LIPN

lipase family member N, the group of Lipases

Basic information

Region (hg38): 10:88759982-88779626

Previous symbols: [ "LIPL4" ]

Links

ENSG00000204020 ∙ NCBI:643418 ∙ OMIM:613924 ∙ HGNC:23452 ∙ Uniprot:Q5VXI9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive congenital ichthyosis 8 (Limited), mode of inheritance: AR
• lamellar ichthyosis (Supportive), mode of inheritance: AR
• autosomal recessive congenital ichthyosis 8 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ichthyosis, congenital, autosomal recessive 8	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	Dermatologic	12780701; 21439540
There are suggestions that treatment may be tailored by more precise (ie, genetic) diagnosis

ClinVar

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

• Autosomal recessive congenital ichthyosis 8 (1 variants)
• Lamellar ichthyosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPN 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				3	5	8
missense			38	4	4	46
nonsense			4			4
start loss						0
frameshift	1			1		2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			3	1		4
non coding				2	31	33
Total	1	0	43	10	40

Highest pathogenic variant AF is 0.0000198

Variants in LIPN

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

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

Position	Type	Phenotype	Significance	ClinVar
10-88761090-T-G			Benign (Nov 12, 2018)
10-88761440-T-C		not specified	Uncertain significance (Apr 26, 2023)
10-88761454-A-G		not specified	Uncertain significance (Jan 03, 2024)
10-88761463-G-T		not specified	Uncertain significance (Mar 09, 2023)
10-88761469-C-G		not specified	Uncertain significance (Oct 03, 2023)
10-88761514-G-A		not specified	Uncertain significance (Jun 03, 2022)
10-88761516-A-G			Uncertain significance (May 22, 2024)
10-88761518-G-C			Uncertain significance (Apr 26, 2023)
10-88761718-GCTAT-G			Benign (Jun 19, 2021)
10-88761718-GCTATCTAT-G			Benign (Jun 20, 2021)
10-88761718-GCTATCTATCTAT-G			Benign (Jun 20, 2021)
10-88761718-G-GCTAT			Benign (Jun 21, 2021)
10-88761755-CTATCTATG-C			Benign (Jun 20, 2021)
10-88761759-CTATG-C			Benign (Jun 21, 2021)
10-88761763-G-C			Benign (Jun 19, 2021)
10-88761779-TTATCTATC-T			Benign (Jun 20, 2021)
10-88761859-G-A			Benign (Nov 12, 2018)
10-88762188-A-G		not specified	Uncertain significance (May 24, 2023)
10-88762189-G-A		not specified	Uncertain significance (Jul 13, 2021)
10-88762228-A-G		not specified	Uncertain significance (Jan 03, 2024)
10-88762252-A-G		not specified	Uncertain significance (Aug 23, 2021)
10-88762301-C-G		not specified	Uncertain significance (Oct 05, 2021)
10-88762318-T-C			Likely benign (Sep 09, 2022)
10-88762425-T-C			Benign (Jun 19, 2021)
10-88764412-C-T		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIPN	protein_coding	protein_coding	ENST00000404459	9	16837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000310	0.943	124501	0	93	124594	0.000373

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0970	211	207	1.02	0.00000995	2626
Missense in Polyphen		78	79.935	0.97579		1046
Synonymous	0.657	63	70.0	0.900	0.00000336	709
Loss of Function	1.75	10	18.0	0.554	8.43e-7	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000687	0.000686
Ashkenazi Jewish	0.00299	0.00299
East Asian	0.00	0.00
Finnish	0.000187	0.000186
European (Non-Finnish)	0.000313	0.000283
Middle Eastern	0.00	0.00
South Asian	0.0000990	0.0000980
Other	0.000502	0.000496

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a highly specific role in the last step of keratinocyte differentiation. May have an essential function in lipid metabolism of the most differentiated epidermal layers. {ECO:0000269|PubMed:17562024}.
• Disease: DISEASE: Ichthyosis, congenital, autosomal recessive 8 (ARCI8) [MIM:613943]: A form of autosomal recessive congenital ichthyosis, a disorder of keratinization with abnormal differentiation and desquamation of the epidermis, resulting in abnormal skin scaling over the whole body. The main skin phenotypes are lamellar ichthyosis (LI) and non-bullous congenital ichthyosiform erythroderma (NCIE), although phenotypic overlap within the same patient or among patients from the same family can occur. Lamellar ichthyosis is a condition often associated with an embedment in a collodion-like membrane at birth; skin scales later develop, covering the entire body surface. Non-bullous congenital ichthyosiform erythroderma characterized by fine whitish scaling on an erythrodermal background; larger brownish scales are present on the buttocks, neck and legs. {ECO:0000269|PubMed:21439540}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Intolerance Scores

• loftool: 0.686
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.144
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lipn
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: lipid catabolic process;cellular lipid metabolic process;cornification
• Cellular component: extracellular region;intracellular membrane-bounded organelle
• Molecular function: lipoprotein lipase activity;lipase activity