LEAP2

protein-coding

liver enriched antimicrobial peptide 2

Gene summary

This gene encodes a cysteine-rich cationic antimicrobial peptide that is expressed predominantly in the liver. The mature peptide has activity against gram-positive bacteria and yeasts. [provided by RefSeq, Sep 2014]

MANE transcript

NM_052971.3

Inheritance

—

ClinVar variants

U:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.1

Max pathogenic AF

—

Genomic locus

chr5:132,873,444-132,875,046

External References & Databases

Ensembl (ENSG00000164406)

Transcript & Mutation Effects

hg38 • Region Span ~1.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LEAP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052971.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	0	0	15

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052971.3	RefSeq	NP_443203.1	3	MANE Select
ENST00000296877.3	Ensembl	ENSP00000296877.2	3	MANE Select
ENST00000872294.1	Ensembl	ENSP00000542353.1	3	Standard
ENST00000872294.2	Ensembl	ENSP00000542353.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Antimicrobial peptides
Innate Immune System
Immune System

Biological Process

antimicrobial humoral response
defense response to bacterium

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296877
Coding exons: 3
Length: 2725
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125746
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0112	44	44.2	0.995	0.00000248	490
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00055	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has an antimicrobial activity. {ECO:0000269|PubMed:20845358}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.557
RVIS EVS: 0.17
RVIS percentile EVS: 65.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.655

Gene Damage Prediction

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