LIPF

lipase F, gastric type, the group of Lipases

Basic information

Region (hg38): 10:88664440-88678814

Links

ENSG00000182333 ∙ NCBI:8513 ∙ OMIM:601980 ∙ HGNC:6622 ∙ Uniprot:P07098 ∙ 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 LIPF gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPF 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						0
missense			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in LIPF

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

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

Position	Type	Phenotype	Significance	ClinVar
10-88667350-A-G		not specified	Uncertain significance (Sep 01, 2021)
10-88667352-G-T		not specified	Uncertain significance (Jul 17, 2023)
10-88667386-A-T		not specified	Uncertain significance (Apr 12, 2023)
10-88668723-A-G		not specified	Uncertain significance (Jan 04, 2024)
10-88668738-T-C		not specified	Uncertain significance (Dec 07, 2023)
10-88669866-C-T		not specified	Uncertain significance (Jun 29, 2022)
10-88669913-C-T		not specified	Uncertain significance (Nov 08, 2022)
10-88669944-T-C		not specified	Uncertain significance (Oct 17, 2023)
10-88671857-C-A		not specified	Uncertain significance (Dec 13, 2023)
10-88671931-A-G		not specified	Uncertain significance (Feb 26, 2024)
10-88673722-G-T		not specified	Uncertain significance (Sep 13, 2023)
10-88675590-G-A			Likely benign (Mar 29, 2018)
10-88675596-A-T		not specified	Uncertain significance (Dec 03, 2021)
10-88675632-T-C		not specified	Uncertain significance (Dec 13, 2022)
10-88676209-G-T		not specified	Uncertain significance (Feb 16, 2023)
10-88678488-T-C		not specified	Uncertain significance (Jan 04, 2022)
10-88678494-T-A		not specified	Uncertain significance (Jun 02, 2023)
10-88678511-G-A		not specified	Uncertain significance (Oct 05, 2023)
10-88678592-T-G		not specified	Uncertain significance (Sep 01, 2021)
10-88678598-C-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIPF	protein_coding	protein_coding	ENST00000394375	10	14374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000721	0.983	125679	0	67	125746	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.421	195	212	0.919	0.00000974	2724
Missense in Polyphen		58	66.13	0.87707		887
Synonymous	-0.298	75	71.8	1.04	0.00000344	733
Loss of Function	2.11	8	17.5	0.456	7.41e-7	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000941	0.000940
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000214	0.000211
Middle Eastern	0.000326	0.000326
South Asian	0.000206	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Glycerolipid metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Fatty Acid Beta Oxidation;Triacylglyceride Synthesis;Glycerophospholipid metabolism;triacylglycerol degradation;Digestion of dietary lipid;Digestion;Digestion and absorption (Consensus)

Recessive Scores

• pRec: 0.0992

Intolerance Scores

• loftool: 0.631
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.0697
• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.154

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lipf

Gene ontology

• Biological process: malate metabolic process;triglyceride metabolic process;lipid catabolic process;cellular lipid metabolic process;oxidation-reduction process
• Cellular component: cellular_component;extracellular region;mitochondrion;intracellular membrane-bounded organelle
• Molecular function: triglyceride lipase activity;lipid binding;lipase activity;malate dehydrogenase activity