LEAP2

liver enriched antimicrobial peptide 2

Basic information

Region (hg38): 5:132873444-132875046

Links

ENSG00000164406 ∙ NCBI:116842 ∙ OMIM:611373 ∙ HGNC:29571 ∙ Uniprot:Q969E1 ∙ 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 LEAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEAP2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in LEAP2

This is a list of pathogenic ClinVar variants found in the LEAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-132873711-T-C		not specified	Uncertain significance (Dec 17, 2023)
5-132873727-G-T		not specified	Uncertain significance (Sep 11, 2024)
5-132873741-T-C		not specified	Uncertain significance (Nov 08, 2022)
5-132873971-G-A		not specified	Uncertain significance (Dec 12, 2023)
5-132873975-T-C		not specified	Uncertain significance (Jun 10, 2024)
5-132873998-C-T		not specified	Uncertain significance (Aug 08, 2023)
5-132874046-G-A		not specified	Uncertain significance (Jan 20, 2025)
5-132874047-C-T		not specified	Uncertain significance (Jan 29, 2024)
5-132874056-G-A		not specified	Uncertain significance (Jul 19, 2022)
5-132874074-T-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LEAP2	protein_coding	protein_coding	ENST00000296877	3	2725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00127	0.425	125713	0	33	125746	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0112	44	44.2	0.995	0.00000248	490
Missense in Polyphen		14	17.739	0.7892		209
Synonymous	-0.543	19	16.2	1.17	7.83e-7	157
Loss of Function	-0.174	4	3.64	1.10	1.54e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000640	0.000641
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.000217	0.000217
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has an antimicrobial activity. {ECO:0000269|PubMed:20845358}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.557
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0849
• hipred: N
• hipred_score: 0.170
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Leap2

Gene ontology

• Biological process: antimicrobial humoral response;defense response to bacterium
• Cellular component: extracellular region