2022)
22-50503488-G-A		not specified	Uncertain significance (Aug 16, 2022)
22-50503494-C-A		not specified	Uncertain significance (Sep 27, 2021)
22-50503500-T-C		not specified	Uncertain significance (May 18, 2022)
22-50503504-C-T		not specified	Uncertain significance (Jun 02, 2023)
22-50503512-G-A		not specified	Likely benign (Feb 12, 2024)
22-50503521-G-A		not specified	Uncertain significance (Oct 12, 2022)
22-50503530-C-T		not specified	Likely benign (Aug 05, 2023)
22-50503575-C-T		not specified	Uncertain significance (Aug 23, 2021)
22-50503584-A-T		not specified	Uncertain significance (Mar 11, 2024)
22-50503597-A-G		not specified	Uncertain significance (Dec 28, 2022)
22-50503606-C-T		not specified	Likely benign (Oct 05, 2021)
22-50503618-G-C		not specified	Uncertain significance (Sep 25, 2023)
22-50503621-G-T		not specified	Uncertain significance (Aug 28, 2023)
22-50503677-C-T		not specified	Uncertain significance (May 26, 2022)
22-50503678-G-A		not specified	Uncertain significance (Sep 17, 2021)
22-50503828-G-A		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMF2	protein_coding	protein_coding	ENST00000474879	14	4760

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.40e-50	2.65e-12	125500	1	167	125668	0.000669

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.52	577	430	1.34	0.0000284	4374
Missense in Polyphen		217	174.78	1.2416		1817
Synonymous	-7.08	324	197	1.64	0.0000130	1547
Loss of Function	-3.80	61	36.3	1.68	0.00000181	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00399	0.00378
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00111	0.00109
Finnish	0.000129	0.0000924
European (Non-Finnish)	0.000288	0.000273
Middle Eastern	0.00111	0.00109
South Asian	0.00133	0.00127
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maturation of specific proteins in the endoplasmic reticulum. May be required for maturation and transport of active lipoprotein lipase (LPL) through the secretory pathway (By similarity). {ECO:0000250}.
• Pathway: Transport of small molecules;Assembly of active LPL and LIPC lipase complexes;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling (Consensus)

Intolerance Scores

• loftool: 0.887
• rvis_EVS: -1.29
• rvis_percentile_EVS: 5

Haploinsufficiency Scores

• pHI: 0.143
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmf2

Zebrafish Information Network

• Gene name: lmf2b
• Affected structure: blood circulation
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: protein maturation
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane
• Molecular function: protein binding